The nicotinic acetylcholine receptor (AChR) is a complex protein, which functions as a ligand-gated ion channel on the postsynaptic membrane at the neuromuscular junction and mediates signal transmission from neuron to muscle. Research on the AChR has had a long history and has benefited from the endeavors of scientists from many disciplines. The intensive, multidisciplinary studies have yielded valuable knowledge about this molecule, which serves as a model for the understanding of many fundamental questions in biological sciences. Chapter 1 presents a review of the AChR.
\r\n\r\nAs a tissue-specific and developmental stage-specific molecule, AChR is under temporal and spatial control for its synthesis. Chapter 2 reports a qualitative and quantitative study of AChR gene activity during muscle cell differentiation, using a cDNA clone isolated from a murine muscle cell line, which codes for the \u03b3 subunit of the mouse AChR. The results indicate that the regulation of mRNA accumulation levels is a major mechanism in the differential synthesis of the AChR.
\r\n\r\nThe marriage between AChR and molecular biology resulted in many cDNA clones which, after being introduced to African frogs, produced the next generation \u2014 Xenopus oocytes with exotic AChRs on them. Chapter 3 describes the attempt to localize \"determinants\" that specify species subunit identity in the AChR by constructing chimeric cDNA clones composed of fragments from different origins, taking advantage of the Xenopus oocyte expression system. The results from surface toxin-binding assay and two-electrode voltage-clamp recording suggested that while the species specificity can be dictated by certain subunits, the determination of subunit identity does not reside at a defined locus in the fragments tested.
\r\n\r\nDoes the complex composition of multisubunits in the AChR bear any functional significance? Chapter 4 addresses this question through the study of mouse-Torpedo AChR hybrids. The complete substitution of AChR subunits between mouse and Torpedo receptors generated all 16 combinations, and a systematic analysis of these hybrids revealed an interesting pattern with respect to the voltage sensitivity in the ACh-induced response: The identity of the \u03b2 subunit determines, while the interaction between the \u03b2 and \u03b4 subunits modulates, the AChR voltage sensitivity. The results, therefore, suggest that different subunits of AChR may play a central role in different functional properties.
\r\n\r\nPatch-clamp technique has offered an opportunity for analyzing transmembrane current flow with the high resolution of single-channel recording. Chapter 5 describes such a study on homologous and hybrid AChRs. Voltage influence on the three parameters were evaluated, and the results indicate that the single channel conductance is independent of membrane potential and that the channel closing and opening rates together constitute the basis for the voltage sensitivity in whole-cell recording with the closing rate making the major contribution. Also investigated were the subunit roles in species specificity of channel-open duration and voltage dependence. The results are in agreement with those reported on channel duration and support the conclusions of our previous work on the subunit involvement in determining the voltage sensitivity of the AChR response.
", "doi": "10.7907/fj5c-4h83", "publication_date": "1987", "thesis_type": "phd", "thesis_year": "1987" }, { "id": "thesis:11394", "collection": "thesis", "collection_id": "11394", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02152019-094650551", "type": "thesis", "title": "Structure and Expression of the Actin Gene Family of Drosophila melanogaster", "author": [ { "family_name": "Matthews", "given_name": "Beverley Bond", "clpid": "Matthews-Beverley-Bond" } ], "thesis_advisor": [ { "family_name": "Meyerowitz", "given_name": "Elliot M.", "clpid": "Meyerowitz-E-M" }, { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Meyerowitz", "given_name": "Elliot M.", "clpid": "Meyerowitz-E-M" }, { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" }, { "family_name": "Lewis", "given_name": "Edward B.", "clpid": "Lewis-E-B" }, { "family_name": "Rothenberg", "given_name": "Ellen V.", "clpid": "Rothenberg-E-V" }, { "family_name": "Wold", "given_name": "Barbara J.", "clpid": "Wold-B-J" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "We have isolated the six actin genes of Drosophila melanogaster from a Drosophila genomic DNA library and have compared structural features of the genes by restriction mapping, electron microscopy and DNA sequencing. We found that at least two of the actin genes contain intervening sequences which interrupt the genes at different positions. Several of the genes were shown to be lacking intervening sequences in the analogous positions. This nonconservation of intron position is in striking contrast to the strong conservation of intron positions seen in other gene families. The DNA sequences of the protein coding regions of the genes are highly conserved while the intron and untranslated sequences are not. The primary sequences of all the Drosophila actins resemble mammalian cytoplasmic actins more than mammalian muscle actins.
\r\n\r\nWe studied the distribution of actin mRNAs in different developmental stages and in different dissected body parts with the use of gene specific hybridization probes which we isolated from the 3' untranslated portions of the genes. We found that the genes fall into three main categories with respect to their patterns of expression in Drosophila. Trancripts from two of the genes are found throughout Drosophila development. They are expressed at higher levels in ovaries and embryonic cultured cells than in muscle containing tissue and are thought to be cytoplasmic actins. Two others encode thoracic muscle actins. Their transcripts accumulate predominantly in the thoracic regions of the adult where the flight and jump muscles are found. The other two genes are most active in larvae and in adult abdomens. They are thought to encode actins used in the larval, pupal, and adult intersegmental muscles.
\r\n\r\nWe studied the structure of the cytoplasmic actin gene, act5C, in detail and found that it encodes at least six different mRNAs. At the 5' end there are two nonhomologous leader exons which are alternately spliced to the remainder of the gene. At the 3' end of the gene, three sites of polyadenylation are used. The 3' variation is the principal cause of the transcript length heterogeneity observed in the transcripts. In whole animal RNA, the two leader exons are expressed with the same pattern through development and with all three polyadenylation sites. There is some developmental variability in the use of the three polyadenylation sites.
\r\n\r\nIn order to determine if each exon is preceded by a functional promoter and to identify sequences important for transcription initiation from each exon, we made fusions between act5C promoter fragments and the bacterial chloramphenicol acetyltransferase (CAT) gene and tested these for promoter activity in transient assays in Kc cells. We found that each exon is preceded by a separate, functional promoter. At least two regions of DNA sequences are necessary for optimal expression from exon 1. One of these lies greater than 1.9 kb upstream from the exon 1 cap site. All of the sequences required for exon 2 transcription lie within 450 bases of its cap site. There is evidence from some constructions that transcription initiation from exon 1 may inhibit transcription initiation from ex on 2.
", "doi": "10.7907/05zz-5w73", "publication_date": "1987", "thesis_type": "phd", "thesis_year": "1987" }, { "id": "thesis:11834", "collection": "thesis", "collection_id": "11834", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10212019-143142376", "type": "thesis", "title": "The Molecular Structure of the Beadex and Heldup-A Loci of Drosophila melanogaster", "author": [ { "family_name": "Mattox", "given_name": "William Wayne", "clpid": "Mattox-William-Wayne" } ], "thesis_advisor": [ { "family_name": "Lewis", "given_name": "Edward B.", "clpid": "Lewis-E-B" }, { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Lewis", "given_name": "Edward B.", "clpid": "Lewis-E-B" }, { "family_name": "Wold", "given_name": "Barbara J.", "clpid": "Wold-B-J" }, { "family_name": "Meyerowitz", "given_name": "Elliot M.", "clpid": "Meyerowitz-E-M" }, { "family_name": "Simon", "given_name": "Melvin I.", "clpid": "Simon-M-I" }, { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "Genetic studies indicate that excess-of-function Beadex mutations and loss-of-function heldup-a mutations affect different parts of a single bipartite genetic unit. In order to investigate the molecular nature of the Beadex and heldup-a mutations we isolated DNA from a 49 kilobase region surrounding the sites at which these mutations occur. We found gross structural alterations associated with one heldup-a mutation and each of the 13 different Beadex mutations that we examined. As expected from previous genetic studies these loci are separated by only a short molecular distance which is at most 1.5 kilobases. The structural alterations associated with the thirteen Beadex excess-of-function mutations examined are clustered within a three kilobase region. Several of these mutations are found to be associated with the deletion of part of an 800 bp region. This indicates that an element that normally represses gene activity is located within this region: A 200 base pair segment which is required for the function of the wild-type heldup-a locus is defined using a heldup-a mutation which results from a small deletion.
\r\n\r\nTwo RNA transcripts have been found which span this 200 base pair segment. One of these two transcripts, a four kilobase RNA, is expressed during stages in which the Beadex structural gene product is expected to be active. The structure of this transcript is affected by one heldup-a mutation and each of five Beadex mutations that were examined. However, only one of the Beadex mutant alleles expresses significantly elevated levels of this RNA. Other RNA species in the region surrounding the the Beadex and heldup-a loci were not affected either in amount or size by Beadex mutations.
\r\n\r\nWe have also reintroduced a wild-type 10.4 kilobase fragment, which includes the region m which Beadex and heldup-a mutations map, into the Drosophila genome by P element mediated transformation. This introduced fragment fails both to complement loss-of-function heldup-a mutations and to enhance an excess-of-function phenotype. This result indicates that some sequences required for the normal heldup-a function must be located outside this 10.4 kilobase region.
", "doi": "10.7907/c2k4-a231", "publication_date": "1987", "thesis_type": "phd", "thesis_year": "1987" }, { "id": "thesis:11356", "collection": "thesis", "collection_id": "11356", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01222019-155306456", "primary_object_url": { "basename": "Parker_VP_1985.pdf", "content": "final", "filesize": 31373314, "license": "other", "mime_type": "application/pdf", "url": "/11356/1/Parker_VP_1985.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Studies of Gene Structure: I. Expression of Human \u03b1-Globin Genes in COS Cells. II. Isolation and Characterization of the Myosin Light Chain Genes from Drosophila melanogaster", "author": [ { "family_name": "Parker", "given_name": "Vann Phillips", "clpid": "Parker-Vann-Phillips" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Attardi", "given_name": "Giuseppe", "clpid": "Attardi-G" }, { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" }, { "family_name": "Meyerowitz", "given_name": "Elliot M.", "orcid": "0000-0003-4798-5153", "clpid": "Meyerowitz-E-M" }, { "family_name": "Strauss", "given_name": "James H.", "clpid": "Strauss-J-H" }, { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "The first part of this thesis describes the establishment of COS cells as an effective host for the replication and expression of genes cloned into plasmids containing the SV40 viral replication origin. The human \u03b1-globin gene was cloned into a pBR322 derivative which contained a 311 base pair SV40 fragment. These plasmids were replicated to high copy number. The \u03b1-globin gene was transcribed to produce high levels of RNA which was indistinguishable from human \u03b1-globin mRNA. Deletion mutants were generated which defined the region from 55 to 87 base pairs upstream from the mRNA cap site as necessary for high levels of transcription of this gene. This region includes the conserved sequence CCAAT found in a similar position upstream from many eukaryotic genes.
\r\n\r\nThe second part of this thesis describes the cloning of muscle specific genes from Drosophila melanogaster and a detailed analysis of the two myosin light chain genes. A genomic library was screened with RNA isolated from the late pupal stage of development. Recombinant DNA clones which mapped to 24 independent locations were identified. The clones containing the myosin light chain genes were identified from within this group. A cDNA library was generated from late pupal RNA. Clones homologous to each of the myosin light chains were identified and their cloned inserts were sequenced. Their classification as Drosophila myosin light chain genes was established by comparing the derived amino acid sequence to the protein sequence of the chicken myosin light chains. Each myosin light chain is single copy. The alkali myosin light chain maps to the chromosomal locus 98B. It hybrid selects RNA which may be translated in vitro to yeild several polypeptides of molecular weight 18,000 to 19,000 daltons. The gene for myosin light chain-2 maps to the chromosomal locus 99E and is shown to encode two proteins of apparent molecular weights 26,000 and 17,000 daltons. Each protein has a putative divalent cation binding domain.
", "doi": "10.7907/msv6-0s82", "publication_date": "1985", "thesis_type": "phd", "thesis_year": "1985" }, { "id": "thesis:11366", "collection": "thesis", "collection_id": "11366", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01302019-123859876", "primary_object_url": { "basename": "Levy_DE_1985.pdf", "content": "final", "filesize": 64210096, "license": "other", "mime_type": "application/pdf", "url": "/11366/1/Levy_DE_1985.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Expression of Endogenous Retroviruses in Inbred Mice : Coordinate Regulation and Structure of Multiple Transcription Units", "author": [ { "family_name": "Levy", "given_name": "David E.", "orcid": "0000-0002-7320-7788", "clpid": "Levy-David-E" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" }, { "family_name": "Rothenberg", "given_name": "Ellen V.", "orcid": "0000-0002-3901-347X", "clpid": "Rothenberg-E-V" } ], "thesis_committee": [ { "family_name": "Rothenberg", "given_name": "Ellen V.", "orcid": "0000-0002-3901-347X", "clpid": "Rothenberg-E-V" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" }, { "family_name": "Lerner", "given_name": "R.", "clpid": "Lerner-R" }, { "family_name": "Wilson", "given_name": "M.", "clpid": "Wilson-M" }, { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "The control of expression of the murine antigen Gix and of other products of endogenous retroviruses, in strain 129 mice and in its congeneic partner strain 129 Gix-, is an example of the coordinate expression of a dispersed family of independent transcription units. In order to provide a molecular description of the Gix phenotype, evidence is presented, from DNA and RNA hybridization analyses using heterologous viral probes, indicating that this phenotype is specified by a distinct regulatory gene, defined genetically, that acts in trans to control the levels of accumulation of specific mRNA species. The steady state levels of several, structurally distinct polyadenylated RNA species are reduced in Gix- mice, and a major reduction in transcription of these sequences accompanies this drop in abundance. Tissue specific patterns of accumulation of different sized RNA species were detected in numerous organs of the mouse, and the majority of these distinct transcripts were collectively regulated.
\r\n\r\nThe isolation and characterization of cDNA copies of these endogenous retroviral transcripts demonstrated that they were derived from multiple, distinct transcription units. Differences among these RNA species were detected by S1 nuclease protection analyses , which confirmed the tissue specific patterns of RNA accumulation. The nucleotide sequences of endogenous virus cDNA clones fully documented the expression of distinct genes, the nature of the sequence heterogeneity, and the relationship of these normal cellular constituents to exogenous, infectious virus. The polymorphism was found to result from both single nucleotide changes and from deletions of different lengths of coding and non-coding information. Comparison of these sequences with exogenous virus demonstrated that the endogenous transcripts are closely related to the recombinant sequences of eukemogenic, mink cell focus forming viruses.
\r\n\r\n", "doi": "10.7907/165r-9v89", "publication_date": "1985", "thesis_type": "phd", "thesis_year": "1985" }, { "id": "thesis:11389", "collection": "thesis", "collection_id": "11389", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02112019-112435563", "primary_object_url": { "basename": "Falke_JJ_1985.pdf", "content": "final", "filesize": 108586280, "license": "other", "mime_type": "application/pdf", "url": "/11389/1/Falke_JJ_1985.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "The Behavior and Structure of the Band 3 Anion Transport Site: a \u00b3\u2075Cl and \u00b3\u2077Cl NMR Study", "author": [ { "family_name": "Falke", "given_name": "Joseph John", "orcid": "0000-0002-3704-4694", "clpid": "Falke-Joseph-John" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" }, { "family_name": "Chan", "given_name": "Sunney I.", "orcid": "0000-0002-5348-2723", "clpid": "Chan-S-I" }, { "family_name": "Hopfield", "given_name": "John J.", "clpid": "Hopfield-J-J" }, { "family_name": "Beauchamp", "given_name": "Jesse L.", "orcid": "0000-0001-8839-4822", "clpid": "Beauchamp-J-L" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The transport of ions across cellular and organellar membranes is a widespread and fundamental process in biology. The goal of the present work is a molecular picture describing the ion translocation event in band 3, the most heavily used ion transport protein in typical vertebrate systems. The strategy employed involves 35Cl NMR, which is shown both theoretically and experimentally to be a sensitive probe of two microscopic events: 1) the migration of Cl- from solution to the vicinity of a macromolecular binding site, and 2) the binding of Cl- to the site. The technique reveals 35Cl- linebroadening due to two classes of Cl- binding sites on isolated, native red cell membranes. One class is composed solely of low affinity Cl- binding sites of unknown function (KD > > 0.5 M), while the other class is composed solely of band 3 transport sites (KD = 80 \u00b1 20 mM) which are identified by their affinity for substrate (Cl-), competing substrates (HCO-3, F-, Br-, I-) and inhibitor (4,4'-dinitrostilbene-2,2'-disulfonate, or DNDS). A 35Cl NMR method is developed to ascertain the sidedness of Cl- binding sites relative to a compartment barrier such as a membrane: this approach shows that the low-affinity and transport sites are each found on both surfaces of the membrane.
\r\n\r\nThe sequence of events in the Cl- transport cycle is investigated by monitoring the behavior of the transport sites when the concentration of DNDS, p-nitrobenzenesulfonate (pNBS), Cl-, Br-, or H+ is varied. DNDS and pNBS, which are known to bind to outward-facing transport sites, each recruit all of the transport sites on both sides of the membrane to the inhibited outward-facing conformation, indicating that the inward- and outward-facing transport sites observed in the absence of inhibitor are merely different conformations of a single site. In addition, the transport sites on both sides of the membrane together behave like a homogeneous population of sites when [Cl-], [Br-], or pH is varied. These results are quantitatively consistent with the pingpong model for the transport cycle (Gunn and Frolich (1979) J. Gen. Physiol. 74, 351-374), in which a single transport site alternates between the inward- and outward-facing states and can only change states when occupied by bound anion. The rates of Cl- binding and dissociation at both inward- and outward-facing transport sites are investigated with 35Cl and 37Cl NMR, and it is shown that each of these rates exceeds 105 events sec-1 site-1 -- much faster than the known turnover rate of the chloride transport cycle (430 events sec-1 site-1, 0\u00b0C). Assuming that the rates of the influx and efflux half-turnovers of the transport cycle differ by 102 or less, it follows that the translocation of the chloride*transport site complex is the rate-limiting step in both half-turnovers (see Figure).
