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    • Plusieurs versions

    Determining thermodynamic properties of molecular interactions from single crystal studies

    Vander Zanden, Crystal M, Carter, Megan, Ho, Pui Shing
    Methods, November 2013, Vol.64(1), pp.12-18 [Revue évaluée par les pairs]

    • Plusieurs versions

    Principles of physical biochemistry

    Holde, Kensal Edward van
    • Plusieurs versions

    Circular Dichroism and Molecular Modeling Yield a Structure for the Complex of Human Immunodeficiency Virus Type 1 Trans-Activation Response RNA and the Binding Region of Tat, the Trans-Acting Transcriptional Activator

    Loret, Erwann P., Georgel, Philippe, Johnson,, W. Curtis, Ho, Pui Shing
    Proceedings of the National Academy of Sciences of the United States of America, 15 October 1992, Vol.89(20), pp.9734-9738 [Revue évaluée par les pairs]

    • Plusieurs versions

    The Inherent Properties of DNA Four-way Junctions: Comparing the Crystal Structures of Holliday Junctions

    Eichman, Brandt F, Ortiz-Lombardı́a, Miguel, Aymamı́, Joan, Coll, Miquel, Ho, Pui Shing
    Journal of Molecular Biology, 2002, Vol.320(5), pp.1037-1051 [Revue évaluée par les pairs]

    • Plusieurs versions

    Hydrogen Bond Enhanced Halogen Bonds: A Synergistic Interaction in Chemistry and Biochemistry

    Riel, Asia Marie S, Rowe, Rhianon K, Ho, Ethan N, Carlsson, Anna-Carin C, Rappé, Anthony K, Berryman, Orion B, Ho, Pui Shing
    Accounts of chemical research, 15 October 2019, Vol.52(10), pp.2870-2880 [Revue évaluée par les pairs]

    • Plusieurs versions

    Hydration of methylated and nonmethylated B-DNA and Z-DNA

    Ho, Pui Shing, Quigley, Gary J, Tilton, Robert F, Rich, Alexander
    The Journal of Physical Chemistry, 01 February 1988, Vol.92(4), pp.939-945
    ACS Publications (American Chemical Society)
    • Dissertation
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    Sequence dependent conformational variations in DNA Holliday junctions

    Hays, Franklin
    ProQuest Dissertations and Theses
    © ProQuest LLC All rights reserved, ProQuest Dissertations & Theses Global: The Sciences and Engineering Collection, ProQuest Dissertations and Theses Global A&I: The Sciences and Engineering Collection, ProQuest Dissertations & Theses Full Text, ProQuest Dissertations & Theses A&I, ProQuest Dissertations & Theses: Global, ProQuest One Academic
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    Titre: Sequence dependent conformational variations in DNA Holliday junctions
    Auteur: Hays, Franklin
    Contributeur: Ho, Pui Shing (advisor)
    Editeur: ProQuest Dissertations Publishing
    Date: 2005
    Sujet: Biochemistry ; Molecular Biology ; Biochemistry ; Molecular Biology ; Pure Sciences ; Biological Sciences ; Conformational Mapping ; DNA Conformation ; Holliday Junctions ; Sequence-Dependent Conformation
    Description: Four-stranded DNA junctions (also known as Holliday junctions) are structural intermediates involved in a growing number of biological processes including DNA repair, genetic recombination, and viral integration. Although previous studies have focused on understanding the conformational variability and sequence-dependent formation of Holliday junctions in solution there have been relatively few insights into junction structure at the atomic level. Recent crystallographic studies have demonstrated that the more compact stacked-X junction form has an antiparallel alignment of DNA strands and standard Watson-Crick base pairs across the central crossover region. Junction formation within this crystallographic system was seen to be dependent on a common trinucleotide sequence motif (“ACC-triplet” at the 6th, 7th and 8th positions of the decanucleotide sequence d(CCnnnN6N7N8GG)) containing a series of stabilizing direct and solvent-mediated hydrogen bonding interactions. This thesis addresses...
    Fait partie de: ProQuest Dissertations and Theses
    Identifiant: 978-0-542-05846-2 (ISBN)

    • Dissertation
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    The effect of cytosine methylation on DNA structure

