Described are studies involving a new class of nucleoside analogs we have developed to test the importance of specific biomolecular interactions. Our nonpolar nucleoside isosteres are designed to closely mimic the shape of natural nucleosides, but to lack their ability to form polar hydrogen bonded or other electrostatic interactions. This work has led to valuable new insights into the roles of polar and steric interactions in DNA-DNA and protein-DNA binding, and in DNA replication. The long-term goals of this work are to utilize nonpolar nucleoside analogs to gain fundamental understanding of the importance of polar and steric effects in protein-DNA (RNA) binding and in DNA/RNA secondary structure. Over the shorter term covered by this proposal, the specific aims are (1) analysis of protein-DNA interactions for two transcription factors, and the study of DNA bending in the absence of protein; (2) examination of polar and steric effects in DNA replication and editing; and (3) study of the roles of polar and geometric effects in DNA mismatch repair. This work is important to biomedical research in two main ways. First, DNA-DNA and protein-DNA interactions are a fundamental part of most disease states, and so this work will help advance the basic understanding of the molecular basis of diseases, and eventually, in development of molecular therapies for disease. Second, a number of insights gained here may be more directly applied to future medical diagnostics and therapeutics, by offering new ways to modulate protein-DNA interactions and stabilize nucleic acid secondary structure.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM052956-07
Application #
6386195
Study Section
Molecular and Cellular Biophysics Study Section (BBCA)
Program Officer
Lewis, Catherine D
Project Start
1995-08-01
Project End
2004-03-31
Budget Start
2001-04-01
Budget End
2002-03-31
Support Year
7
Fiscal Year
2001
Total Cost
$268,785
Indirect Cost
Name
Stanford University
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
800771545
City
Stanford
State
CA
Country
United States
Zip Code
94305
Maki, Angele S; Kim, TaeWoo; Kool, Eric T (2004) Direct comparison of A- and T-strand minor groove interactions in DNA curvature at A tracts. Biochemistry 43:1102-10
Lai, Jacob S; Kool, Eric T (2004) Selective pairing of polyfluorinated DNA bases. J Am Chem Soc 126:3040-1
Gao, Jianmin; Liu, Haibo; Kool, Eric T (2004) Expanded-size bases in naturally sized DNA: evaluation of steric effects in Watson-Crick pairing. J Am Chem Soc 126:11826-31
Francis, Anthony W; Helquist, Sandra A; Kool, Eric T et al. (2003) Probing the requirements for recognition and catalysis in Fpg and MutY with nonpolar adenine isosteres. J Am Chem Soc 125:16235-42
Lai, Jacob S; Qu, Jin; Kool, Eric T (2003) Fluorinated DNA bases as probes of electrostatic effects in DNA base stacking. Angew Chem Int Ed Engl 42:5973-7
Liu, Haibo; Gao, Jianmin; Lynch, Stephen R et al. (2003) A four-base paired genetic helix with expanded size. Science 302:868-71
Delaney, James C; Henderson, Paul T; Helquist, Sandra A et al. (2003) High-fidelity in vivo replication of DNA base shape mimics without Watson-Crick hydrogen bonds. Proc Natl Acad Sci U S A 100:4469-73
Rausch, Jason W; Qu, Jin; Yi-Brunozzi, Hye Young et al. (2003) Hydrolysis of RNA/DNA hybrids containing nonpolar pyrimidine isosteres defines regions essential for HIV type 1 polypurine tract selection. Proc Natl Acad Sci U S A 100:11279-84
Maki, Angele; Brownewell, Floyd E; Liu, Dongyu et al. (2003) DNA curvature at A tracts containing a non-polar thymine mimic. Nucleic Acids Res 31:1059-66
Washington, M Todd; Helquist, Sandra A; Kool, Eric T et al. (2003) Requirement of Watson-Crick hydrogen bonding for DNA synthesis by yeast DNA polymerase eta. Mol Cell Biol 23:5107-12

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