\r\n\r\nThe structure of the transport machinery is investigated using transport inhibitors and proteases. The reversible inhibitor niflumic acid (NIF) has no effect on the transport site linebroadening: this inhibitor slows the translocation of bound Cl- in both the influx and efflux half-turnovers. The covalent, arginine-specific reagents phenylglyoxal (PG) and 1,2-cyclohexanedione (CHD) each eliminate the transport site linebroadening: PG modifies an essential residue in the transport site and CHD slows the migration of Cl- between the site and solution. The observed PG-sensitivity and pH-dependence of the transport site linebroadening (pKA = 11.1 \u00b1 0.1, [Cl-] = 250 mM) indicate that an arginine residue provides the positive charge in at least one conformation of the transport site. A search is conducted for the minimal structure containing the intact transport site: this search begins with the removal of an innessential part of the transport domain, followed by monitoring of the transport site linebroadening for change. A variety of treatments leave some or all of the transport site linebroadening intact, including: 1) removal of the red cell membrane nonintegral proteins, 2) proteolytic removal of the soluble N-terminal domain of band 3, or 3) extensive proteolysis of band 3 by papain, which reduces band 3 to its transmembrane peptides (3-9 kDa). These results indicate that the essential arginine, as well as all other residues essential for Cl- migration and binding to the transport site, are located on the papain-generated transmembrane peptides. The structural data presented here strongly support a picture in which the transport site, including the essential arginine, is buried in the membrane where it is resistant to proteolysis; and access of the buried site to solution Cl- is provided by a channel that can be blocked by CHD. In summary, the minimal sequence of events in the Cl- transport cycle can be schematically illustrated by
\r\n\r\n[Illustration. See abstract in scanned thesis for details]
\r\n\r\nA model is also presented that describes the molecular details of the ion translocation event: the translocation is proposed to begin when the transport site positive charge is neutralized by anion binding, so that a sliding hydrophobic barrier can move past the site and thereby expose the site to the opposite solution, as illustrated by
\r\n\r\n[Illustration. See abstract in scanned thesis for details]
\r\n\r\nA sliding barrier model could explain the translocation event in many other membrane transport systems as well.
", "doi": "10.7907/j15r-rw02", "publication_date": "1985", "thesis_type": "phd", "thesis_year": "1985" }, { "id": "thesis:11279", "collection": "thesis", "collection_id": "11279", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11212018-100547724", "primary_object_url": { "basename": "Kuo_C-L_1984.pdf", "content": "final", "filesize": 28474761, "license": "other", "mime_type": "application/pdf", "url": "/11279/1/Kuo_C-L_1984.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Use of Temperature Sensitive Mutants to Study Yeast DNA Replication", "author": [ { "family_name": "Kuo", "given_name": "Chia-lam", "clpid": "Kuo-Chia-lam" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" }, { "family_name": "Campbell", "given_name": "Judith L.", "orcid": "0000-0001-8291-5551", "clpid": "Campbell-J-L" }, { "family_name": "Raftery", "given_name": "Michael A.", "clpid": "Raftery-M-A" }, { "family_name": "Richards", "given_name": "John H.", "clpid": "Richards-J-H" }, { "family_name": "Emr", "given_name": "Scott D.", "orcid": "0000-0002-5408-6781", "clpid": "Emr-S-D" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "An improved in vitro DNA replication system in Brij-treated Saccharomyces cerevisiae has been used to screen a random population of temperature-sensitive strains for mutants specifically defective in DNA synthesis. Twenty mutants defective in in vitro DNA synthesis have been isolated. Seven of them fall into three complementation groups -- cdc2, cdc8, and cdc16 -- involved in the control of the cell-division cycle. Because synthesis in vitro represents propagation of replication forks active in in vivo at the time of permeabilization, our findings that cdc2 and cdc16 mutants can incorporate dTMP into DNA in such permeabilized cells at 23\u00b0c but not at 37\u00b0c supports the conclusion that these two mutations directly affect DNA synthesis. Such an involvement was previously suggested by in vivo analysis for CDC2 but was less clear for CDC16. The usefulness of our screening procedure is further demonstrated by the isolation of replication mutants in previously undescribed complementation groups. One strain shows a serious defect in in vivo DNA synthesis but normal RNA synthesis.
\r\n\r\nThe in vitro system has also been used to purify the CDC8 protein. cdc8 mutant strains are temperature-sensitive for DNA chain elongation and the CDC8 gene product is required for DNA synthesis in vitro in permeabilized yeast cells. Extracts of wild-type A364a yeast restore DNA synthesis in Brij-treated cdc8 mutant. A small, heat-stable protein responsible for this complementation has been partially purified from wild-type cells.
\r\n\r\nThe CDC8 gene has been isolated on recombinant plasmids. The yeast-E. coli shuttle vector YCp50 was used to prepare a recombinant plasmid pool containing the entire yeast genome. Plasmids capable of complementing the temperature-sensitive cdc8-1 mutation were isolated by transformation of a cdc8-1 mutant and selection for clones able to grow at the nonpermissive temperature. The entire complementing activity is carried on a 0.75-kilobase fragment, as revealed by deletion mapping and DNA sequencing. This fragment lies 1 kilobase downstream from the well characterized sup4 gene, a gene known to be genetically linked to CDC8 thus confirming the cloned gene corresponds to the chromosomal CDC8 gene. Two additional recombinant plasmids that complement the cdc8-1 mutation but that do not contain the 0.75-kilobase fragment or any flanking DNA were also identified in this study. These plasmids may contain genes that compensate for the cdc8-1 mutation.
\r\n\r\nBy the following criteria, we have shown that thymidylate kinase, which catalyzes the phosphorylation of thymidine-5'-monophosphate to thymidine-5'-diphosphate in the pathway of synthesis of dTTP from dTMP, is the product of the CDC8 gene. First, transformed strains carrying the CDC8 gene on a stable high-copy-number plasmid express higher levels of both the gene transcript and the kinase activity than does wild type. Secondly, extracts of strains bearing different alleles of cdc8 show no detectable thymidylate kinase activity. Third, the DNA sequence of CDC8 gene reveals an open reading frame that encodes a protein of 216 amino acids with the same amino terminal sequence as thymidylate kinase purified from yeast.
", "doi": "10.7907/gekb-yq20", "publication_date": "1984", "thesis_type": "phd", "thesis_year": "1984" }, { "id": "thesis:11885", "collection": "thesis", "collection_id": "11885", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:11042019-115006064", "primary_object_url": { "basename": "snyder-mp-1983.pdf", "content": "final", "filesize": 5671154, "license": "other", "mime_type": "application/pdf", "url": "/11885/1/snyder-mp-1983.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Organization and Expression of a Cluster of Drosophila Cuticle Genes", "author": [ { "family_name": "Snyder", "given_name": "Michael Paul", "orcid": "0000-0003-0784-7987", "clpid": "Snyder-Michael-Paul" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" }, { "family_name": "Meyerowitz", "given_name": "Elliot M.", "orcid": "0000-0003-4798-5153", "clpid": "Meyerowitz-E-M" }, { "family_name": "Parker", "given_name": "Carl Stevens", "orcid": "0000-0001-9795-4211", "clpid": "Parker-C-S" }, { "family_name": "Attardi", "given_name": "Giuseppe", "clpid": "Attardi-G" }, { "family_name": "Davidson", "given_name": "Eric H.", "clpid": "Davidson-E-H" }, { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "A 50 kb DNA segment of the Drosophila genome has been cloned and characterized. This segment lies at chromosomal location 44D and contains two small gene families. One family is comprised of four related cuticle genes clustered within 7.9 kb of DNA. The four genes encode four of the five major third instar larval cuticle proteins. These cuticle genes are coordinately expressed in the integument of third instar larvae, and they are not abundantly expressed in other developmental stages. A fifth cuticle-like gene lies within this gene cluster. It is judged to be a pseudogene, because several features of its structure and the absence of transcripts suggest that it is nonfunctional. Sequence comparisons indicate it arose by an unequal crossing over event involving two closely related and adjacent cuticle genes.
\r\n\r\nEleven kb away from the cuticle gene cluster lies another gene family. This family is comprised of three genes that are 55-60% homologous in DNA sequence and clustered within 8 kb of DNA. The three genes are expressed together in larval stages and adults but show a different pattern of developmental expression from the third instar larval cuticle protein genes. Thus two small gene families can lie adjacent on the chromosome and exhibit different patterns of developmental expression, even though individual genes within a clustered family are coordinately expressed.
\r\n\r\nAdditionally, a Drosophila strain has been studied which fails to synthesize one of the cuticle proteins. A molecular characterization of this strain is reported, which includes the finding of a transposable element in the promoter region of the unexpressed gene.
", "doi": "10.7907/mfee-te69", "publication_date": "1983", "thesis_type": "phd", "thesis_year": "1983" }, { "id": "thesis:17679", "collection": "thesis", "collection_id": "17679", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09152025-181743359", "primary_object_url": { "basename": "Robinson_RR_1981.pdf", "content": "final", "filesize": 26543413, "license": "other", "mime_type": "application/pdf", "url": "/17679/1/Robinson_RR_1981.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Sequence Analysis of a tRNA Gene Cluster: Drosophila Leucine-tRNA Genes contain Intervening Sequences", "author": [ { "family_name": "Robinson", "given_name": "Randy Richard", "clpid": "Robinson-Randy-Richard" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "A recombinant DNA phage containing a cluster of Drosophila\r\nmelanogaster tRNA genes has been isolated and analyzed. In situ\r\nhybridization localizes this phage to chromosomal region 50AB, a known\r\ntRNA site. Nucleotide sequencing of the entire Drosophila tRNA coding\r\nregion reveals seven tRNA genes spanning 2.5 kb of chromosomal DNA.\r\nThis cluster is separated from other tRNA regions on the chromosome\r\nby at least 2.7 kb on one side, and 9.6 kb on the other. Two tRNA genes\r\nare nearly identical and contain intervening sequences in the anticodon\r\nloop. These two genes are assigned to be tRNALeu genes because of\r\nsignificant sequence homology with yeast tRNA3Leu, and secondary structure\r\nhomology with yeast tRNA3Leu intervening sequences. In addition, an 8\r\nbase sequence (AAAAUCUU) is conserved in the same location in the inter-\r\nvening sequences of Drosophi1a tRNALeu genes and a yeast tRNA3Leu gene.\r\nSimilar sequences occur in all other tRNAs containing intervening\r\nsequences. The remaining five genes are identica1 tRNAIle genes, which\r\nare identical to a tRNAIle gene from chromosomal region 42A. The 5'\r\nflanking regions are only weakly homologous, but each set of isoacceptors\r\ncontains short regions of strong homology approximately 20 nucleotides\r\npreceding the tRNA coding sequences: GCNTTTTG preceding tRNAIles; and\r\nGANTTTGG preceding tRNALeus. The genes are irregularly organized on both\r\nDNA strands; spacing regions are divergent in sequence and length.\r\nPreliminary in vitro transcription experiments with isolated restriction\r\nfragments demonstrate that both tRNALeu genes and at least two of the\r\nfive tRNAIle genes are selectively transcribed in vitro by cytoplasmic\r\nextracts from HeLa cells.", "doi": "10.7907/p9cn-c915", "publication_date": "1981", "thesis_type": "phd", "thesis_year": "1981" }, { "id": "thesis:18475", "collection": "thesis", "collection_id": "18475", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04062026-221212098", "primary_object_url": { "basename": "Early_PW_1980.pdf", "content": "final", "filesize": 31573311, "license": "other", "mime_type": "application/pdf", "url": "/18475/1/Early_PW_1980.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Mouse Immunoglobulin Heavy Chain Gene Organization and Rearrangement: Genetic Bases for Antibody Diversity and Regulated Expression", "author": [ { "family_name": "Early", "given_name": "Philip Warren", "clpid": "Early-Philip-Warren" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" }, { "family_name": "Hood", "given_name": "Leroy E.", "orcid": "0000-0001-7158-3678", "clpid": "Hood-L-E" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "Immunoglobulin heavy chains each display one of a wide range of diverse antigenbinding\r\nvariable regions. At least one class of immunoglobulin, IgM, contains heavy chains\r\nwhich exist as two forms, either bound to the outside of a cell membrane or linked by\r\ndisulfide bonds in secreted antibodies. I have used recombinant DNA techniques to isolate\r\nand determine the nucleotide sequences of genes encoding mouse immunoglobulin heavy\r\nchains. This has enabled me to examine genetic bases for the diversity of heavy chain\r\nvariable regions and for the synthesis of membrane-bound and secreted forms of IgM\r\nheavy chains.
\r\n\r\nI found that genes encoding heavy chain variable regions are created somatically\r\nby joining three segments of DNA: VH, D, and JH The JH gene segments are closely\r\nlinked to the IgM heavy chain constant region gene in germline DNA, where they are\r\nwidely separated from VH gene segments. In an immunoglobulin-producing cell, one VH\r\nand one JH gene segment are joined, together with a D sequence which is probably also\r\na germline gene segment, to form the expressed heavy chain variable region gene. Both\r\ncombinatorial association of gene segments and variations in the exact sites of DNA\r\njoining between gene segments can contribute to heavy chain variable region diversity.\r\nBased on observations of certain conserved nucleotides and spacer sequences adjacent\r\nto unrearranged immunoglobulin gene segments, I propose a mechanism for variable\r\nregion gene rearrangement during differentiation.
\r\n\r\nSecreted and membrane-bound forms of IgM heavy chains were found to be\r\nencoded by separate mRNAs transcribed from the same gene. These mRNAs differ only\r\nat their 3' ends, where one encodes a 20 amino acid secretory C-terminal segment, and\r\nthe other encodes a 41 amino acid transmembrane C-terminal segment. Synthesis of\r\nthe two forms of lgM heavy chain mRNA appears to be developmentally regulated by\r\ncontrolling the site of 3' terminal polyadenylation. The site of polyadenylation defines\r\nthe lengths of RNA transcripts and thereby determines which of two alternative RNA\r\nsplicing patterns will be followed, leading to mRNAs encoding either the secreted or\r\nmembrane-bound forms of IgM heavy chains.
", "doi": "10.7907/c5ya-yy20", "publication_date": "1980", "thesis_type": "phd", "thesis_year": "1980" }, { "id": "thesis:18405", "collection": "thesis", "collection_id": "18405", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03062026-161324227", "primary_object_url": { "basename": "Conrad _SE_1979.pdf", "content": "final", "filesize": 47510662, "license": "other", "mime_type": "application/pdf", "url": "/18405/1/Conrad _SE_1979.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "I. Sequence Organization of Drosophila melanogaster 5S rRNA and 4S RNA Genes. II. In Vitro Studies on Replication of Plasmid DNAs", "author": [ { "family_name": "Conrad", "given_name": "Susan Ellen", "clpid": "Conrad-Susan-Ellen" } ], "thesis_advisor": [ { "family_name": "Campbell", "given_name": "Judith L.", "orcid": "0000-0001-8291-5551", "clpid": "Campbell-J-L" }, { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Campbell", "given_name": "Judith L.", "orcid": "0000-0001-8291-5551", "clpid": "Campbell-J-L" }, { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" }, { "family_name": "Attardi", "given_name": "Giuseppe", "clpid": "Attardi-G" }, { "family_name": "Maniatis", "given_name": "Thomas P.", "clpid": "Maniatis-T-P" }, { "family_name": "Strauss", "given_name": "James H.", "clpid": "Strauss-J-H" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "I. The sequence organizations of Drosophila melanogaster 4S RNA (tRNA)\r\nand 5S rRN A genes have been investigated. Segments of Drosophila DNA containing\r\nthese genes have been propagated in recombinant plasmids using Escherichia coli\r\nas a host and Co1E1 as a vector.
\r\n\r\nElectron microscope partial denaturation mapping, mapping by ferritin\r\nlabeling and restriction enzyme-gel electrophoresis analysis all indicate that the\r\nDrosophila DNA inserts of the 5S rRNA gene containing plasmids consist of tandem\r\nrepeats of 5S genes and spacer regions. The repeat length is approximately 380\r\nnucleotide pairs (ntp), corresponding to a gene of length 120 ntp and a spacer\r\nof length 260 ntp. Little heterogeneity in the lengths of the repeats has been\r\ndetected.
\r\n\r\nA tRNA gene containing clone has been characterized by electron microscopic\r\nmethods and by restriction endonuclease mapping. Four tRNA genes were\r\ndetected on a 9.34 kb fragment of DNA. Three of these genes appear to be\r\nidentical and different from the fourth. No evidence was found for extensive\r\nsequence homology in the sequences surrounding the genes. In situ hybridization\r\nwith cRNA transcribed from the plasmid showed localization at region 42A of\r\nchromosome 2R.
\r\n\r\nII. An improved system for in vitro replication of Escherichia coli plasmid\r\nDNAs has been developed and characterized. Endogenous DNA is removed from\r\nthe extracts, making replication dependent upon exogenous DNA even when plasmid\r\ncontaining cells are used as a source of extracts. Replication in this system requires\r\nE. coli DNA polymerases I and III, RNA polymerase, DNA gyrase, and the products\r\nof at least five genes required for E. coli replication (dnaB, dnaC, dnaG, dnaP, dnaZ).
\r\n\r\nThis system has been used to study the replication properties of the\r\nampicillin resistant plasmid RSF1030. We have found that, like Co1E1, RSF1030\r\nreplicates unidirectionally from a unique origin. We have also investigated the\r\nreplication of pFH118, a high copy number mutant derived from Co1E1. The\r\nmutation in pFH118 is due to the insertion of 20-30 base pairs into the coding\r\nsequence for a 100 nucleotide RNA that is transcribed during DNA replication.\r\nResults of reversion studies suggest that this RN A plays a role in determining\r\nplasmid copy number. Furthermore, the RN As transcribed from Co1E1 and RSF1030\r\nhave significant sequence homology, although the plasmids were isolated independently\r\nand have been thought to have no sequence homology.
", "doi": "10.7907/d94z-c749", "publication_date": "1979", "thesis_type": "phd", "thesis_year": "1979" }, { "id": "thesis:17843", "collection": "thesis", "collection_id": "17843", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01282026-233715971", "primary_object_url": { "basename": "Bender_W_1978.pdf", "content": "final", "filesize": 60115146, "license": "other", "mime_type": "application/pdf", "url": "/17843/1/Bender_W_1978.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Electron Microscopic Studies of Sequence Arrangement: Poly(A) Mapping, RNA Tumor Viruses, and Slime Mold Actin Genes", "author": [ { "family_name": "Bender", "given_name": "Welcome", "clpid": "Bender-Welcome" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "No abstract.", "doi": "10.7907/ssje-ve39", "publication_date": "1978", "thesis_type": "phd", "thesis_year": "1978" }, { "id": "thesis:17808", "collection": "thesis", "collection_id": "17808", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01072026-213406911", "primary_object_url": { "basename": "Kung_H-S_1976.pdf", "content": "final", "filesize": 48672784, "license": "other", "mime_type": "application/pdf", "url": "/17808/1/Kung_H-S_1976.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Structure of RNA Tumor Virus Genome", "author": [ { "family_name": "Kung", "given_name": "James Hsing-Jien", "clpid": "Kung-James-Hsing-Jien" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Part I of the thesis describes the characterization of the RNA\r\nstructure of the RNA tumor viruses.