    Vargason, Jeffrey
    ProQuest Dissertations and Theses
    © ProQuest LLC All rights reserved, ProQuest Dissertations & Theses Global: The Sciences and Engineering Collection, ProQuest Dissertations and Theses Global A&I: The Sciences and Engineering Collection, ProQuest Dissertations & Theses Full Text, ProQuest Dissertations & Theses A&I, ProQuest Dissertations & Theses: Global, ProQuest One Academic
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    Titre: The effect of cytosine methylation on DNA structure
    Auteur: Vargason, Jeffrey
    Contributeur: Ho, Pui Shing (advisor)
    Editeur: ProQuest Dissertations Publishing
    Date: 2002
    Sujet: Biophysics ; Biochemistry ; Molecular Biology ; Biophysics ; Biochemistry ; Molecular Biology ; Pure Sciences ; Biological Sciences ; Cytosine ; DNA Structure ; Holliday Junctions ; Methylation
    Description: DNA methylation is common in prokaryotes and eukaryotes and has been implicated in various biological roles including gene silencing, X-chromosome inactivation, and genomic imprinting. 5-methylcytosine the “fifth base” of the genetic code comprises 1–3% of the human genome and is primarily found on cytosines within the context of the CpG sequence. Although progress has been made in understanding the biological roles of 5-methylcytosine, we are only beginning to uncover how it changes the local structure and global conformation of DNA. This thesis deals with the local perturbations in structure and hydration and the global conformational changes induced by the presence of 5-methylcytosine in DNA as determined by single crystal x-ray diffraction. 5-methylcytosine induces a novel conformation in the structure of duplex DNA. This conformation has characteristics of both the A-DNA and B-DNA conformations as well as some unique defining characteristics. This distinct duplex provides a structural...
    Fait partie de: ProQuest Dissertations and Theses
    Identifiant: 978-0-493-58395-2 (ISBN)

    • Dissertation
    Sélectionner

    Studies on the hydrophobic effect and its contribution to the stability, crystallization, and helix packing of Z-DNA

    Kagawa, Todd
    ProQuest Dissertations and Theses
    © ProQuest LLC All rights reserved, ProQuest Dissertations & Theses Global: The Sciences and Engineering Collection, ProQuest Dissertations and Theses Global A&I: The Sciences and Engineering Collection, ProQuest Dissertations & Theses Full Text, ProQuest Dissertations & Theses A&I, ProQuest Dissertations & Theses: Global, ProQuest One Academic
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    Titre: Studies on the hydrophobic effect and its contribution to the stability, crystallization, and helix packing of Z-DNA
    Auteur: Kagawa, Todd
    Contributeur: Ho, Pui Shing (advisor)
    Editeur: ProQuest Dissertations Publishing
    Date: 1994
    Sujet: Biophysics ; Biophysics ; Biological Sciences
    Description: The studies presented here use the B- to Z-DNA transition and Z-DNA crystallization as model systems to determine the contribution of solvent interactions to macromolecular structures. The substituent groups of naturally occurring and modified nucleotide bases affect the hydration and thus the stability of right-handed B-DNA and left-handed Z-DNA. The free energy for alternating pyrimidine-purine sequences in the B- and Z-conformations are quantitated as solvent free energies (SFE) from their solvent-accessible surfaces. The effect of methylation of the C5 carbon of pyrimidine bases on the stability of Z-DNA was analyzed in comparisons of d(TA) versus d(UA) dinucleotides. In the minor groove, the N2 amino group of purine bases was examined by comparing the stability of d(CG) versus d(CI), and d(TA) versus d(TA$\sp\prime$) dinucleotides as Z-DNA. These comparisons correctly accounted for the observed effects of the major and minor groove substituent groups on the relative stability of Z-DNA....
    Fait partie de: ProQuest Dissertations and Theses

    • Dissertation
    Sélectionner

    Crystal structures of DNA four -way junctions

    Eichman, Brandt
    ProQuest Dissertations and Theses
    © ProQuest LLC All rights reserved, ProQuest Dissertations & Theses Global: The Sciences and Engineering Collection, ProQuest Dissertations and Theses Global A&I: The Sciences and Engineering Collection, ProQuest Dissertations & Theses Full Text, ProQuest Dissertations & Theses A&I, ProQuest Dissertations & Theses: Global, ProQuest One Academic
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    Titre: Crystal structures of DNA four -way junctions
    Auteur: Eichman, Brandt
    Contributeur: Ho, Pui Shing (advisor)
    Editeur: ProQuest Dissertations Publishing
    Date: 2000
    Sujet: Biophysics ; Biochemistry ; Biophysics ; Biochemistry ; Pure Sciences ; Biological Sciences ; Crystal Structures ; DNA Binding Drug ; Four-Way Junctions ; Holliday Junctions ; Psoralen
    Description: DNA four-way junctions (also known as Holliday junctions) are the primary structural intermediate during recombination, an important process responsible for biological evolution and maintenance of genomes. These junctions arise from the assembly of four nucleic acid strands to produce double-helical regions extending from a central point. Although much progress has been made in understanding the general structural and functional properties of four-way junctions, we are only now beginning to elucidate the atomic interactions that stabilize such structures. This thesis deals with the sequence- and drug-dependent formation of Holliday junctions at the atomic level, as determined by single-crystal x-ray diffraction. The first crystal structure of a DNA four-way junction from an inverted repeat sequence is described here. The conformation of the junction corresponds to that of the stacked-X form previously characterized in solution, in which helical arms are coaxially stacked to form two pseudo-continuous...
    Fait partie de: ProQuest Dissertations and Theses
    Identifiant: 978-0-493-03132-3 (ISBN)