Abstract

This proposal addresses structure-dynamics-function relationships in DNA helices containing carcinogenic and mutagenic lesions at specific positions in oligonucleotides of defined sequence. We propose to combine two dimensional homonuclear and heteronuclear NMR methods with structure reconstruction algorithms to define features of the solution conformation of these DNA helices at and adjacent to the damage sites. The hydrogen exchange characteristics of the imino protons will be evaluated at infinite buffer catalyst concentration to estimate local base pair opening lifetimes at the individual base pair level. Specific projects include (1) characterization of oligonucleotide duplexes containing 04-and 02-alkylthymidine carcinogenic lesions ranging from methyl to isopropyl substituents. The base pairing potential of these alkylated pyrimidines with A and G will be probed to elucidate the origin of the observed transition and transversion errors associated with this lesion. (2) We propose to characterize structural and dynamics details at stable mutagenic abasic site lesions incorporated into oligonucleotide duplexes. Both furanose-intact and -open abasic sites will be investigated with A and T on partner strands opposite the lesion. Specific intermolecular interactions between tyrosine/tryptophan containing peptides and the abasic site will be characterized in detail. (3) The pairing properties of the mutagenic 2-aminopurine and 2,6-diaminopurine lesions with T and C will be monitored by proton and nitrogen-15 NMR parameters. We shall attempt to differentiate between Wobble base pairing and protonated base pair formation for the 2-aminopurine-cytosine interaction. (4) These mutagenic and carcinogenic lesions will be incorporated adjacent to consensus promotor regions involved in transcriptional regulation and adjacent to replication forks. The functional properties of regulatory sites as modulated by these lesions will be characterized by the proposed structural and hydrogen exchange experiments.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Research Project (R01)
Project #
5R01CA046533-02
Application #
3189819
Study Section
Biophysics and Biophysical Chemistry B Study Section (BBCB)
Project Start
1988-03-05
Project End
1993-02-28
Budget Start
1989-03-01
Budget End
1990-02-28
Support Year
2
Fiscal Year
1989
Total Cost
Indirect Cost

  Institution

Name
Columbia University (N.Y.)
Department
Type
Schools of Medicine
DUNS #
064931884
City
New York
State
NY
Country
United States
Zip Code
10027

  Publications

Reeves, Dara A; Mu, Hong; Kropachev, Konstantin et al. (2011) Resistance of bulky DNA lesions to nucleotide excision repair can result from extensive aromatic lesion-base stacking interactions. Nucleic Acids Res 39:8752-64
Rechkoblit, Olga; Delaney, James C; Essigmann, John M et al. (2011) Implications for damage recognition during Dpo4-mediated mutagenic bypass of m1G and m3C lesions. Structure 19:821-32
Rechkoblit, Olga; Kolbanovskiy, Alexander; Malinina, Lucy et al. (2010) Mechanism of error-free and semitargeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4. Nat Struct Mol Biol 17:379-88
Cai, Yuqin; Kropachev, Konstantin; Xu, Rong et al. (2010) Distant neighbor base sequence context effects in human nucleotide excision repair of a benzo[a]pyrene-derived DNA lesion. J Mol Biol 399:397-409
Kropachev, Konstantin; Kolbanovskii, Marina; Cai, Yuqin et al. (2009) The sequence dependence of human nucleotide excision repair efficiencies of benzo[a]pyrene-derived DNA lesions: insights into the structural factors that favor dual incisions. J Mol Biol 386:1193-203
Zhang, Na; Ding, Shuang; Kolbanovskiy, Alexander et al. (2009) NMR and computational studies of stereoisomeric equine estrogen-derived DNA cytidine adducts in oligonucleotide duplexes: opposite orientations of diastereomeric forms. Biochemistry 48:7098-109
Cai, Yuqin; Patel, Dinshaw J; Geacintov, Nicholas E et al. (2009) Differential nucleotide excision repair susceptibility of bulky DNA adducts in different sequence contexts: hierarchies of recognition signals. J Mol Biol 385:30-44
Rechkoblit, Olga; Malinina, Lucy; Cheng, Yuan et al. (2009) Impact of conformational heterogeneity of OxoG lesions and their pairing partners on bypass fidelity by Y family polymerases. Structure 17:725-36
Broyde, Suse; Wang, Lihua; Rechkoblit, Olga et al. (2008) Lesion processing: high-fidelity versus lesion-bypass DNA polymerases. Trends Biochem Sci 33:209-19
Broyde, Suse; Wang, Lihua; Zhang, Ling et al. (2008) DNA adduct structure-function relationships: comparing solution with polymerase structures. Chem Res Toxicol 21:45-52

Showing the most recent 10 out of 45 publications