\r\n\r\nThe genome of type C RNA tumor viruses is an RNA complex\r\nwhich sediments at \"50-60\"S in a nondenaturing aqueous electrolyte.\r\nUpon exposure to denaturing conditions, it can be dissociated\r\ninto subunits of \"30-40\"S plus small \"4-10\"S RNA's. The structure\r\nand molecular weight of the \"50-60\"S and \"30-40\"S RNA species have\r\nbeen studied by electronmicroscopy, gel electrophoresis and sedimentation\r\nanalysis. It was found that type C viruses, isolated from\r\ndifferent origins (feline, murine, simian and baboon) all contain as\r\ntheir genomes \"50-60\"S RNA species which have similar secondary\r\nstructure patterns. The \"50-60\"S molecule has a molecular length\r\nabout 16-20 Kb (~6x106 daltons) as measured by electronmicroscopy.\r\nIt contains two characteristic secondary structure features (i) a\r\ncentral T-shaped structure (the dimer linkage structure) (ii) two\r\nloops symmetrically positioned on each side of the dimer linkage\r\nstructure. Melting of the dimer linkage structure resulted in a concomitant\r\ndissociation of the 52S molecule into two half-size subunits,\r\neach about 8-10 Kb. PolyA mapping by electronmicroscopy shows\r\nthat the \"50-60\"S molecules contain two polyA segments, one at each\r\nend.
\r\n\r\nThese results suggest that the \"50-60\"S RNA consists of two\r\n8-10 Kb or \"30-40\"S subunits, each with a characteristic secondary\r\nstructure loop. These two subunits which are possibly identical are\r\njoined at their 5' ends within the dimer linkage structure. The primary\r\nnucleotide sequence, the molecular weight and the stability of\r\nthe \"50-60\"S RNA is different for each different virus. Yet, the finding\r\nthat these different viral RNA's contain similar secondary structure\r\npatterns suggests that such features are functionally important.\r\nIf this is true, it is possible that they are present in all type C virus\r\ngenomes.
\r\n\r\nIn part II, an electronmicroscopic technique for studying\r\nsingle-stranded RNA is described. This technique has been applied\r\nto determine the molecular weight, to study the secondary structure\r\nand to map the polyA sequence of RNA isolated from an arbovirus\r\n(Sindbis).
\r\n\r\nThis spreading technique utilizes glyoxal as a denaturing\r\nagent. Glyoxal reacts preferentially with guanine residues of polynucleotides\r\nand blocks their hydrogen binding donor functions. Single-stranded\r\nRNA, after treatment with glyoxal, appears as an extended\r\nfilament whose length can be accurately measured by electronmicroscopy.\r\nBy this means, the molecular weight of Sindbis virus RNA\r\nis determined to be 4.7 \u00b1 0.4 x 106 daltons. Glyoxal treatment is\r\nuseful for the electronmicroscopic mapping of polyA sequences on\r\nRNA molecules, since the RNA is extended without affecting the\r\npolydT binding which is the basis for polyA mapping. Using this method,\r\na polyA sequence has been mapped at one end of Sindbis virus\r\nRNA. Many circular molecules are seen when Sindbis RNA is treated\r\nfor only short periods with glyoxal, then spread for electron\r\nmicroscopy. Under more denaturing conditions, linear molecules\r\nare seen. It is proposed that the two ends of Sindbis viral RNA contain\r\nmutually complementary sequences which normally are base-paired\r\nto form circular molecules. Under the more denaturing conditions\r\nhydrogen bonding is disrupted, which produces linear molecules.
", "doi": "10.7907/a4x7-sy65", "publication_date": "1976", "thesis_type": "phd", "thesis_year": "1976" }, { "id": "thesis:16228", "collection": "thesis", "collection_id": "16228", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10312023-213025015", "type": "thesis", "title": "I. Electron Microscope Heteroduplex Analysis of DNA Sequences in F-Prime Factors. II. Electron Microscope Studies of \u03bb and Mu Prophages. III. An Electron Microscope Study of Sindbis Virus RNA", "author": [ { "family_name": "Hsu", "given_name": "Ming-Ta", "clpid": "Hsu-Ming-Ta" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "This thesis is composed of three parts. Part I is concerned with studies of the DNA sequences of several F-prime factors and the sequence relations among them using electron microscope heteroduplex methods. It was found that the DNA sequence of the F factor can be roughly divided into three regions: 1) a region about one-fourth of the molecule which is concerned with the fertility functions of the F factor. 2) a region about one-third of the molecule which is rich in A+T sequence and contains the sequences used to interact with the bacterial chromosome for the integration or excision of F factor DNA. J) a region which contains the genes for autonomous replication and female phage resistance and the structural element for conjugal transfer.
\r\n\r\nThe structure of the bacterial DNA carried in several classical episomes, F100, F152, F8 and some of their derivatives was studied extensively. Bacterial markers between fep and uvrB were analyzed both genetically and physically. A method was developed to reconstruct the original episomes from their deletion variants. The results confirm the history that F100 and F152 were derived from the same Hfr. The formation of a new episome, F80, from F8 suggested that there is a hot spot in the E. coli chromosome for the recombination with F sequence between 93.2 and 94.5/0.0F.
\r\n\r\nIn part II, the structures of \u03bb and Mu prophages and Mu phage DNA were studied. The \u03bb prophage carried in an F-prime factor was found by electron microscope heteroduplex analysis to be circularly permuted relative to the vegetative viral DNA. On the other hand, Mu prophage DNA was shown to be collinear with the viral DNA. The integrated Mu prophage DNA was used as a marker for physical mapping of bacterial genes in E. coli.
\r\n\r\nSequence heterogeneity in Mu phage and prophage DNA's was also studied. The G loop heterogeneity was found to be present in both phage and prophage DNA.'s and was shown to be due to sequence inversion. The heterogeneous split ends sequences were found to be absent in the several prophages studied.
\r\n\r\nPart III contains an electron microscope study of viral RNA of Sindbis virus and a method for mapping poly A sequences in RNA molecules. Under weak denaturing conditions Sindbis virus RNA appears in circular form with a double stranded \"handle\" of about 250 nucleotides long. This implies that Sindbis RNA contains complementary\r\nsequences at or near the ends of the molecule.
\r\n\r\nA technique using glyoxal as a denaturing agent for mapping polyA sequences in RNA was developed. Glyoxal attaches to guanine base irreversibly and thus removes the secondary structure of RNA without inhibiting the renaturation capacity of polyA sequences in the molecule. A polyA sequence was found at or near one end of Sindbis\r\nRNA by this method.
", "doi": "10.7907/c22c-kg15", "publication_date": "1974", "thesis_type": "phd", "thesis_year": "1974" }, { "id": "thesis:10680", "collection": "thesis", "collection_id": "10680", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02072018-084611335", "type": "thesis", "title": "Genetic Sequences by Electron Microscopy", "author": [ { "family_name": "Chow", "given_name": "Louise Tsi", "clpid": "Chow-Louise-Tsi" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "Caltech Distinguished Alumni Award" }, { "literal": "div_chem" } ], "abstract": "Part I: Sequence homology between the DNA molecules of the \r\ntwo temperate Bacillus subtilis bacteriophages, SPO2 and \u00d8 105,\r\nhas been mapped by electron microcope observation of heteroduplexes.\r\nThere is a region of partial homology covering about 14 % of the\r\ngenome (3.8 x 106 daltons) close to the center of the heteroduplex\r\nmolecule, flanked by completely non-homologous regions of lengths\r\nabout 1.2 x 107 and 1.0 x 107 daltons on the two sides. Within the\r\ncentral homologous region there is a characteristic pattern of duplex \r\nregions and single-strand loops. The amount of duplex decreases as \r\nthe denaturing power of Ue solvent used for preparing the electron \r\nmicroscope grids increases; this indicates that the DNA molecules\r\nof the two phages are only partially homologous w ithin the homology \r\nregion. The heteroduplex patterns show that there are no completely \r\nhomologous nor completely non-homologous gene size sequences within \r\nthe central region of partial homology. Since the phages are sero\u00adlogically \r\nrelated, we conclude that the antigenic determinants for serological \r\ncross-reactivity in the phage tails are coded for by genes in the central \r\nregion of homology. This conclusion is consistent with available genetic \r\ndata. Comparison of genetic and physical data indi\u00adcates that the genes \r\nfor DNA synthesis and for clear plaque formation in the two phages are \r\nnon-homologous. The molecuiar weights of SPO2 DNA and \u00d8 105 DNA are both\t\r\ncalculated as 26.3 (\u00b1 0.3) x 106 daltons, from length measurements \r\nrelative to \u00d8x 174 RF II DNA. Both DNA's have cohesive ends and are capable \r\nof reversible cycli\u00adzation the joined ends dissociate more readily that \r\ndo those of \u03bb DNA. Our physical studies show that each phage DNA consists \r\nof a unique linear sequence and is not circularly permuted, in agreement with \r\nthe conclusion from genetic studies that both phage maps are linear.
\r\n\r\nPart II: Circular duplex structures of the correct length are \r\nobserved in the electron microscope in hybridization mixture of \r\nlysogen DNA and mature phage DNA for the case of the temperate \r\nBacillus subtilis SPO2. This result shows that the sequence order\r\nof the prophage is a circular per mutation of that of the mature phage. \r\nBy making heteroduplexes of prophage DNA with that of the SPO2 \r\ndeletion mutants R90 and S25, the att site of the phage has been\r\nmapped at 61.2 \u00b1 0.6 % from one end of the mature phage DNA,\r\nwhich has a length of 38,600 base-pairs. In the same coordinate \r\nsystem, the R90 deletion extends from 58.9 \u00b1 0.7 to 66.8 \u00b1 0.8 % \r\non the SPO2 chromosome whereas the S25 deletion extends from\r\n63.2 \u00b1 0.6 to 66.9 \u00b1 0.7 % In similar experiments with lysogen and\r\nmature phage DNA's of the temperate B. subtilis phage, \u00d8 105, no \r\ncircular structures were seen. This result shows that the sequence \r\norder in the prophage and the phage are collinear, without circular \r\npermutaion. Short duplex segments, of length 4830 \u00b1 250 base pairs, \r\nwith two single-strand arms at each end are seen at a low frequency \r\nafter denaturation and renaturation of B. sublitis DNA. Several lines \r\nof ecidence support the hy pothesis that these duplex segments are\r\nformed by out-of-register renaturation of the 16s+23s ribosomal \r\nRNA genes (rDNA) of B. subtilis. They are of the correct length. \r\nTheir formation is inhibited if homologous but not if heterologous\r\nribosomal RNA is added to the hybridization mixture. The frequency \r\nof occurrence of the duplex structures is consistent with the rDNA\r\nhypothesis. Heteroduplex molecules are seen with two or three rDNA \r\nduplex segments separated by single-strand substitution loops with \r\nspecific lengths for each of the two single-strand arms of any one \r\nloop. On the basis these structures, linkage groups containing\t7\r\nto 9 rDNA sets (each set containing one 16s and one 23s rDNA gene) \r\nseparated by spacer DNA's are proposed. The evidence indicates\r\nthat if 5s rDNA is present in the set it is located near one end to \r\ngive a gene order 16s-23s-5s. All of the 16s rDNA genes are \r\nlinked to 23s rDNA and vice versa with little or no spacer DNA \r\nbetween a 16s and a 23s sequence. The spacer DNA between 23s \r\nand 5s must also be short. The propnage SPO2 bacterial att \r\nsite maps at a distance 6200 bases away from a 16s+23s rDNA set \r\nwhich is itself separated by a very short spacer (less than \r\n600 bases) from a second rDNA set.
\r\n\r\nPart III: The genetic sequences of seventeen different \u03bbdv's \r\nobtained Dr. D.E. Berg have been mapped on \u03bb DNA by the elec\u00adtron \r\nmicroscope heteroduplex method. The physical results are\r\nin agreement with the genetic analyses of the contents of the \u03bbdv's. \r\nDifferent \u03bbdv's exist predominantly either as monomers, or as \r\ndimers, or as trimers in recA- carrier cells. Higher order \r\noli\u00adgomers are also found in all\u03bb \u03bbdv preparations, Most of the \u03bbdv's \r\noriginated from \u03bb phage carrying the nin deletion are observed to \r\ncontain inverted partial duplications (and are called amphimers).\r\nThat is, the \u03bbdv's carry a duplication of all or some of the sequences \r\nin an inverted order on the same strand. There are four types \r\nof inverted repeat structures: (1) complete inversion and duplication,\r\n(2) partial inversion and duplication with a long (5.7 % of \u03bb+) non\u00ad-\r\ninverted, non-duplicated (or unique) sequence on the left end \r\ncovering the immunity region (oriented according to the \u03bb map), (3) \r\npartial inversion and duplication with a long (5.1 %) and a short\r\n(2.2 %) unique sequence on the left and the tight ends respectively,\r\n(4) partial inversion and duplication with a very short (<0.7 %) \r\nunique sequence on the right end of the \u03bbdv's near the nin deletion. \r\nWhen the closed circular molecules of these inverted \u03bbdv's are \r\nnicked lightly, denatured by alkali, and then reneutralized, the\r\ncomplementary sequences on the same DNA strand \"snap back\" \r\nto form double-stranded linear molecules. The unique sequences,\r\nif any, appear as single-stranded loops at one or both ends when \r\nthe above treated DNA preparations are mounted by the formamide \r\ntechnique. Lambda phage that does not carry the nin deletion does \r\nnot produce \u03bbdv's with inverted repeats. Denaturation of the open \r\ncircular molecules of these non-inverted \u03bbdv's generates, as \r\nexpected, only single-stranded circular and single-stranded linear \r\nmolecules when mounted by the formamide technique. The nin \r\ndeletion is believed to have caused somehow the formation of the\r\n\u03bbdv's containing inverted repeats. The left end points of many \u03bbdv's \r\nmap around 73 % on the \u03bb map while the right boundaries of many\r\n\u03bbdv's map in the vicinity of the nin deletion which extends from\r\n83.8 to 89 .6 % on \u03bb+, indicative of two regions of high \r\nrecombination frequency.
", "doi": "10.7907/YNNT-V341", "publication_date": "1973", "thesis_type": "phd", "thesis_year": "1973" }, { "id": "thesis:10674", "collection": "thesis", "collection_id": "10674", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02052018-145823945", "primary_object_url": { "basename": "Mohr_dc_1973.pdf", "content": "final", "filesize": 41039741, "license": "other", "mime_type": "application/pdf", "url": "/10674/1/Mohr_dc_1973.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Study of the Possibility of the Detection of Fluorescent Dyes by Cathodoluminescence in the Scanning Electron Microscope and Partial Denaturation Maps of Lambda DNA using Methylmercuric Hydroxide", "author": [ { "family_name": "Mohr", "given_name": "Douglas Crane", "clpid": "Mohr-Douglas-Crane" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Part I. The possibilities of using ethidium \r\nbromide, quinacrine hydrochloride, and dansyl chloride \r\nas cathodoluminescent stains for scanning electron\r\nmicroscopy have been investigated. Nucleic acid specimens\r\nstained with the dyes gave best results when they were\r\nembedded in frozen glycerol and examined at liquid\r\nnitrogen temperature. Under these conditions, the\r\nexcitation cross section for ethidium bromide is about\r\n0.5 A2 and the destruction cross section 5 A2. The\r\nother dyes were destroyed quite rapidly.
\r\n\r\nEven under the best conditions, the minimum amount\r\nof ethidium bromide detectable by cathodoluminescence is\r\nabout the same as detectable by fluorescence microscopy.
\r\n\r\nPart II. Methylmercuric hydroxide preferentially\r\nreacts with thymine. This reaction disrupts the Watson-Crick\r\nbase pairing, the mercurated regions appearing as\r\nloops in the electron microscope. Lambda DNA has been\r\npartially denatured by methylmercuric hydroxide and\r\nmounted for electron microscopy by the basic film\r\ntechnique.
\r\n\r\nThe results indicate that there are four regions\r\nwhich readily denature, located on one side of the lambda\r\ngenome. This result is in agreement with other thermal\r\nand alkaline partial denaturation data.
", "doi": "10.7907/1F4Q-0K50", "publication_date": "1973", "thesis_type": "phd", "thesis_year": "1973" }, { "id": "thesis:9881", "collection": "thesis", "collection_id": "9881", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06212016-081819448", "primary_object_url": { "basename": "Robberson_dl_1972.pdf", "content": "final", "filesize": 46068496, "license": "other", "mime_type": "application/pdf", "url": "/9881/1/Robberson_dl_1972.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "I. A Study by Electron Microscopy of the RNA and RNA-DNA Hybrids of Hela Mitochondria. II. Replication of Closed Circular DNA in Mouse L Cells", "author": [ { "family_name": "Robberson", "given_name": "Donald Lewis", "clpid": "Robberson-Donald-Lewis" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_biol" } ], "abstract": "The thesis consists of two parts. In Part I, electron microscope analysis of HeLa mitochondrial RNA-DNA hybrids isolated from CsSO4 gradients demonstrates that more than 85% of the heavy strand of HeLa mitochondrial DNA is transcribed in vivo.
\r\n\r\nA modified basic protein film method of spreading RNA in a strongly denaturing solvent for examination in the electron microscope has been developed and applied to determine the size of the HeLa mitochondrial specific ribosomal RNA (rRNA) components. Length measurements on purified 12S and 16S mitochondrial rRNA, on mixtures of the two, and on mixtures of 12S with 18S cytoplasmic rRNA have given molecular lengths of 0.27 \u03bc, 0.42 \u03bc, and 0. 55 \u03bc for the 12S, 16S, and 18S rRNAs, respectively. If these molecular lengths are proportional to molecular weight, and if the molecular weight of 18S cytoplasmic rRNA is taken as 0.71 x 106, as determined by sedimentation equilibrium, the molecular weights of the 12S and 16S components are 0.35 x 106 and 0.54 x 106, respectively. These molecular weight values are in good agreement with the relative values predicted from sedimentation velocity measurements, but not with the relative values based on gel electrophoresis.
\r\n\r\nElectron microscopy of hybrids between the heavy strand of HeLa mitochondrial DNA and HeLa mitochondrial rRNA demonstrates that the genes for 16S and 12S HeLa mitochondrial rRNAs are situated adjacent, or very close, to each other on mitochondrial DNA. The length of the DNA segment separating the two genes is estimated to correspond to less than 500 nucleotide pairs.
