The goal of this project is to provide a molecular picture (theory) of DNA on surfaces in solution which is consistent with known thermodynamic and structural data. We will make detailed calculations with our new methods in an attempt to make the most direct possible comparisons with recent and planned thermodynamic, structural and biophysical experiments. We will consider the relation of thermodynamic solubilities, binding and allowed conformations of nucleotides to their solution environment and salt concentration. A key question is understanding the experimentally observed possibility of both increased affinity and increased selectivity near surfaces for certain surface/solution condition combinations. Using theoretical methods, we will quantify the balance between general solution effects (such as screening and solvation) and specific effects due to the surface and molecular association in solutions in determining the thermodynamics of DNA. A goal of this work is the development and application of new theoretical techniques to solve solvation/conformation related design problems of oligonucleotide covered surfaces. Test cases and applications have been chosen to maximize overlap with existing data or collaborations that will yield data of specific relevance to DNA analyses on surfaces. ? ?

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
3R01GM066813-01A2S1
Application #
7024373
Study Section
Genome Study Section (GNM)
Program Officer
Wehrle, Janna P
Project Start
2004-04-01
Project End
2008-03-31
Budget Start
2004-04-01
Budget End
2005-03-31
Support Year
1
Fiscal Year
2005
Total Cost
$16,681
Indirect Cost
Name
University of Houston
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
036837920
City
Houston
State
TX
Country
United States
Zip Code
77204
Wang, Qian; Irobalieva, Rossitza N; Chiu, Wah et al. (2017) Influence of DNA sequence on the structure of minicircles under torsional stress. Nucleic Acids Res 45:7633-7642
Myers, Christopher G; Pettitt, B Montgomery (2017) Phage-like packing structures with mean field sequence dependence. J Comput Chem 38:1191-1197
Esadze, Alexandre; Chen, Chuanying; Zandarashvili, Levani et al. (2016) Changes in conformational dynamics of basic side chains upon protein-DNA association. Nucleic Acids Res 44:6961-70
Chen, Chuanying; Pettitt, B Montgomery (2016) DNA Shape versus Sequence Variations in the Protein Binding Process. Biophys J 110:534-544
Bates, David; Pettitt, B Montgomery; Buck, Gregory R et al. (2016) Importance of disentanglement and entanglement during DNA replication and segregation: Comment on: ""Disentangling DNA molecules"" by Alexander Vologodskii. Phys Life Rev 18:160-164
Wang, Qian; Pettitt, B Montgomery (2016) Sequence Affects the Cyclization of DNA Minicircles. J Phys Chem Lett 7:1042-6
Wang, Qian; Myers, Christopher G; Pettitt, B Montgomery (2015) Twist-induced defects of the P-SSP7 genome revealed by modeling the cryo-EM density. J Phys Chem B 119:4937-43
Wang, Qian; Pettitt, B Montgomery (2014) Modeling DNA thermodynamics under torsional stress. Biophys J 106:1182-93
Myers, Christopher G; Pettitt, B Montgomery (2013) Communication: Origin of the contributions to DNA structure in phages. J Chem Phys 138:071103
Theruvathu, Jacob A; Yin, Y Whitney; Pettitt, B Montgomery et al. (2013) Comparison of the structural and dynamic effects of 5-methylcytosine and 5-chlorocytosine in a CpG dinucleotide sequence. Biochemistry 52:8590-8

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