\r\n\r\nA coupling procedure has been developed for the efficient covalent attachment of periodate oxidized RNA to an insoluble matrix of hydrazide-derived sepharose, which is subsequently available for nucleic acid hybridization.
\r\n\r\nIn Part II of the thesis, the properties of a new structure of mitochondrial DNA are discussed. In two strains of mouse L cells, it was found that approximately one half of the closed mitochondrial DNA molecules contain a short three-stranded DNA region in which a short single strand of progeny DNA containing about 350 nucleotides is inserted into the closed circular duplex with the displacement of a corresponding stretch of the still circular parental strand. The three-stranded region is called a D-loop because of its formal shape and because it appears to\r\nhave been formed by displacement replication. Double-length mitochondrial DNA molecules often contain two D-loops which are always at diametrically opposed positions on the 20 megadalton circle. This latter result is taken to indicate that one of the forks in each D-loop marks a unique site for the initiation of replication.
\r\n\r\n", "doi": "10.7907/JKBR-M955", "publication_date": "1972", "thesis_type": "phd", "thesis_year": "1972" }, { "id": "thesis:9697", "collection": "thesis", "collection_id": "9697", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05022016-133803954", "primary_object_url": { "basename": "Kim_jp_1972.pdf", "content": "final", "filesize": 55078813, "license": "other", "mime_type": "application/pdf", "url": "/9697/1/Kim_jp_1972.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Studies on T-Even Bacteriophage DNA", "author": [ { "family_name": "Kim", "given_name": "Jungsuh Park", "clpid": "Kim-Jungsuh-Park" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Part I. The regions of sequence homology and non-homology between the DNA molecules of T2, T4, and T6 have been mapped by the electron microscopic heteroduplex method. The heteroduplex maps have been oriented with respect to the T4 genetic map. They show characteristic, reproducible patterns of substitution and deletion loops. All heteroduplex molecules show more than 85% homology. Some of the loop patterns in T2/T4 heteroduplexes are similar to those in T4/T6.
\r\n\r\nWe find that the rII, the lysozyme and ac genes, the D region, and gene 52 are homologous in T2, T4, and T6. Genes 43 and 47 are probably homologous between T2 and T4. The region of greatest homology is that bearing the late genes. The host range region, which comprises a part of gene 37 and all of gene 38, is heterologous\r\nin T2, T4, and T6. The remainder of gene 37 is partially homologous in the T2/T4 heteroduplex (Beckendorf, Kim and Lielausis, 1972) but it is heterologous in T4/T6 and in T2/T6. Some of the tRNA genes are homologous and some are not. The internal protein genes in general seem to be non-homologous.
\r\n\r\nThe molecular lengths of the T-even DNAs are the same within the limit of experimental error; their calculated molecular weights are correspondingly different due to unequal glucosylation. The size of the T2 genome is smaller than that of T4 or T6, but the terminally repetitious region in T2 is larger. There is a length distribution of the terminal repetition for any one phage DNA, indicating a variability in length of the DNA molecules packaged within the phage.
\r\n\r\nPart II. E. coli cells infected with phage strains carrying extensive deletions encompassing the gene for the phage ser-tRNA are missing the phage tRNAs normally present in wild type infected cells. By DNA-RNA hybridization we have demonstrated that the DNA complementary to the missing tRNAs is also absent in such deletion mutants. Thus the genes for these tRNAs must be clustered\r\nin the same region of the genome as the ser-tRNA gene. Physical mapping of several deletions of the ser-tRNA and lysozyme genes, by examination of heteroduplex DNA in the electron microscope, has enabled us to locate the cluster, to define its maximum size, and to order a few of the tRNA genes within it. That such deletions can be isolated indicates that the phage-specific tRNAs from this cluster are dispensable.
\r\n\r\nPart III. Genes 37 and 38 between closely related phages T2 and T4 have been compared by genetic, biochemical, and hetero-duplex studies. Homologous, partially homologous and non-homologous regions of the gene 37 have been mapped. The host range determinant which interacts with the gene 38 product is identified.
\r\n\r\nPart IV. A population of double-stranded \u00d8X-RF DNA molecules carrying a deletion of about 9% of the wild-type DNA has been discovered in a sample cultivated under conditions where the phage lysozyme gene is nonessential. The structures of deleted monomers, dimers, and trimers have been studied by the electron microscope heteroduplex method. The dimers and trimers are shown to be head-to-tail repeats of the deleted monomers. Some interesting examples of the dynamical phenomenon of branch migration in vitro have been observed in heteroduplexes of deleted dimer and trimer strands with undeleted wild-type monomer viral strands.
\r\n\r\n\r\n", "doi": "10.7907/XYBG-3K08", "publication_date": "1972", "thesis_type": "phd", "thesis_year": "1972" }, { "id": "thesis:10669", "collection": "thesis", "collection_id": "10669", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:02012018-135717308", "primary_object_url": { "basename": "Bowman_rd_1971.pdf", "content": "final", "filesize": 19739887, "license": "other", "mime_type": "application/pdf", "url": "/10669/1/Bowman_rd_1971.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Hydrodynamic Shear Breakage of Native DNA", "author": [ { "family_name": "Bowman", "given_name": "Ray Douglas", "clpid": "Bowman-Ray-Douglas" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Shear breakage is the process by which high molecular weight\r\npolymers are broken one or more times by shear stress generated in\r\nliquid velocity gradients. This thesis is a kinetic study of the \r\nbreakage of native DNA from the coliphage \u03bbb2b5c (contour length 12.8 \u00b5)\r\nin dilute aqueous solution. Breakage of this DNA is produced by flow\r\nthrough a capillary. In all our experiments, each DNA molecule\r\nbreaks only once to form two approximately half-sized molecules.\r\nThe shear stress required to induce breakage is about 103 dynes/cm2.\r\nWe find that the kinetics of breakage are first order and that the first\r\norder rate constant is a function of the fifteenth power of the shear\r\ngradient at 25\u00b0C. The shear stress required to produce breakage at\r\na particular rate increases linearly with DNA concentration over the\r\nrange 0.05 \u00b5g DNA/ml to 7.5 \u00b5g DNA/ml. We observe a very large\r\ntemperature coefficient for the breakage rate which arises from the\r\neffect of temperature on the viscosity of the DNA solution. This\r\nresult indicates that the rate limiting step for DNA shear breakage is\r\nthe speed at which random coil DNA unfolds to an extended configuration\r\nwhen it enters the capillary's liquid velocity gradient. We\r\ndiscuss a kinetic model and a simple theoretical model which have\r\nproperties similar to those observed experimentally.\r\n", "doi": "10.7907/5f4m-ns78", "publication_date": "1971", "thesis_type": "phd", "thesis_year": "1971" }, { "id": "thesis:9099", "collection": "thesis", "collection_id": "9099", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08122015-102840138", "primary_object_url": { "basename": "hyman-rw-1970.pdf", "content": "final", "filesize": 20088343, "license": "other", "mime_type": "application/pdf", "url": "/9099/1/hyman-rw-1970.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "On the Interaction of Actinomycin and DNA", "author": [ { "family_name": "Hyman", "given_name": "Richard Walter", "clpid": "Hyman-Richard-Walter" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Experiments have been accomplished that (a) further define the nature of the strong, G-containing DNA binding sites for actinomycin D (AMD), and (b) quantitate the in vitro inhibition of E. coli RNA polymerase\r\nactivity by T7 DNA-bound AMD.
\r\n\r\nTwenty-five to forty percent of the G's of crab dAT are disallowed\r\nas strong AMD binding sites. The G's are measured to be \r\nrandomly distributed, and, therefore, this datum cannot be explained\r\non the basis of steric interference alone. Poly dAC:TG binds as much\r\nAMD and as strongly as any natural DNA, so the hypothesis that the\r\nunique strong AMD binding sites are G and a neighboring purine is\r\nincorrect. The datum can be explained on the basis of both steric\r\ninterference and the fact that TGA is a disallowed sequence for strong\r\nAMD binding.
\r\n\r\nUsing carefully defined in vitro conditions, there is one RNA\r\nsynthesized per T7 DNA by E. coli RNA polymerase. The rate of the\r\nRNA polymerase-catalyzed reaction conforms to the equation\r\n\r\n1/rate = 1/kA(ATP) + 1/KG(GTP) + 1/KC(CTP) + 1/KU(UTP)\r\n\r\nT7 DNA-bound AMD has only modest effects on initiation and termination\r\nof the polymerase-catalyzed reaction, but a large inhibitory effect\r\non propagation. In the presence of bound AMD, kG and kC are decreased,\r\nwhereas kA and kU are unaffected. These facts are interpreted to mean that on the microscopic level, on the average, the rates of incorporation of ATP and UTP are the same in the absence or\r\npresence of bound AMD, but that the rates of incorporation of GTP and\r\nCTP are decreased in the presence of AMD.
\r\n", "doi": "10.7907/RJRA-PV20", "publication_date": "1970", "thesis_type": "phd", "thesis_year": "1970" }, { "id": "thesis:9092", "collection": "thesis", "collection_id": "9092", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08102015-160156690", "primary_object_url": { "basename": "Lee_cs_1970.pdf", "content": "final", "filesize": 48213338, "license": "other", "mime_type": "application/pdf", "url": "/9092/1/Lee_cs_1970.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "I. Studies on Bacteriophage DNA's and Minicircular DNA's in M. lysodeikticus and E. coli 15. II. Flow Dichroism of DNA Solutions", "author": [ { "family_name": "Lee", "given_name": "Chong Sung", "clpid": "Lee-Chong-Sung" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Part I
\r\n\r\nChapter 1.....A physicochemical study of the DNA molecules\r\nfrom the three bacteriophages, N1, N5, and N6, which infect the bacterium,\r\nM. lysodeikticus, has been made. The molecular weights, as measured\r\nby both electron microscopy and sedimentation velocity, are 23 x 106\r\nfor N5 DNA and 31 x 106 for N1 and N6 DNA's. All three DNA's are capable\r\nof thermally reversible cyclization. N1 and N6 DNA's have identical\r\nor very similar base sequences as judged by membrane filter hybridization\r\nand by electron microscope heteroduplex studies. They have identical\r\nor similar cohesive ends. These results are in accord with the close\r\nbiological relation between N1 and N6 phages. N5 DNA is not closely\r\nrelated to N1 or N6 DNA. The denaturation Tm of all three DNA's is the\r\nsame and corresponds to a (GC) content of 70%. However, the buoyant\r\ndensities in CsCl of Nl and N6 DNA's are lower than expected,\r\ncorresponding to predicted GC contents of 64 and 67%. The buoyant\r\ndensities in Cs2SO4 are also somewhat anomalous. The buoyant density\r\nanomalies are probably due to the presence of odd bases. However, direct\r\nbase composition analysis of N1 DNA by anion exchange chromatography\r\nconfirms a GC content of 70%, and, in the elution system used, no peaks\r\ndue to odd bases are present.
\r\n\r\nChapter 2.....A covalently closed circular DNA form has been\r\nobserved as an intracellular form during both productive and abortive\r\ninfection processes in M. lysodeikticus. This species has been isolated\r\nby the method of CsC1-ethidium bromide centrifugation and examined with\r\nan electron microscope.
\r\n\r\nChapter 3.....A minute circular DNA has been discovered as\r\na homogeneous population in M. lysodeikticus. Its length and molecular\r\nweight as determined by electron microscopy are 0.445 \u03bc and 0.88 x 106\r\ndaltons respectively. There is about one minicircle per bacterium.
\r\n\r\nChapter 4.....Several strains of E. coli 15 harbor a prophage.\r\nViral growth can be induced by exposing the host to mitomycin C or to\r\nuv irradiation. The coliphage 15 particles from E. coli 15 and E, coli\r\n15 T- appear as normal phage with head and tail structure; the particles\r\nfrom E. coli 15 TAU are tailless. The complete particles exert a\r\ncolicinogenic activity on E.coli 15 and 15 T-, the tailless particles\r\ndo not. No host for a productive viral infection has been found and the\r\nphage may be defective. The properties of the DNA of the virus have\r\nbeen studied, mainly by electron microscopy. After induction but before\r\nlysis, a closed circular DNA with a contour length of about 11.9 \u03bc is\r\nfound in the bacterium; the mature phage DNA is a linear duplex and\r\n7.5% longer than the intracellular circular form. This suggests the\r\nhypothesis that the mature phage DNA is terminally repetitious and\r\ncircularly permuted. The hypothesis was confirmed by observing that\r\ndenaturation and renaturation of the mature phage DNA produce circular\r\nduplexes with two single-stranded branches corresponding to the terminal\r\nrepetition. The contour length of the mature phage DNA was measured\r\nrelative to \u03c6X RFII DNA and \u03bb DNA; the calculated molecular weight is\r\n27 x 106. The length of the single-stranded terminal repetition was\r\ncompared to the length of \u03c6X 174 DNA under conditions where single-stranded\r\nDNA is seen in an extended form in electron micrographs. The length of\r\nthe terminal repetition is found to be 7.4% of the length of the nonrepetitious\r\npart of the coliphage 15 DNA. The number of base pairs in\r\nthe terminal repetition is variable in different molecules, with a fractional\r\nstandard deviation of 0.18 of the average number in the terminal\r\nrepetition. A new phenomenon termed \"branch migration\" has been discovered\r\nin renatured circular molecules; it results in forked branches, with\r\ntwo emerging single strands, at the position of the terminal repetition.\r\nThe distribution of branch separations between the two terminal\r\nrepetitions in the population of renatured circular molecules was studied.\r\nThe observed distribution suggests that there is an excluded volume\r\neffect in the renaturation of a population of circularly permuted molecules\r\nsuch that strands with close beginning points preferentially\r\nrenature with each other. This selective renaturation and the phenomenon\r\nof branch migration both affect the distribution of branch separations;\r\nthe observed distribution does not contradict the hypothesis of a\r\nrandom distribution of beginning points around the chromosome.
\r\n\r\nChapter 5....Some physicochemical studies on the minicircular\r\nDNA species in E. coli 15 (0.670 \u03bc, 1.47 x 106 daltons) have been made.\r\nElectron microscopic observations showed multimeric forms of the minicircle\r\nwhich amount to 5% of total DNA species and also showed presumably\r\nreplicating forms of the minicircle. A renaturation kinetic study\r\nshowed that the minicircle is a unique DNA species in its size and base\r\nsequence. A study on the minicircle replication has been made under\r\ncondition in which host DNA synthesis is synchronized. Despite\r\nexperimental uncertainties involved, it seems that the minicircle replication\r\nis random and the number of the minicircles increases\r\ncontinuously throughout a generation of the host, regardless of host\r\nDNA synchronization.
\r\n\r\nPart II
\r\n\r\nThe flow dichroism of dilute DNA solutions (A260\u22480.1) has been\r\nstudied in a Couette-type apparatus with the outer cylinder rotating\r\nand with the light path parallel to the cylinder axis. Shear gradients\r\nin the range of 5-160 sec.-1 were studied. The DNA samples were whole,\r\n\"half,\" and \"quarter\" molecules of T4 bacteriophage DNA, and linear\r\nand circular \u03bbb2b5c DNA. For the linear molecules, the fractional\r\nflow dichroism is a linear function of molecular weight. The dichroism\r\nfor linear A DNA is about 1.8 that of the circular molecule. For a given\r\nDNA, the dichroism is an approximately linear function of shear gradient,\r\nbut with a slight upward curvature at low values of G, and some trend\r\ntoward saturation at larger values of G. The fractional dichroism\r\nincreases as the supporting electrolyte concentration decreases.
", "doi": "10.7907/K05B-3W74", "publication_date": "1970", "thesis_type": "phd", "thesis_year": "1970" }, { "id": "thesis:3675", "collection": "thesis", "collection_id": "3675", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-09212004-105308", "primary_object_url": { "basename": "Davis_rw_1970.pdf", "content": "final", "filesize": 21389716, "license": "other", "mime_type": "application/pdf", "url": "/3675/1/Davis_rw_1970.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "A Study of the Base Sequence Arrangements in DNA by Electron Microscopy", "author": [ { "family_name": "Davis", "given_name": "Ronald Wayne", "clpid": "Davis-Ronald-Wayne" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "Caltech Distinguished Alumni Award" }, { "literal": "div_chem" } ], "abstract": "The study of base sequence arrangements in DNA molecules was accomplished by coupling electron microscopy (EM) with DNA hybridization. Modifications of the basic protein film technique were used. EM methods for examining both double-stranded and single-stranded DNA were used.
\r\n\r\nMany EM studies have a tendency to be rather descriptive in nature. However, it has been my aim to approach problems from a more quantitative aspect. The major problem in quantitative EM of DNA is length fluctuations. It was discovered that the standard deviation in the length of a homogeneous sample of DNA molecules is directly proportional to the square root of the length.
\r\n\r\nAn EM method was developed for determining the size and location of deletion mutations and substitutions in the \u03bb bacteriophage DNA. Heteroduplexes with one strand from the wild type and one strand from the mutant were formed by renaturation. The location of the nonhomology regions can be accurately mapped. A number of mutants were selected that are unable to integrate and by EM studies of the heteroduplexes it was discovered that there is a specific site in the \u03bb DNA (0.574 from the left end) and a specific site in the E. coli DNA where the integration takes place. It was also shown that this specific site in \u03bb DNA would not form stable base pairing with the specific site in the E. coli DNA. This means that the two sites have a base sequence similarity of less than 10 base pairs. A physical gene map of the left arm of the \u03bb DNA molecule was constructed by comparing the physical and genetic location of a large number of mutations.
\r\n\r\nThe DNA isolated from a defective lysogenic phage of E. coli 15 was studied. After induction there is a closed circular DNA in vivo. However, the DNA is packaged as a linear molecule in the phage head. The mature linear DNA is 7.5% longer than the in vivo closed circular DNA. This was found to be because the mature linear DNA is both terminally repetitious (TR) and circularly permuted. Circular molecules are obtained by denaturing and renaturing the linear molecules. These in vitro circular molecules have two single-stranded DNA branches, each equal in length to the TR. The amount of the TR was found to be slightly heterogeneous. Therefore, the amount of linear DNA that is packaged in the phage head is slightly variable and there is no mechanism for packaging exactly the same amount of DNA.
\r\n\r\nThe mitochondria of human leukemic leukocytes contain covalently closed circular DNA molecules of twice the molecular weight found in mitochondria of normal leukocytes. Heteroduplexes containing one dimer length strand and two complementary monomer length strands were formed by renaturation. These heteroduplex DNA molecules appear as figure eights. They were carefully examined for DNA substitutions or deletions but none were found. Therefore, the dimer molecule is composed of exactly two monomer molecules.
\r\n\r\nEM studies of the SV40 DNA showed that it is heterogeneous in length. From heteroduplex studies it was learned that this DNA is heterogeneous in base sequence as well. About half of the self-renatured molecules contained non-homology regions. The size (up to 1/2 the molecule) and the number of non-homology regions varied considerably. Unique classes of heteroduplex molecules could not be found and no reasonable conclusions could be given for the nature or origin of the heterogeneity.
\r\n\r\nThe replicating intermediates in the in vivo synthesis of \u00d8X174 DNA were studied. The single-stranded DNA is synthesized from a double-stranded template as a linear molecule. The replicating intermediate appears as a double-stranded circular molecule with a linear single-stranded branch attached to the circle. The linear branch was never found to be longer than the mature circular DNA and is presumably released after one round of replication on the template and then cyclized by an as yet undetermined means.
\r\n\r\nRNA was synthesized on T\u2087 DNA in vitro. The resulting RNA-RNA polymerase-DNA complex was visualized in the EM. By synchronizing initiation and mapping the location of the RNA at various times it was discovered that synthesis is always initiated close to one unique end, and thus, presumably at a unique site. At one min there is one PNA per DNA. At high RNA polymerase concentrations, closely spaced sequential initiations occur from the one active initiation site. The rate of propagation was measured as about 45 bases/sec.
", "doi": "10.7907/1QZW-ZP91", "publication_date": "1970", "thesis_type": "phd", "thesis_year": "1970" }, { "id": "thesis:3709", "collection": "thesis", "collection_id": "3709", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-09232002-113015", "primary_object_url": { "basename": "Wetmur_jg_1967.pdf", "content": "final", "filesize": 15327669, "license": "other", "mime_type": "application/pdf", "url": "/3709/1/Wetmur_jg_1967.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Studies on the Kinetics of Renaturation of DNA", "author": [ { "family_name": "Wetmur", "given_name": "James Gerard", "clpid": "Wetmur-James-Gerard" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document. \r\n\r\nA temperature jump system is described for studying fast DNA renaturation reactions. The reaction is found to be second order as seen in the time course of the reaction and in the concentration dependence of the rate. The stepwise base-pairing model of Saunders and Ross is extended to allow varying DNA base composition. Rate constants calculated with this model are compared with experimental rate constants at varying temperatures.\r\n\r\nT4 and T7 DNAs were fragmented by various procedures. The molecular weight of denatured DNA was determined by alkaline sedimentation. For a given DNA, fragmented into different molecular weights, the rate of renaturation is found to be proportional to the square root of the molecular weight. The rate of renaturation of DNA was measured in sucrose, glycerol, ethylene glycol and sodium perchlorate solutions. The melting temperature of DNA is changed by different amounts in each solvent. Nevertheless, the rate constant multiplied by the viscosity and divided by the renaturation temperature is found to be a constant. Thus, the rate determining step must be hydrodynamically limited.\r\n\r\nThe complexity of the DNA of an organism is defined as the total DNA complement of the organism. The rates of renaturation of SV40, T7, Nl, T4, E coli and Ascites tumor DNA (non-repeated sequences) are inversely proportional to the complexity. After complexity correction, the rate of renaturation is found to depend slightly on the GC content of the DNA. The stepwise renaturation model predicts this result.\r\n\r\nA method is described for positively staining electron microscope grids prepared by the method of Kleinschmidt and Zahn.\r\n\r\nSome properties of N1 DNA are described. The DNA has a buoyant density corresponding to 64% GC, a molecular weight of 33 X 10[^6]and the property of reversible cyclization like lambdoid phage DNAs.", "doi": "10.7907/YB2H-T758", "publication_date": "1967", "thesis_type": "phd", "thesis_year": "1967" }, { "id": "thesis:3580", "collection": "thesis", "collection_id": "3580", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-09172002-162743", "primary_object_url": { "basename": "Galley_wc_1967.pdf", "content": "final", "filesize": 8941631, "license": "other", "mime_type": "application/pdf", "url": "/3580/1/Galley_wc_1967.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Triplet Energy Delocalization in Polynucleotide-Acridine Complexes", "author": [ { "family_name": "Galley", "given_name": "William Claude", "clpid": "Galley-William-Claude" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nTransfer of triplet electronic excitation energy from the purine and/or pyrimidine moities of native DNA and adenine polynucleotides to the acridine dye 9-aminoacridine has been demonstrated at 77 [degrees] K. The occurrence of such transfers indicates that there is pi electron overlap between the purine and/or pyrimidine bases and the dye bound to the polymer.\r\n\r\nThe acridine dye has then been used as a trap for the polymer triplet excitation energy. The polymer to dye dependence of the base to dye transfer efficiency indicates that triplet energy is delocalized in native DNA and adenine polynucleotides. Kinetic studies provide evidence that the pathlength for triplet energy transfer in native DNA is determined by trapping within the polymer rather than by diffusion.\r\n\r\nDelayed fluorescence from the dye bound to DNA has been observed and its origin in the triplet state of the polymer has been confirmed at high polymer to dye ratios. In addition it has been shown that delayed fluorescence can arise from triplet-triplet annihilation between dyes at low polymer to dye ratios.", "doi": "10.7907/QTHP-8Y47", "publication_date": "1967", "thesis_type": "phd", "thesis_year": "1967" }, { "id": "thesis:9189", "collection": "thesis", "collection_id": "9189", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10012015-160718695", "primary_object_url": { "basename": "Olivera_bm_1966.pdf", "content": "final", "filesize": 39770446, "license": "other", "mime_type": "application/pdf", "url": "/9189/1/Olivera_bm_1966.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "The Interactions of Basic Proteins and DNA : I. Electrophoresis of the Nucleic Acids. II. The Cytochrome C/DNA Complex. III. Studies of the Electrophoresis and Melting Behavior of Nucleohistones. IV. The Dissociation of Histone from Calf Thymus Chromatin", "author": [ { "family_name": "Olivera", "given_name": "Baldomero Marquez", "clpid": "Olivera-Baldomero-Marquez" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "I. ELECTROPHORESIS OF THE NUCLEIC ACIDS
\r\nA zone electrophoresis apparatus using ultraviolet optics has been constructed to study nucleic acids at concentrations less than 0.004%. Native DNA has a mobility about 15% higher than denatured DNA over a range of conditions. Otherwise, the electrophoretic mobility is independent of molecular weight, base composition or source. DNA mobilities change in the expected way with pH but the fractional change in mobility is less than the calculated change in charge. A small decrease in mobility accompanies an increase in ionic strength. RNA\u2019s from various sources have mobilities slightly lower than denatured DNA except for s-RNA which travels slightly faster. The important considerations governing the mobility of nucleic acids appear to be the nature of the hydrodynamic segment, and the binding of counterions. The differences between electrophoresis and sedimentation stem from the fact that all random coil polyelectrolytes are fundamentally free draining in electrophoresis.
\r\nII. THE CYTOCHROME C/DNA COMPLEX
\r\nThe basic protein, cytochrome c, has been complexed to DNA. Up to a cytochrome:DNA mass ratio of 2, a single type of complex is formed. Dissociation of this complex occurs between 0.05F and 0.1F NaCl. The complexing of cytochrome to DNA causes a slight increase in the melting temperature of the DNA, and a reduction of the electrophoretic mobility proportional to the decrease in net charge. Above a cytochrome:DNA mass ratio of 2.5, a different type of complex is formed. The results suggest that complexes such as are formed in the Kleinschmidt technique of electron microscopy would not exist in bulk solution and are exclusively film phenomena.
\r\nIII. STUDIES OF THE ELECTROPHORESIS AND MELTING BEHAVIOUR OF NUCLEOHISTONES
\r\nElectrophoresis studies on reconstituted nucleohistones indicate that the electrophoretic mobility for these complexes is a function of the net charge of the complex. The mobility is therefore dependent on the charge density of the histone complexing the DNA, as well as on the histone/DNA ratio. It is found that the different histones affect the transition from native to denatured DNA in different ways. It appears that histone I is exchanging quite rapidly between DNA molecules in 0.01 F salt, while histone II is irreversibly bound. Histone III-IV enhances the capacity of non-strand separated denatured DNA to reanneal. Studies on native nucleoproteins indicate that there are no gene-sized uncomplexed DNA regions in any preparations studied.
\r\nIV. THE DISSOCIATION OF HISTONE FROM CALF THYMUS CROMATIN
\r\nCalf thymus nucleoprotein was treated with varying concentrations of NaCl. The identity of the histones associated and dissociated from the DNA at each salt concentration was determined by gel electrophoresis. It was found that there is no appreciable histone dissociation below 0.4 F NaCl. The lysine rich histones dissociate between 0.4 and 0.5 F NaCl. Their dissociation is accompanies by a marked increase in the solubility of the chromatin. The moderately lysine rich histones dissociate mainly between 0.8 and 1.1 F NaCl. There are two arginine rich histone components: the first dissociates between 0.8 F and 1.1 F NaCl, but the second class is the very last to be dissociated from the DNA (dissociation beginning at 1.0 F NaCl). By 2.0 F NaCl, essentially all the histones are dissociated.
\r\nThe properties of the extracted nucleoprotein were studied. The electrophoretic mobility increases and the melting temperature decreases as more histones are dissociated from the DNA. A comparison with the dissociation of histones from DNA in NaClO4 shows that to dissociate the same class of histones, the concentration of NaCl required is twice that of NaClO4.
\r\n", "doi": "10.7907/6NP0-3K17", "publication_date": "1966", "thesis_type": "phd", "thesis_year": "1966" }, { "id": "thesis:9194", "collection": "thesis", "collection_id": "9194", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10052015-092714954", "primary_object_url": { "basename": "Ohlenbusch_hh_1966.pdf", "content": "final", "filesize": 86067623, "license": "other", "mime_type": "application/pdf", "url": "/9194/1/Ohlenbusch_hh_1966.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Part I. Electric Birefringence Studies of Deoxyribonucleic Acids. Part II. Selective Dissociation of Nucleohistone Complexes", "author": [ { "family_name": "Ohlenbusch", "given_name": "Heiko Herbert Emil Walter", "clpid": "Ohlenbusch-Heiko-Herbert-Emil-Walter" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Part I
\r\nThe electric birefringence of dilute DNA solutions has been studied in considerable detail and on a large number of samples, but no new and reliable information was discovered concerning the tertiary structure of DNA. The large number of variables which effect the birefringence results is discussed and suggestions are made for further work on the subject.
\r\nThe DNA molecules have been aligned in a rapidly alternating (10 to 20 kc/sec) square wave field confirming that the orientation mechanism is that of counterion polarization. A simple empirical relation between the steady state birefringence, \u0394nst, and the square of the electric field, E, has been found: \u0394nst = E2/(a E2 + b), where a = 1/\u0394ns and b = (E2/\u0394nst)E\u2192o. \u0394ns is the birefringence extrapolated to infinite field strength.
\r\nThe molecules show a distribution of relaxation times from 10-4 to 0.2 sec, which is consistent with expectations for flexible coil molecules. The birefringence and the relaxation times decrease with increasing salt concentrations. They also depend on the field strength and pulse duration in a rather non-reproducible manner, which may be due in part to changes in the composition of the solution or in the molecular structure of the DNA (other than denaturation). Further progress depends on the development of some control over these effects.
\r\nPart II
\r\nThe specificity of the dissociation of reconstituted and native deoxyribonucleohistones (DNH) by monovalent salt solutions has been investigated. A novel zone ultracentrifugation method is used in which the DNH is sedimented as a zone through a preformed salt gradient, superimposed on a stabilizing D2O (sucrose) density gradient. The results, obtained by scanning the quartz sedimentation tubes in a spectrophotometer, were verified by the conventional, preparative sedimentation technique. Procedures are discussed for the detection of microgram quantities of histones, since low concentrations must be used to prevent excessive aggregation of the DNH.
\r\nThe data show that major histone fractions are selectively dissociated from DNH by increasing salt concentrations: Lysine rich histone (H I) dissociates gradually between 0.1 and 0.3 F, slightly lysine rich histone (H II) dissociates as a narrow band between 0.35 and 0.5 F, and arginine rich histone (H III, H IV) dissociates gradually above 0.5 F NaClO4.
\r\nThe activity of the partially dissociated, native DNH in sustaining RNA synthesis, their mobility and their unusual heat denaturation and renaturation behavior are described. The two-step melting behavior of the material indicates that the histones are non-randomly distributed along the DNA, but the implications are that the uncovered regions are not of gene-size length.
\r\n", "doi": "10.7907/GA9Z-6S65", "publication_date": "1966", "thesis_type": "phd", "thesis_year": "1966" }, { "id": "thesis:726", "collection": "thesis", "collection_id": "726", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-02242003-090009", "primary_object_url": { "basename": "jensen_rh_1965.pdf", "content": "final", "filesize": 6663692, "license": "other", "mime_type": "application/pdf", "url": "/726/1/jensen_rh_1965.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Complexes of Silver (I) with Nucleic Acids", "author": [ { "family_name": "Jensen", "given_name": "Ronald Harry", "clpid": "Jensen-Ronald-Harry" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The equilibrium properties of the Ag (I) complexes of DNA have been studied potentiometrically and spectrophotometrically at ionic strength of 0.1 M (NaC10[subscript 4]) and at pH's from 5.6 to 8.0. There are at least two different complexes which form at low silver ion concentrations. The strength of association of one complex (type I binding) is pH independent. The type I complexing reaction releases no protons from the DNA. A second complex (type II binding) is stronger at high pH. This complexing causes the release of approximately one proton per Ag (I) bound.\r\n\r\nDNA which is rich in GC binds Ag (I) more strongly than does AT rich DNA. However, at pH's between 5.6 and 8.0 more protons are released from AT-rich DNA's.\r\n\r\nIt is proposed that the first complex (type I) involves only GC base pairs, with silver (I) adding to the sigma electrons of a ring nitrogen or interacting with the pi electrons. In the second complex (type II), Ag (I) replaces an N-1 (purine) to N-3 (pyrimidine) hydrogen bond, thus displacing one proton.\r\n\r\nThe complexing behavior of various polynucleotides, nucleotides and substituted purines was studied, and the DNA complexes are discussed in the light of these results.\r\n\r\nA cesium sulfate equilibrium density gradient ultracentrifugation technique has been developed in which buoyant density differences between different DNA's are generated by the specific formation of their Ag (I) complexes. When Ag (I) is bound to the extent of one silver ion per DNA base pair, the buoyant density of either native or denatured DNA increases by about .17 g/cc.\r\n\r\nCompetition experiments in which Ag (I) was added to a mixture of two different DNA's resulted in specific binding of the Ag (I) by one of the DNA species. At equilibrium in the ultracentrifuge two widely separated DNA bands were observed. The buoyant density difference between these bands corresponded to the difference in Ag (I) binding by the two species of DNA.\r\n\r\nA survey was done of various useful preparative separations based on this technique. One such preparative separation has been accomplished, and the separated components have been characterized.", "doi": "10.7907/7V9M-6D68", "publication_date": "1965", "thesis_type": "phd", "thesis_year": "1965" }, { "id": "thesis:4405", "collection": "thesis", "collection_id": "4405", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-11052002-161025", "primary_object_url": { "basename": "Wirth_th_1964.pdf", "content": "final", "filesize": 8497972, "license": "other", "mime_type": "application/pdf", "url": "/4405/1/Wirth_th_1964.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Mercury-Amine Complexes and Aromatic Mercurials: a Study of Compounds Containing Mercury-Nitrogen and Mercury-Carbon Bonds in Aqueous Solution", "author": [ { "family_name": "Wirth", "given_name": "Thomas Henry", "clpid": "Wirth-Thomas-Henry" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe Hg(II) complexes of aniline, guanidine, and ammonia have been studied potentiometrically in aqueous solution with a mercury electrode. The stability of the HgR[subscript 2][superscript ++] complexes of these compounds correlates well with their basicities. An RHgOH[superscript +] complex (R = guanidine) has been identified potentiometrically and its stability determined.\r\n\r\nPotentiometric evidence for the existence of a 1: 1 Hg(I)-aniline complex was confirmed spectrophotometrically. The complex is less stable than the corresponding complex of Hg(II). No 2: 1 complex (Hg[subscript 2] L[subscript 2][superscript ++]) was observed.\r\n\r\nThe 1: 1 complexes of aniline and para-mercurated aniline with Hg(II) were studied spectrophotometrically. Cationic, ring mercurated anilines bind Hg(II) strongly; no decrease in complex stability occurs as -Hg[superscript +] groups are added to the aromatic ring. Complexes of Hg(II) with mercurated anilines exhibit a unique ultraviolet absorption band at 330-335 m[mu] in aqueous solution.\r\n\r\nSlow but pronounced spectral changes occur in aqueous Hg(C1O[subscript 4])[subscript2]-HC1O[subscript 4] solutions containing small amounts of [psi]NH[subscript 3C1O[subscript 4] which are allowed to stand. These changes have been interpreted in terms of mercuration of the aniline and the formation of Hg(II) complexes with the products.\r\n\r\nSingle crystals of an explosive Hg(II)-aniline compound C[subscript 6]NH[subscript 3]Hg[subscript 3](C1O[subscript 4)[subscript 2] [...] 4H[subscript 2]O have been prepared.\r\n\r\nEquilibrium in the mercuration of benzene and p-methoxy anisole has been studied at room temperature in aqueous HC1O[subscript 4]NaC1O[subscript 4] solution in the presence of excess organic. An analytical procedure utilizing the U.V. absorption of the HgC1[subscript 4][superscript =] complex was used. The equilibrium quotient of the reaction C[subscript 6]H[subscript 6] + Hg[superscript ++] = C[subscript 6H[subscript 5]Hg[superscript +] +H [superscript +] lies in the range 70-500.", "doi": "10.7907/2P2A-GE19", "publication_date": "1964", "thesis_type": "phd", "thesis_year": "1964" }, { "id": "thesis:7034", "collection": "thesis", "collection_id": "7034", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05162012-070830184", "type": "thesis", "title": "Studies of the Metal Ion Complexes of Purines and Pyrimidines by Electrophoresis and Other Methods", "author": [ { "family_name": "Vasi\u013cevskis", "given_name": "J\u0101nis", "clpid": "Vasilevskis-J\u0101nis" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "A density-gradient-stabilized electrophoresis apparatus has been designed and built.
\r\n\r\nSpectrophotometric and electrophoretic measurements are used to investigate the hydrogen ion, mercuric ion, and methylmercuric ion complexes of purine and pyrimidine derivatives. The results are used to infer the charge of the complexes.
\r\n\r\nThe problem of determining the charge of an ion from its mobility and diffusion coefficient is also considered.
\r\n", "doi": "10.7907/Y9PS-DG32", "publication_date": "1963", "thesis_type": "phd", "thesis_year": "1963" }, { "id": "thesis:7249", "collection": "thesis", "collection_id": "7249", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10302012-085345824", "primary_object_url": { "basename": "Stewart_rf_1963.pdf", "content": "final", "filesize": 36560088, "license": "other", "mime_type": "application/pdf", "url": "/7249/1/Stewart_rf_1963.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Polarized Absorption Spectra of Purines and Pyrimidines", "author": [ { "family_name": "Stewart", "given_name": "Robert Farrell", "clpid": "Stewart-Robert-Farrell" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The polarized absorption spectra for single crystals of 1-methylthymine and 9-methyladenine and hydrogen-bonded complex of the two have been determined. A \r\nmicrospectro-photometer was constructed to carry out these measurements. A technique for preparing thin sections of the single crystals with thicknesses down to 10^(-5) cm has been developed. Special attention has been given to intensity determinations for the several ultraviolet absorption spectra.", "doi": "10.7907/Y85T-DN22", "publication_date": "1963", "thesis_type": "phd", "thesis_year": "1963" }, { "id": "thesis:6554", "collection": "thesis", "collection_id": "6554", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:07282011-100303520", "primary_object_url": { "basename": "Dove_wf_1962.pdf", "content": "final", "filesize": 33834690, "license": "other", "mime_type": "application/pdf", "url": "/6554/1/Dove_wf_1962.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "The Helix-Coil Transition in DNA: Effects of the Interactions with Small-Ion and of the Composition of DNA", "author": [ { "family_name": "Dove", "given_name": "William Franklin", "clpid": "Dove-William-Franklin" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "We have studied the effects of ion binding and DNA composition on the helix-coil denaturation of the DNA macromolecule. Among the systems studied, none gave a marked increase in the composition dependence of the denaturation conditions, an increase which would\r\nallow extensive fractionation of a compositionally disperse DNA sample.\r\n\r\nThe binding of protons to DNA is extensive even before hyperchromicity and irreversible changes in intrinsic viscosity are observed, and includes protonation of the cytosine heterocycle. It is intriguing that this cytosine protonation seems to require the breaking of hydrogen\r\nbonds in the Watson-Crick structure.\r\n\r\nThe binding of Mg^(++), Co^(++), or Ag^+ at low ionic strengths markedly stabilizes the helical conformation. We have evaluated the extent to which high concentrations of Na^+ ion reduce the binding of Mg^(++) and H^+ ions.\r\n\r\nBroad transitions are observed at low ionic strengths of Na^+ ion, and in the presence of the equivalent ratios r=0.2 Ag^+, r=0.5 Co^(++), or r=0.5 Mg^(++). In the latter two cases, this broadening maybe due to the selective binding of cations to native DNA, but the broadening observed at low Na^+ concentrations may be due to a change in Zimm's parameters \u03c3_o and/or \u03c3_j.\r\n\r\nThe inactivation of the transforming ability of pneumococcal\r\nDNA for three characteristics was studied at 0.1 and 3x10^(-4) ionic strengths. Differences in denaturation temperature were observed which could not be correlated with the compositions deduced by Rolfe and Ephrussi-Taylor from density differences. At low ionic strengths, extremely broad inactivation curves were observed, and can be explained by the renaturation made possible by the existence of short helical regions in low ionic strength denaturations.", "doi": "10.7907/SYPJ-C611", "publication_date": "1962", "thesis_type": "phd", "thesis_year": "1962" }, { "id": "thesis:5796", "collection": "thesis", "collection_id": "5796", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05112010-154607309", "primary_object_url": { "basename": "Rapaport_sa_1962.pdf", "content": "final", "filesize": 14599182, "license": "other", "mime_type": "application/pdf", "url": "/5796/1/Rapaport_sa_1962.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "I. Determination of the Quantum Yield of Thymidine Dinucleoside Irradiated by Ultra-Violet Light. II. Studies on the Inactivation by Ultra-Violet light of T\u2084D Bacteriophage Containing 5-Bromodesoxyuridine Substituted DNA", "author": [ { "family_name": "Rapaport", "given_name": "Seymour Alvin", "clpid": "Rapaport-Seymour-Alvin" } ], "thesis_advisor": [ { "family_name": "Delbruck", "given_name": "Max", "clpid": "Delbr\u00fcck-M" }, { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "It has been found that when frozen thymine solutions are irradiated by ultra-violet light a photoreversible steady state is formed between thymine and a thymine diner. The suggestion has been made that such photoreversible chemical reactions might be involved in the photoreactivable mutations that occur upon irradiation of viruses with ultra-violet light. In order to give further credence to this thymine dinucleoside, TpT, was prepared and irradiated by ultra-violet light as described in Part I. A wavelength dependent photosteady state was found tobe established by this, and the quantum yield of the reaction of TpT to its photoproduct determined. The existence of this steady state and the magnitude of the quantum yield (0.002) support the supposition that similar reactions may cause the photoreversible mutations in viral DNA.\r\n\r\nPart II describes the determination of the action spectrum of in activation of plaque forming ability of T_4 bacteriophages grown in the presence of the thymidine analogue 5-bromodesoxyuridine (5-BD). Under these conditions 5-BD is substituted intothe DNA in place of thymidine. Such substituted DNA has been found to have increased sensitivity to UV light at 254 m\u03bc. The action spectrum was determined to more precisely define this increase in sensitivity and to obtain additional information regarding the UV inactivation of DNA. It was found that 5-BD substituted T_4 was uniformly more sensitive to UV than unsubstituted T_4; this effect was most striking in the 302 to 334 m\u03bc region where a factor of increased sensitivity up to 500 to 1000 times was noted. Furthermore, unlike unsubstituted T_4, killing of 5-BD substituted T_4 was found to follow \"one hit\" kinetics. The action spectrum indicated that 5-BD was directly involved in the initial steps of inactivation and was compatible with the possibility of transfer of absorbed light energy along the polynucleotide chain.", "doi": "10.7907/V4NH-KB09", "publication_date": "1962", "thesis_type": "masters", "thesis_year": "1962" }, { "id": "thesis:6599", "collection": "thesis", "collection_id": "6599", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08182011-150313553", "primary_object_url": { "basename": "Wulff_dl_1962.pdf", "content": "final", "filesize": 12550495, "license": "other", "mime_type": "application/pdf", "url": "/6599/1/Wulff_dl_1962.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "On Nucleic Acid Photochemistry", "author": [ { "family_name": "Wulff", "given_name": "Daniel Lewis", "clpid": "Wulff-Daniel-Lewis" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "I. Frozen aqueous solutions of thymine and N, N'-dimethylthymine have been irradiated at 2537 \u00c5 to yield two dimers from N,N'-dimethylthymine and a single dimer from thymine. In all cases irradiation of the dimer in liquid aqueous solution at 2537 \u00c5 causes reversion to the monomer. One of the photodimers obtained from N,N'-dimethylthymine is identical to a product obtained by exhaustively N\u2013methylating the single photodimer obtained from thymine. Nuclear magnetic resonance and ultraviolet absorption data support a structure containing a cyclobutane ring.\r\n\r\nII. Action spectra for formation of thymine dimer in E. coli\r\nDNA have been taken. The initial quantum yield is not strongly dependent on wavelength. The ratio of thymine dimer to thymine in the photo-stationary state is much more dependent on wavelength. At the 235 m\u00b5 photo steady state 1.7% of the thymine is present as dimer. This shifts\r\nto 6.5% at 254 m\u00b5 and to 20% at 275 m\u00b5. While the change in the position of the photosteady state with wavelength fails to fit a simple model, the data do indicate that not all thymines are capable of participating in dimer formation.\r\n\r\nIII. Irradiation of ultraviolet irradiated DNA with photoreactivating light (370 m\u00b5) in the presence of an extract from baker's yeast containing photoreactivating enzyme causes the disappearance of thymine photodimer. The agent causing thymine photodimer to disappear is heat\r\nlabile. These results suggest that the molecular basis of photoreactivation of biological damage to microorganisms is the reconversion of thymine photodimer to thymine.\r\n", "doi": "10.7907/ENS3-PQ39", "publication_date": "1962", "thesis_type": "phd", "thesis_year": "1962" }, { "id": "thesis:5730", "collection": "thesis", "collection_id": "5730", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04212010-142614826", "primary_object_url": { "basename": "Wallace_fa_1960.pdf", "content": "final", "filesize": 957667, "license": "other", "mime_type": "application/pdf", "url": "/5730/1/Wallace_fa_1960.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "pH Titration Studies of the Acid Denaturation of Calf Thymus Deoxyribosenucleic Acid", "author": [ { "family_name": "Wallace", "given_name": "Frederic Andrew", "clpid": "Wallace-Frederic-Andrew" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The acid denaturation of calf thymus deoxyribosenucleic acid (DNA) has been studied both by PH and \r\nspectrophotometric titration in the temperature range \r\n10 - 30\u00b0C and at ionic strengths 0.1 F and 0.5 F. The \r\nnumber of hydrogen ions bound by the DNA at any given \r\npH increased with increasing temperature and decreased \r\nwith increasing ionic strength. The number bound at \r\nany given pH was greater after denaturation. A model \r\nfor acid denaturation is proposed. The site of protonation of cytosine is discussed.\r\n", "doi": "10.7907/MME6-8038", "publication_date": "1961", "thesis_type": "masters", "thesis_year": "1961" }, { "id": "thesis:2949", "collection": "thesis", "collection_id": "2949", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-07202006-091354", "primary_object_url": { "basename": "Yamane_t_1960.pdf", "content": "final", "filesize": 5641708, "license": "other", "mime_type": "application/pdf", "url": "/2949/1/Yamane_t_1960.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "I. Complexes of Mercury (I) with Polyphosphate and Dicarboxylate Anions and Mercury (II) Pyrophosphate Complexes. II. The Interaction of Mercuric Chloride with Deoxyribonucleic Acid", "author": [ { "family_name": "Yamane", "given_name": "Tetsuo", "clpid": "Yamane-Tetsuo" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\n\r\nPart I: It has been discovered that mercurous mercury forms complexes with pyrophosphate, tripolyphosphate, oxalate, [...]-dimethylmalonate, and succinate. These complexes are stable towards disproportionation to mercury (II) complexes and mercury. If L(-q) is the anion, the principal complexes are Hg2L2(-2q+2) and Hg2(OH)L(-q+1). The formation constants were determined from the potential of a mercury-mercurous electrode in ligand solutions. Theory and experiment agree that mercurous complexes of ligands (such as NH3 and CN-) which form strong covalent bonds to mercury are unstable towards disproportionation to give mercuric complexes but \"ionic\" chelating ligands can form stable mercurous complexes.\r\n\r\nThe mercury (II) pyrophosphate complex was studied from the potential of a Pt electrode in Hg2(I), Hg(II), pyrophosphate solutions at pH 7-10. The principal species is Hg(OH)(P2O7)(-3), with a formation constant of (2.8\u00b10.6)10(17)M-2.\r\n\r\nPart II: The interaction of mercury (II) with DNA was studied. The formation of the DNA-Hg(II) complex is reversible according to spectrophotometric, viscometric, and biological criteria. Based on the ultraviolet absorption spectra and on the number of protons liberated from DNA during complexation, the binding sites of Hg(II) to DNA are discussed.", "doi": "10.7907/D5YM-BF81", "publication_date": "1960", "thesis_type": "phd", "thesis_year": "1960" }, { "id": "thesis:2975", "collection": "thesis", "collection_id": "2975", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-07242006-152841", "primary_object_url": { "basename": "Taylor_rl_1960.pdf", "content": "final", "filesize": 6247197, "license": "other", "mime_type": "application/pdf", "url": "/2975/1/Taylor_rl_1960.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "I. A Study of Vibrational Relaxation in Carbon Monoxide by Shock-Waves and Infra-Red Emission. II. A Study of the Effect of a Resonant Transfer of Energy on the Vibrational Relaxation of Gas Mixtures", "author": [ { "family_name": "Taylor", "given_name": "Raymond Leonard", "clpid": "Taylor-Raymond-Leonard" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "I: Pure CO gas was rapidly heated by the passage of a shock wave, and the vibrational relaxation time determined from measurements of the time history of the intensity of the 1st overtone transition at 2.35[microns]. The relaxation time was measured over a temperature range of 1400-3000\u00b0K and at pressures from 1 1/2 - 4 atmospheres. At 1400\u00b0K and 1 atm. a value of 650 \u00b1 50 [micro]sec. was obtained. A large impurity effect was discovered and is believed to be caused by traces of water vapor.\r\n\r\nII: The effect of an efficient, near-resonant exchange of vibration energy between O2 and N2 molecules on the vibration relaxation behavior was investigated. The near-resonant and non-resonant vibrations transition probabilities were estimated from current theory. It was shown that the resonant process can provide a catalytic path for the rapid vibrational relaxation of the slower component (N2). The hypothetical calculations are compared with experiment, and\tinterpretation of the \"impurity effect\" of H2O is given in terms of a resonant process.", "doi": "10.7907/61Z9-2S65", "publication_date": "1960", "thesis_type": "phd", "thesis_year": "1960" }, { "id": "thesis:5735", "collection": "thesis", "collection_id": "5735", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04222010-093442090", "primary_object_url": { "basename": "Helman_wp_1960.pdf", "content": "final", "filesize": 998326, "license": "other", "mime_type": "application/pdf", "url": "/5735/1/Helman_wp_1960.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Absorption and Dispersion of Sound in Reacting and Relaxing Fluids", "author": [ { "family_name": "Helman", "given_name": "William Phillip", "clpid": "Helman-William-Phillip" } ], "thesis_advisor": [ { "family_name": "Mazo", "given_name": "Robert M.", "clpid": "Mazo-R-M" }, { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The hydrodynamic equations for a chemically reacting and internally relaxing fluid are obtained in a suitable form, and, are then used to find the dispertion and absorption of plane infinitesimal sound waves, Only the case of no viscosity, heat conduction, and diffusion is considered. It is shown that the interference effects between relaxation processes are not, in general, negligible compared to the relaxation effects themselves. A specific example, that of oxygen gas at 2500\u00b0 K is considered giving an idea of the relative magnitudes of the several effects which are involved.\r\n", "doi": "10.7907/DW69-PB79", "publication_date": "1960", "thesis_type": "masters", "thesis_year": "1960" }, { "id": "thesis:517", "collection": "thesis", "collection_id": "517", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-02062006-102644", "primary_object_url": { "basename": "Engleman_r_1959.pdf", "content": "final", "filesize": 8243061, "license": "other", "mime_type": "application/pdf", "url": "/517/1/Engleman_r_1959.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "On the Recombination Rate of Iodine Atoms in the Presence of Various Gases", "author": [ { "family_name": "Engleman", "given_name": "Rolf", "clpid": "Engleman-Rolf" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Wulf", "given_name": "Oliver Reynolds", "clpid": "Wulf-O-R" }, { "family_name": "Buchman", "given_name": "Edwin R.", "clpid": "Buchman-E-R" }, { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" }, { "family_name": "Lauritsen", "given_name": "Thomas", "clpid": "Lauritsen-T" }, { "family_name": "Mazo", "given_name": "Robert Marc", "clpid": "Mazo-R-M" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The rate of iodine atom recombination in the presence of various gases has been studied by the flash photolysis technique. The temperature dependence of the rate constant has been determined for recombination in helium, hydrogen, benzene, and methyl iodide. The negative temperature dependences are fitted by the form, k∝1/Tn, where n(He) = 0.80, n(H2 = 1.48, n(C6H6 = 2.53, and n(CH3I = 3.24.
\r\n\r\nThe iodine atom recombination rate constant was also measured at 50\u00b0C. for ethyl iodide, hydrogen iodide, carbon monoxide, and nitric oxide. The rate constants relative to helium at 50\u00b0C. are:
\r\n
\r\nHe 1.00 C2H5I 179.
\r\nH2 3.33 NI 21.1
\r\nC6H6 61.1 CO 4.07
\r\nCH3I 88.8 NO >1.4 x 104
\r\n
\r\nNitric oxide appears to be a very efficient third body gas and only a lower limit on the rate constant could be established.
Calculations have been made for some possible mechanisms of iodine atom recombination. A classical three body collision model is proposed for atom recombinations. The classical equations of motion were programmed to be solved numerically on a digital computer and some trajectories were examined.
", "doi": "10.7907/KAVE-WG75", "publication_date": "1959", "thesis_type": "phd", "thesis_year": "1959" }, { "id": "thesis:5765", "collection": "thesis", "collection_id": "5765", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05032010-130844301", "primary_object_url": { "basename": "Kraus_ba_1958.pdf", "content": "final", "filesize": 3334074, "license": "other", "mime_type": "application/pdf", "url": "/5765/1/Kraus_ba_1958.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "The Photoisomerization of Azobenzene at 77\u00b0K in a Rigid Solvent and at Room Temperature", "author": [ { "family_name": "Kraus", "given_name": "Bernhard August", "clpid": "Kraus-Bernhard-August" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The photoisomerization of azobenzene has been studied at room temperature in ethanol and P. Me.H., and at 77\u00b0K in a P.Me.H. rigid solvent. At room temperature, the photostationary state composition is 74% trans (and 26 % cis) in ethanol and 77 % trans in P.Me.H.; it is 98 % trans in P.Me.H. at 77\u00b0K. It has been shown that both the trans to cis and the cis to trans photoisomerizations occur in the rigid solvent at liquid nitrogen temperature.\r\n\r\nThe spectra and molar extinction coefficients have been determined at room temperature for trans azobenzene in ethanol and P.Me.H. Other spectra were taken of azobenzene: at the photostationary state, at room temperature in ethanol and P.Me.H., and at 77\u00b0K in P.Me.H.; at 77\u00b0K of 100 % and 77 % trans in P.Me.H.\r\n\r\nIt has been shown that the photoisomerization occurs more readily by irradiation in the visible, than in the ultraviolet region. A new low temperature cell has been designed and used.\r\n", "doi": "10.7907/RDAG-4773", "publication_date": "1958", "thesis_type": "masters", "thesis_year": "1958" }, { "id": "thesis:3974", "collection": "thesis", "collection_id": "3974", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10072004-150337", "primary_object_url": { "basename": "Huffman_re_1958.pdf", "content": "final", "filesize": 4478771, "license": "other", "mime_type": "application/pdf", "url": "/3974/1/Huffman_re_1958.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "I. Kinetics of the Thermal Decomposition of Nitrogen Dioxide Behind Shock Waves. II. Kinetics of the Ferrous Ion-Oxygen Reaction in Sulfuric Acid Solution", "author": [ { "family_name": "Huffman", "given_name": "Robert Eugene", "clpid": "Huffman-Robert-Eugene" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nShock waves into argon containing a small amount of N02 have been used to study the kinetics of the thermal decomposition of nitrogen dioxide from 1100 to 2300[degrees]K. Mole fractions of N02 varied from 2.8 x 10[...] to 1.5 x 10[...]; the ratio argon/N02 varied from 5.6 to 350; the argon concentration varied by a factor of twenty; and the N02 concentration varied by a factor of ten. Under these conditions, the results indicate that two separate reaction mechanisms are operative. One path has the rate law [...] with [...] and is apparently the unimolecular decomposition of N02 at the second order limit. The other path has the rate law [...] with an activation energy of 22[plus or minus]6 kcal/mole. This path is believed to be the bimolecular decomposition of N02 first observed by Bodenstein. However, extrapolation of this mechanism to the shock tube temperatures gives results about eight times too low. The reason for this discrepancy is not known. One interpretation is that there is another bimolecular reaction path for the decomposition of N02. A good possibility for such a path is the bimolecular formation of N02, recently postulated by Ashmore and Levitt, and its subsequent rapid decomposition, either by reaction with N02 or by unimolecular dissociation into N02 and 0. This discrepancy has also recently been observed by Steinburg and Lyon in a concurrent investigation. However, the mechanism and conclusions of that study are not supported by the present investigation.\r\n\r\nPart II consists of a paper that has already been published on the kinetics of the ferrous ion-oxygen reaction in sulfuric acid solution.\r\n", "doi": "10.7907/53F3-0D68", "publication_date": "1958", "thesis_type": "phd", "thesis_year": "1958" }, { "id": "thesis:4356", "collection": "thesis", "collection_id": "4356", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-11012004-144834", "primary_object_url": { "basename": "King_jr_j_1958.pdf", "content": "final", "filesize": 3009139, "license": "other", "mime_type": "application/pdf", "url": "/4356/1/King_jr_j_1958.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "I. Magnetic resonance studies of paramagnetic solutions. II. Kinetics of the ferrous iron-oxygen reaction in acidic phosphate-pyrophosphate solutions\r\n\r\nI. Magnetic Resonance Studies in Paramagnetic Solutions. II. Kinetics of the Ferrous Iron-Oxygen Reaction in Acidic Phosphate-Pyrophosphate Solutions", "author": [ { "family_name": "King", "given_name": "James", "clpid": "King-James" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" }, { "family_name": "McConnell", "given_name": "Harden M.", "clpid": "McConnell-H-M" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe techniques of Nuclear Magnetic Resonance and Electron Paramagnetic Resonance have been used to study the interaction of electrons and nuclei in solution. Results of a study of the interaction between paramagnetic manganeous ions [...] and water molecules indicate that the abnormally large ratio of the proton relaxation times, [...], previously found in the system, can be essentially explained by an isotropic hyperfine interaction between the electrons and protons in the solution. When this interaction is destroyed by complexing the [...] with the hexadentate ligand, ethylenediaminetetraacetate [...], or with the tetradentate ligand, nitrilotriacetate [...], [...] is increased slightly and [...] is increased markedly, so that [...] = [...] and the ratio is unity as expected.\r\n\r\nAn isotropic hyperfine interaction is also found to exist in ferric fluoride solutions. The interaction between the electrons of the ferric ion and the fluoride nuclei produces characteristic resonance spectra for the different complexes in the system. From a study of the system, the existence in solution of the [...] complex is definitely established. A value for the dissociation constant of the complex is obtained and an upper limit is set for the rate of exchange of complexed and uncomplexed fluorides in the system. The amount of 2s - character of the [...] bond in the ferric fluoride complexes is also obtained.\r\n\r\nThe shifts, due to the magnetic susceptibility in the system are treated in Section IV. It is found that the shifts deviate from the values one would expect if the susceptibility in the system were isotropic. Both organic and inorganic systems are treated. The method used to measure these small shifts is also described.\r\n\r\nPart II consists of a published article on the oxygenation of ferrous ion in acidic phosphate-pyrophosphate solutions.", "doi": "10.7907/266P-TV05", "publication_date": "1958", "thesis_type": "phd", "thesis_year": "1958" }, { "id": "thesis:3966", "collection": "thesis", "collection_id": "3966", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-10072004-114343", "primary_object_url": { "basename": "DeMore_wb_1958.pdf", "content": "final", "filesize": 4067016, "license": "other", "mime_type": "application/pdf", "url": "/3966/1/DeMore_wb_1958.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Chemical Processes in Rigid Media at Low Temperatures", "author": [ { "family_name": "DeMore", "given_name": "William Bailey", "clpid": "DeMore-William-Bailey" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nAn apparatus has been developed for studying chemical processes in rigid inert media at low temperatures (4.2[degrees]K, 20[degrees]K., or 77[degrees]K. The materials to be studied are deposited as a thin film on a cold surface by vacuum effusion. Infrared and visible-ultraviolet absorption spectroscopy were used for detection.\r\n\r\nThe CS molecule and the benzyl radical were isolated in hydrocarbon films at 77[degrees]K. CF2 and NO3 were trapped in films of nitrogen at 20[degrees]K. Visible-ultraviolet spectra of these species were obtained.\r\n\r\nThe photolysis of diazomethane in films of nitrogen at 20[degrees]K has been extensively studied. By adding various reactants to the films, evidence for the following reactions has been obtained: [...].\r\n\r\nOzone in nitrogen films is decomposed by ultraviolet light and some nitrous oxide is produced. This is attributed to the reaction [...], which is a hot atom reaction.\r\n\r\nIrradiation of mixtures of O3 and NO2 in nitrogen films yields NO3, N2O5, NO, and HNO3 (due to the presence of water). Irradiation of NO2 and O2 in nitrogen films yields O3 and NO.\r\n\r\nThe results obtained indicate that (1) hot atom or radical reactions occur in the film, and (2) photochemical fragments are energy-rich and may diffuse for a distance of at least a few molecular diameters in the rigid media.", "doi": "10.7907/ZR35-PF54", "publication_date": "1958", "thesis_type": "phd", "thesis_year": "1958" }, { "id": "thesis:2831", "collection": "thesis", "collection_id": "2831", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-07082004-142823", "primary_object_url": { "basename": "Bunker_dl_1957.pdf", "content": "final", "filesize": 3135370, "license": "other", "mime_type": "application/pdf", "url": "/2831/1/Bunker_dl_1957.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Flash Photolysis and the Recombination of Iodine Atoms", "author": [ { "family_name": "Bunker", "given_name": "Don Louis", "clpid": "Bunker-Don-Louis" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe rate of recombination of iodine atoms in the presence of argon has been redetermined by a flash photolysis technique. The measured rate constant agrees with results obtained by the same method in other laboratories. The recombination rate has also been measured at temperatures up to 548[degrees]K; these results are in accord with shock tube data and with other flash photolysis experiments. The rate is found to decrease slowly with increasing temperature, as about [...].\r\n\r\nIn experiments at temperatures between 300 [degrees]K and 493 [degrees]K n-butane has been employed as \"third body.\" It is found to be 13 times more efficient than argon at room temperature; this margin decreases as the temperature is raised. The third-body efficiencies of hydrogen and deuterium have been compared at 323 [degrees]K; they are equal.\r\n\r\nThe above experiments collectively lead to a determination of the rate of the recombination reaction involving I2 itself as third body. This reaction is about 600 times more rapid than that occurring with argon at room temperature, but rapidly becomes insignificant if the temperature is increased. From its temperature dependence [...] Kcal may be deduced for the reaction [...].", "doi": "10.7907/Q36G-BS81", "publication_date": "1957", "thesis_type": "phd", "thesis_year": "1957" }, { "id": "thesis:2750", "collection": "thesis", "collection_id": "2750", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06282004-143746", "primary_object_url": { "basename": "Schott_gl_1956.pdf", "content": "final", "filesize": 6166344, "license": "other", "mime_type": "application/pdf", "url": "/2750/1/Schott_gl_1956.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Chemical Studies in Shock Waves", "author": [ { "family_name": "Schott", "given_name": "Garry Lee", "clpid": "Schott-Garry-Lee" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nShock waves in argon bearing about one percent nitrogen pentoxide vapor have been used to initiate the rapid decomposition of N2O5 between 450[degrees] and 1100[degrees]. The important intermediate in the reaction is the nitrate radical, NO3, whose characteristic absorption bands in the green and red are known. These bands have been identified in flash absorption spectrograms, and quantitative photoelectric measurements of absorption by NO3 have followed its appearance and disappearance in the reaction mixture. Simultaneous measurements with violet light have recorded the production of NO2.\r\n\r\nThe first step in N2O5 decomposition is: [...]. Near 500[degrees]K, the forward rate and the equilibrium in this reaction have been measured. Above 600[degrees]K, the dissociation is rapid and complete, and the rates of the bimolecular decomposition reactions [...] and [...] have been measured. The contributions of these steps have been established by experiments in the presence of excess NO2. The reaction [...] is fast, and although NO2 is unstable with respect to NO and O2 above about 600[degrees]K, the stoichiometric reaction [...] has been observed in the short times of these experiments. The rate equations and the constants and energies measured agree very well with predictions based on mechanisms known at room temperature.\r\n\r\nTwo papers on the rate of dissociation of molecular iodine, by the present author and others, are included. The abstracts accompanying these papers are on pages 118 and 131.", "doi": "10.7907/TQXE-RK75", "publication_date": "1956", "thesis_type": "phd", "thesis_year": "1956" }, { "id": "thesis:4670", "collection": "thesis", "collection_id": "4670", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-11262003-143942", "primary_object_url": { "basename": "Britton_jd_1955.pdf", "content": "final", "filesize": 3102616, "license": "other", "mime_type": "application/pdf", "url": "/4670/1/Britton_jd_1955.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Shock Waves in Chemical Kinetics", "author": [ { "family_name": "Britton", "given_name": "John Doyle", "clpid": "Britton-John-Doyle" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe rates of dissociation of I[subscript 2] in N[subscript 2] and CO[subscript 2], and Br[subscript 2] in A were measured at temperatures around 1300[degrees]K by heating room temperature mixtures by means of shock waves and observing the subsequent reactions. The rates of recombination of both I[subscript 2] and Br[subscript 2] were found to decrease with increasing temperature. The results, combined with room temperature measurements seemed to be best expressed in the form K[subscript R] = A exp([...]/RT). Attempts to measure the efficiency of I[subscript 2] or Br[subscript 2] molecules as third bodies for the recombination gave only rather wide limits to the possible values.\r\n\r\nThe experiments also showed that CO[subscript 2] is vibrationally relaxed at high temperatures in a time short compared to the reaction time of 20-200 microseconds. It was not possible to decide whether or not N[subscript 2] is vibrationally relaxed at this temperature in this short time.\r\n\r\nExtinction coefficients of I[subscript 2] and Br[subscript 2] were measured as a function of the temperature. They appeared to be dependent on the inert gas.", "doi": "10.7907/Y16V-VY27", "publication_date": "1955", "thesis_type": "phd", "thesis_year": "1955" }, { "id": "thesis:47", "collection": "thesis", "collection_id": "47", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01072004-101648", "primary_object_url": { "basename": "king,jr_j_1955.pdf", "content": "final", "filesize": 531516, "license": "other", "mime_type": "application/pdf", "url": "/47/1/king,jr_j_1955.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "The Kinetics of the Oxygenation of Ferrous Ion in Phosphoric Acid Containing Pyrophosphate", "author": [ { "family_name": "King", "given_name": "James", "clpid": "King-James" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\t\r\nThe kinetics of the ferrous-oxygen reaction in an acid solution containing phosphate and pyrophosphate has been investigated. The rate law at [...] is [...]. Sodium perchlorate is used to maintain the ionic strength at 1.0-l.1M. There is inhibition due to ferric ion. This phase of the reaction has not been investigated. It is believed that the inhibition is due to the insolubility of ferric pyrophosphate at high concentrations and to the formation of complexes at low concentrations. The following mechanism, suggested by Weiss, is consistent with the experimental results. [...]. The rate of the reaction is given by [...]. The phosphate and pyrophosphate species catalyse the reaction through complex ion formation.", "doi": "10.7907/9W2D-4P13", "publication_date": "1955", "thesis_type": "masters", "thesis_year": "1955" }, { "id": "thesis:181", "collection": "thesis", "collection_id": "181", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01152004-092735", "type": "thesis", "title": "I. The Rate of Recombination of Iodine Atoms. II. Some Studies of the Trace Quantities of Lead, Uranium, and Thorium in Marine Carbonate Skeletons", "author": [ { "family_name": "Marshall", "given_name": "Royal Richard", "clpid": "Marshall-Royal-Richard" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" }, { "family_name": "Patterson", "given_name": "Clair C.", "clpid": "Patterson-C-C" }, { "family_name": "Brown", "given_name": "Harrison", "clpid": "Brown-Harrison" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "PART I.
\r\n\r\nThe rate constants for the homogeneous recombination of iodine atoms in the gas phase I+I+M \u2192 d[I\u2082]/d[I\u2082][M], have been measured for the gases M=A, n\u0332e\u0332o\u0332-C\u2085H\u2081\u2082 and n\u0332-C\u2085H\u2081\u2082 at room temperature. The rate constants are 4.2 (\u00b10.4) x 10\u2079, 58 (\u00b14) x 10\u2079, and 65 (\u00b16) x 10\u2079 liter\u00b2mole\u207b\u00b2sec\u207b\u00b9, respectively. In these experiments and those with iodine solutions, a short, intense pulse of light from a flash lamp dissociated 1-10% of the iodine molecules in a reaction cell. The photoelectric cell response to a light signal modulated with the change in the iodine atom concentration was amplified and used as the vertical deflection input of an oscilloscope. The oscilloscope trace, a direct indication of the subsequent recombination observed during periods from 0.0002 sec after the flash to as long as 0.01 sec, was recorded photographically.
\r\n\r\nThe rate constants for the recombination of iodine atoms in the liquids CCl\u2084 and n\u0332-C\u2087H\u2081\u2086, d[I\u2082]/d[I\u2082], were found to be at room temperature 0.7 (\u00b10.11) x 10\u00b9\u2070 and 2.2 (\u00b10.4) x 10\u00b9\u2070 liter mole\u207b\u00b9sec\u207b\u00b9, respectively. The primary quantum yields in the solutions were found to 0.19 (\u00b10.05) and 0.41 (\u00b10.26), respectively.
\r\n\r\nPART II.
\r\n\r\nA procedure is described for the chemical isolation from carbonates of microgram quantities of lead, uranium, and thorium suitable for mass spectrometric analyses. The concentration of lead in a Jurassic belemnite as well as a Mississippian Spirifer has been found to be less than 1 ppm while for Strombus gigas, a living species of gastropod, the value 0.19\u00b10.04 ppm was found. The uranium concentration in this gastropod was determined as 0.036\u00b10.002 ppm. The isotopic composition of the lead from the Strombus gigas has also been determined and is compared to other analyses of \"common\" lead.
", "doi": "10.7907/KV4S-PC49", "publication_date": "1955", "thesis_type": "phd", "thesis_year": "1955" }, { "id": "thesis:371", "collection": "thesis", "collection_id": "371", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-01272004-154020", "primary_object_url": { "basename": "Stottlemyer_qr_1954.pdf", "content": "final", "filesize": 4169059, "license": "other", "mime_type": "application/pdf", "url": "/371/1/Stottlemyer_qr_1954.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Investigation of the Behavior of the Aqueous I\u2083\u207b-I\u2082-I\u207b System Following Intense Irradiation", "author": [ { "family_name": "Stottlemyer", "given_name": "Quayton Ray", "clpid": "Stottlemyer-Quayton-Ray" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n \r\nAcidified aqueous solutions containing [...], [...], and [...] have been irradiated by a high intensity flash lamp and the resulting change in the optical density of the solution has been observed spectrophotometrically as a function of time after the flash.\r\n\r\nImmediately following the flash, there is an increase in the optical density of the solution. This is attributed to the photochemical production of the diiodide ion, [...], by reaction (1) and/or reaction (2) and (3). [...] [...] [...].\r\n\r\nThe disappearance of the colored species, in about 1.5--8 milliseconds after the flash, has been found to be kinetically of the second order with respect to that species and has been explained in terms of the recombination of [...], principally by equation (4). [...] [...] [...].\r\n\r\nOn the basis of these assumptions, the value of [...] has been determined at wave lengths 365 mmu. and 435 mmu. for [...] ranging from [...] to [...] M. The experimental dependence of the rate of disappearance of [...] on [...] has been found to agree qualitatively with the theoretical equation: [...].\r\n\r\nThe calculated value of [...] has been found to vary with the wave length of the light used to observe the reaction as predicted by the equation: [...].\r\n\r\nThe presence of [...] in concentrations about [...] caused a slight increase in the value of [...], which was attributed to one or both of the reactions: [...] [...]. [...] in concentrations less than [...] appeared to decrease the rate of disappearance of [...]; for this anomalous effect no explanation is given.\r\n\r\nExperiments performed in which a large percentage of the light absorbed by [...] was cut off by filters produced correspondingly smaller phenomena but gave no conclusive evidence as to the relative proportion of [...] and [...] dissociated by the irradiation.\r\n\r\nAn extensive summary of data is presented.", "doi": "10.7907/CSV2-DQ22", "publication_date": "1954", "thesis_type": "masters", "thesis_year": "1954" }, { "id": "thesis:1445", "collection": "thesis", "collection_id": "1445", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-04222003-090120", "primary_object_url": { "basename": "Carter_pr_1953.pdf", "content": "final", "filesize": 4626731, "license": "other", "mime_type": "application/pdf", "url": "/1445/1/Carter_pr_1953.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "I. Kinetics of the Oxidation of Iron (II) by Bromine. II. Complex Ion Formation in the Systems Iron (III), Phosphoric Acid. III. Kinetics of the Oxidation of Ferrocyanide Ion by Bromine", "author": [ { "family_name": "Carter", "given_name": "Paul Richard", "clpid": "Carter-Paul-Richard" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n \r\nThe kinetics of the oxidation of iron (II) by bromine has been studied spectrophotometrically. At (Br[...]) = 0.50 M, tribromide ion was found to be the reactive bromine species, while evidence for HOBr and Br[subscript 2] reacting with iron (II) was obtained at (Br[...]) [...] 10[superscript -3] M. A mechanism involving Br[...][subscript 2] is suggested, and the observed inhibition by iron (III) eliminates an alternative mechanism involving iron (IV) as an unstable intermediate. The catalytic effect of phosphoric acid was investigated.\r\n\r\nThe ultraviolet light absorption of iron (III) in phosphoric acid was studied. An attempt was made to determine the nature of the complex that is present. The presence of only one complex could not be verified.\r\n\r\nThe oxidation of ferrocyanide ion by bromine was found to proceed at a faster pace than the analogous oxidation of iron (II). Both molecular bromine and tribromide ion were found to react with ferrocyanide ion when (Br[...]) = 0.05 M. The reaction appeared to be first order with respect to bromine and ferrocyanide ion at H[superscript +] = 0.93 M, but was found to deviate from a simple second order behaviour when the hydrogen ion concentration was decreased to 0.50 M.", "doi": "10.7907/PDTJ-FP82", "publication_date": "1953", "thesis_type": "phd", "thesis_year": "1953" }, { "id": "thesis:10518", "collection": "thesis", "collection_id": "10518", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10162017-102130831", "primary_object_url": { "basename": "Ferington_TE_1951.pdf", "content": "final", "filesize": 4608930, "license": "other", "mime_type": "application/pdf", "url": "/10518/1/Ferington_TE_1951.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Observations on the Interaction of Ion Exchange Resins with Some Cupric Compounds", "author": [ { "family_name": "Ferington", "given_name": "Thomas Edwin", "clpid": "Ferington-Thomas-Edwin" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The interaction of the Sulfonic Acid Resin,\r\nNalcite HCR, with CuII halide solutions was studied\r\nin hope of obtaining dissociation constants for the complex \r\nions CuX+. The fact that CuX+ is absorbed by\r\nthe resin to an appreciable extent prevented the\r\nattainmnet of this goal. It was found in the case of\r\nCuF+ that the complex ion is absorbed even more strongly\r\nthan Cu++. The presence of a Cu++-F- complex\r\nwas indicated by spectrophotometric observations.
\r\n\r\nThe action of the carboxylic acid resin, IRC - 50\r\nwas studied in a column. It was found that the \r\nvolume of the resin in the Cu++ salt form depended\r\non the salt with which the resin was treated. In the\r\ncase of solutions of Cu(OAc)2 it was found that Cu(OAc)+\r\nwas taken into the resin as well as Cu++.
\r\n\r\nA titration curve for IRC - 50 with NaOH in\r\nsolutions of ionic strength one is given.
", "doi": "10.7907/CMRX-8587", "publication_date": "1952", "thesis_type": "masters", "thesis_year": "1952" }, { "id": "thesis:10498", "collection": "thesis", "collection_id": "10498", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10102017-110749047", "primary_object_url": { "basename": "Carrington_T_1952.pdf", "content": "final", "filesize": 19425527, "license": "other", "mime_type": "application/pdf", "url": "/10498/1/Carrington_T_1952.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Photoelectric Observation of the Rate of Dissociation of Dinitrogen Tetroxide Behind a Shock Wave", "author": [ { "family_name": "Carrington", "given_name": "Tucker", "clpid": "Carrington-Tucker" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "An experimental method has been developed in which\r\na shock wave is used to heat a gas by definite amount\r\nin a time short compared to the rate of adjustment of the\r\ngas to the new temperature. The rate of attainment of the\r\nnew thermal equilibrium is then followed photoelectrically.\r\nThe apparatus described here can be used to study reactions\r\nwith half times as short as 10-5 seconds.
\r\n\r\n\r\nBy this method the rate of dissociation of dinitrogen\r\ntetroxide in the presence of a large excess of nitrogen\r\nhas been studied over a 48 degree temperature range and\r\nwith an eight fold variation in total pressure. The results\r\nindicate that dissociation is a unimolecular reaction,\r\nnear its second order limit at one atmosphere pressure,\r\nand approaching a first order limit at higher pressures.
", "doi": "10.7907/63P4-AF03", "publication_date": "1952", "thesis_type": "phd", "thesis_year": "1952" }, { "id": "thesis:2534", "collection": "thesis", "collection_id": "2534", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-06102004-141410", "primary_object_url": { "basename": "McConnell_hm_1951.pdf", "content": "final", "filesize": 3924644, "license": "other", "mime_type": "application/pdf", "url": "/2534/1/McConnell_hm_1951.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "I. Investigation of Possible Interactions Between Thallium (I) and Thallium (III) in Solution and in the Crystalline Thallium Sesqui-Halides. II. Spectrophotometric Investigations of the Copper (II) Chloro-Complexes in Aqueous Solutions of Unit Ionic Strength. III. Optical Interaction Between the Chloro-Complexes of Copper (I) and Copper (II) in Solutions of Unit Ionic Strength. Interpretations of the Spectral Absorption of a Copper (I) - Copper (II) Dichloro-Complex. IV. Spectrophotometric Investigation of the Interaction Between Iron (II) and Iron (III) in Hydrochloric Acid Solutions", "author": [ { "family_name": "McConnell", "given_name": "Harden Marsdon", "clpid": "McConnell-Harden-Marsdon" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\t\t\t\t\t\r\n\r\nA radiochemical and spectrophotometric investigation of the interactions between thallium (I) and thallium (III) is used to show that the majority of the thallium (I) and thallium (III) atoms in the crystalline thallium sesquihalides do not occupy equivalent positions in the crystalline lattice and that there is no strong optical interaction between thallium (I) and thallium (III) in aqueous solutions containing perchlorate or chloride ion.\r\n\r\nThe absorption spectra of mixed solutions of copper (II) perchlorate, perchloric acid and hydrochloric acid at a constant ionic strength of 1.00 in the wavelength range 250-300 [...] are interpreted in terms of the equilibria, [...]. The equilibrium constants for these reactions are determined and the enthalpy of formation of [...] is estimated.\r\n\r\nThe non-additive light absorption in the 400-600 mp wavelength range of solutions maintained at unit ionic strength with perchloric acid and containing copper (I) and copper (II) and low concentrations of chloride ion, has been interpreted in terms of an \"interaction complex\", [...]. At higher chloride ion concentrations in solutions of the same ionic strength, interaction complexes of higher chloride coordination (but still containing only one copper (I) and one copper (II) in each complex) are important.\r\n\r\nTwo interpretations of the 400-600 [...] spectral absorption of [...] are advanced and discussed. At present no conclusions can be drawn as to which interpretation is to be preferred.\r\n\r\nThe light absorption in the 450-900 [...] wavelength range by mixed solutions of iron (II) and iron (III) in hydrochloric acid is interpreted as evidence for the formation of unstable but strongly absorbing interaction complexes, each interaction complex containing one atom of iron (II) and one atom of iron (III) and a number of coordinating chloride ligands. The light absorption by interaction complexes decreases with decreasing hydrochloric acid concentration and there is no interaction absorption by solutions containing [...] and no chloride ion.\r\n\r\nAbsorption spectra of iron (II) in solutions of varying hydrochloric acid concentration observed in the 700-900 [...] wavelength range are used to show the presence of iron (II) chloro-complexes.", "doi": "10.7907/M9F6-ZC83", "publication_date": "1951", "thesis_type": "phd", "thesis_year": "1951" }, { "id": "thesis:17483", "collection": "thesis", "collection_id": "17483", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06242025-212122769", "primary_object_url": { "basename": "Sullivan_JH_1950.pdf", "content": "final", "filesize": 20023394, "license": "other", "mime_type": "application/pdf", "url": "/17483/1/Sullivan_JH_1950.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Part I. Kinetics of the Vapor Phase Exchange of Radioactive Bromine Between Trichlorobromomethane and Bromine. Part II. Kinetics of the Forward and Reverse Reactions of the Vapor Phase Thermal Bromination of Chloroform. Part III. A Method of Estimating and Minimizing the Rate of a Radioactive Exchange Reaction", "author": [ { "family_name": "Sullivan", "given_name": "John Henry", "clpid": "Sullivan-John-Henry" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The rate of the homogeneous vapor phase thermal radioactive\r\nexchange reaction
\r\n\r\nCBrCl3 + Br2* \u2192 exchange
\r\n\r\nand the rates of the forward and reverse reactions of the homogeneous \r\nvapor phase thermal bromination of chloroform
\r\n\r\nCHCl3 + Br2 \u21c4 CBrCl3 + HBr (A)
\r\n\r\nhave been measured in the temperature range 420-455\u00b0 K.
\r\n\r\nFor the bromination reaction a mechanism which is consistent\r\nwith all the experimental data is
\r\n\r\nBr2 \u21c4 2Br (d) (5)
\r\n\r\nBr + CHCl3 \u21c4 -CCl3 + HBr (1) (2)
\r\n\r\n-CCl3 + Br2 \u21c4 CBrCl3 + Br. (3) (4)
\r\n\r\nThe rate determining steps are (1) and (4). The rate of the\r\nexchange reaction is given by k0(CBrCl3)(Br) and the equation for\r\nthe rate determining constant k0 = k0(T) is identical to that\r\nfor k4 as a function of temperature. The exchange reaction\r\ntakes place, therefore, by the reaction sequence (d), (4), and (3).
\r\n\r\nThe activation energies of (1) and (4) imply that the CH\r\nbond in CHCl3 is weaker than that in CH4 by at least 6.6 kcal,\r\nand the CBr bond in CBrCl3 is weaker than that in CH3Br by at\r\nleast 11 kcal. The equilibrium constant K = (CBrCl3)(HBr)/\r\n(CHCl3)(Br2) is 1.96 at 442\u00b0 K; the heat of reaction (A) is\r\n-0.9(\u00b10.65) kcal.
\r\n\r\nIn a single exploratory experiment, it was observed that\r\nthe exchange reaction between bromine and trifluorobromomethane\r\nis much slower than that between bromine and trichlorobromomethane.
\r\n\r\nA method of estimating and minimizing the error of measurement of \r\nthe rate of a radioactive exchange reaction is given.
", "doi": "10.7907/nysr-5c25", "publication_date": "1950", "thesis_type": "phd", "thesis_year": "1950" }, { "id": "thesis:17461", "collection": "thesis", "collection_id": "17461", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06162025-180659877", "primary_object_url": { "basename": "Craig_RP_1949.pdf", "content": "final", "filesize": 20076483, "license": "other", "mime_type": "application/pdf", "url": "/17461/1/Craig_RP_1949.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Radiochemical Investigation of the Kinetics of the Electron Exchange Between the Oxidation States of Tin", "author": [ { "family_name": "Craig", "given_name": "Roy Phillip", "clpid": "Craig-Roy-Phillip" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The kinetics of the electron exchange between SnII and SnIV\r\nin 10.0 f HCl have been investigated by the use of a \r\nradio-active tracer. It is found that the rate of exchange\r\nis proportional to the product of the SnII and SnIV concentrations.\r\nIn the HCl concentration range between 9.0 f and 11.0 f,\r\nthe exchange rate is found to be proportional to the 0.3 power of the HCl activity,\r\ngiving the empirical rate equation R = k [SnII] [SnIV] (HCl)0.3
\r\n\r\nRadio-active exchange experiments carried out at 0\u00b0 C.\r\nand at 25.2\u00b0C. show this exchange to have an activation\r\nenergy of 10.7 Kcal. per mole. The exchange is found to be\r\nhomogeneous.
\r\n\r\nIt is found that exposure of the SnII-SnIV solutions\r\nto illumination from a capillary Hg arc gives a marked photochemical\r\nincrease in the rate of electron exchange between\r\nthe two valence states.
\r\n\r\nPreliminary spectrophotometric investigations of cobalt-glycine\r\nsystems also have been made.
", "doi": "10.7907/4e56-hq86", "publication_date": "1950", "thesis_type": "masters", "thesis_year": "1950" }, { "id": "thesis:17402", "collection": "thesis", "collection_id": "17402", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06032025-181307069", "primary_object_url": { "basename": "Maun_EK_1949.pdf", "content": "final", "filesize": 77161373, "license": "other", "mime_type": "application/pdf", "url": "/17402/1/Maun_EK_1949.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "I. The Iodometric Determination of Zinc. II. Investigations in the Chemistry of Rhenium", "author": [ { "family_name": "Maun", "given_name": "Eugene Kingery", "clpid": "Maun-Eugene-Kingery" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" }, { "family_name": "Swift", "given_name": "Ernest H.", "clpid": "Swift-E-H" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Part I describes a study of the iodometric determination\r\nof zinc. The equilibrium of the ferricyanide-ferrocyanide\r\nand iod1de-iodine couples is shifted far to the right by zinc\r\nion, which precipitates ferrocyanide and hence causes iodine\r\nliberation. Conditions based on this principle were developed\r\nfor a rapid, accurate titration of zinc.
\r\n\r\nThe results of a series of investigations of the reactions\r\nof oxidation states of rhenium in aqueous solution\r\nare presented in Part II. These reactions were studied by\r\nspectrophotometric and analytical experiments for the states\r\nReVII, ReV, ReIV, ReI, and R-I.
\r\n\r\nReV was formed rapidly in a light green solution by\r\naddition of 1 or 2 equivalents of stannous chloride to\r\nsolutions of perrhenic acid, HReO4 , in 4 F hydrochloric\r\nacid; this oxidation state has been previously reported,\r\nSimilarly, yellow-brown ReIV was verified as the product\r\nwith further addition of stannous chloride. Brown ReIV\r\nprepared from hydrochloric acid with rhenium dioxide had\r\nreactivity similar to the stannous chloride preparations,\r\nbut yellow-green ReIV Cl=6 was very resistant against a wide\r\nvariety of oxidizing agents.
\r\n\r\nIt was confirmed that Re-I was formed by treatment of\r\ndilute solutions of perrhenic acid, in hydrochloric acid,\r\nby amalgamated zinc. Oxidation of Re-I by HReO4 or O2 formed\r\nfirst brown Re+I and then yellow Re . Titration of Re-I\r\nwith CuII gave Re+I and copper metal.
", "doi": "10.7907/t88x-1113", "publication_date": "1949", "thesis_type": "phd", "thesis_year": "1949" }, { "id": "thesis:17409", "collection": "thesis", "collection_id": "17409", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06042025-200212097", "primary_object_url": { "basename": "Doyle_GJ_1948.pdf", "content": "final", "filesize": 15698381, "license": "other", "mime_type": "application/pdf", "url": "/17409/1/Doyle_GJ_1948.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Kinetics of the Acid-Catalyzed Hydrolysis of Amine Disulfonate Ion. The Third Ionization Constant of Amine Disulfonic Acid", "author": [ { "family_name": "George", "given_name": "Joseph Doyle", "clpid": "George-Joseph-Doyle" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" }, { "family_name": "Yost", "given_name": "Don M.", "clpid": "Yost-D-M" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The rate of the acid-catalyzed hydrolysis of amine\r\ndisulfonate ion, HN(SO3)=2, in water solution has been\r\nthoroughly studied over the temperature range 25-45\u00b0 C.\r\nThe effect of varying the concentration of reactants, the\r\neffect of ionic strength (neutral salt effect), and the\r\neffect of temperature have been studied. All results at\r\nconstant ionic strength confirm the rate equation
\r\n\r\n- d(HN(SO3)=2)/dt = k(H+)(SO3)=2)
\r\n\r\nif the equilibrium between sulfate ion and hydrogen ion is\r\ntaken into account. The uncatalyzed hydrolysis was found\r\nto have an undetectable rate compared to the rate of the\r\ncatalyzed reaction.
\r\n\r\nThe variation of the rate constant with ionic strength\r\nimplies that the charge product of the ions involved in the\r\nrate determining reaction is -2.
\r\n\r\nThe internal energy of activation, \u0394E\u2260, was found to\r\nbe 23.5 \u00b1 1 Kcal., and the entropy of activation, \u0394S\u2260, was\r\nfound to be +7.2 \u00b1 1.5 e.u. for the reaction at zero\r\nionic strength.
\r\n\r\nA mechanism involving an activated complex of amine\r\ndisulfonate ion and hydronium ion may be invoked to explain\r\nthese results.
\r\n\r\nIn addition, the ionization function (classical ionization\r\nconstant) for the equilibrium
\r\n\r\nHN(SO3)=2) = H+ + N(SO3)=2)
\r\n\r\nwas measured in a sodium chloride solution at an ionic\r\nstrength of 1.00 at 25\u00b0 C. It was found that
\r\n\r\n(H+)N(SO3)=2)/HN(SO3)=2) = 3.2 x 10-9.
", "doi": "10.7907/bdxy-bd03", "publication_date": "1948", "thesis_type": "masters", "thesis_year": "1948" }, { "id": "thesis:17240", "collection": "thesis", "collection_id": "17240", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05162025-181639771", "primary_object_url": { "basename": "Browne_CI_1948.pdf", "content": "final", "filesize": 23332301, "license": "other", "mime_type": "application/pdf", "url": "/17240/1/Browne_CI_1948.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Spectrophotometric and Radiochemical Investigation of the Interaction Between the Oxidation States of Tin in Aqueous Solution", "author": [ { "family_name": "Browne", "given_name": "Charles Idol", "clpid": "Browne-Charles-Idol" } ], "thesis_advisor": [ { "family_name": "Davidson", "given_name": "Norman R.", "clpid": "Davidson-N-R" } ], "thesis_committee": [ { "family_name": "Unknown", "given_name": "Unknown" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "The spectrophotometry and radioactive exchange of\r\nSnII and SnIV in hydrochloric acid have been investigated.\r\nIt is found that mixtures of SnII and SnIV in hydrochloric\r\nacid exhibit anomalous absorption of ultra-violet light\r\nand that with the extent of this anomalous absorption is\r\nproportional to the product of the SnII and SnIV concentrations,\r\nimplying absorption by a dimeric complex of\r\nSnII and SnIV.
\r\n\r\nIt is found that SnII and SnIV exchange radioactivity\r\nmoderately slowly (half-exchange time about 7 min.) in 9N\r\nhydrochloric acid. The extent of exchange upon immediate\r\nseparation after mixing is about 17%, which is\r\neither a function of the separation method or an indication\r\nthat only certain chloride complexes of tin exchange.
\r\n\r\nIt is found that CuI and CuII exhibit interaction\r\nabsorption in 6N HCl
", "doi": "10.7907/rn6j-5f45", "publication_date": "1948", "thesis_type": "masters", "thesis_year": "1948" } ]