This application focuses on structural alignments at the DNA duplex level associated with covalent polycyclic aromatic hydrocarbons, food mycotoxins and cis-platin adducts which play a critical role in chemical carcinogenesis. Single stereoisomeric lesion-purine covalent adducts positioned at a known site in a DNA duplex will be studied in a defined sequence context. The solution structure of these lesions will be determined by a combination of NMR and molecular dynamics calculations including iterative relaxation refinement. Parallel studies will measure individual base pair opening parameters from nucleic acid imino proton hydrogen exchange measurements as a function of added catalyst concentration. The emphasis will be on studying the carcinogenic lesion positioned opposite its complementary base, as well as positioned opposite other bases reflecting base substitution mutations and opposite deletion sites reflecting frame shift mutagenesis. The polycyclic aromatic hydrocarbon lesion research will focus on benzo[a]pyrene modified 2-amino guanine adducts and benzo[c]phenanthrene modified 6-amino adenine adducts. Pure stereoisomeric adducts are being studied in order to elucidate the role of chirality in determining whether the polyene ring chromophores are positioned in the grooves or intercalate between base pairs. The potential blockage of the minor groove by B[a]P-dG adducts and the major groove by B[c]Ph-dA adducts is expected to profoundly effect the base pair opening parameters measured from imino proton hydrogen exchange measurements. Such structural and dynamics studies will also be extended to the covalent 2- amino guanine adducts of the bulky quinonoid antibiotics saframycin and cyanocycline. The food mycotoxin lesion research will address structural issues related to the N7 guanine adducts formed by sterigmatocystin and its formamidopyrimidine ring opened FAPY analog positioned opposite cytidine, adenine and single deletion sites. An attempt will be made to generate and compare the structural differences from both the exo- and endo-8,9-epoxides of sterigmatocystin. These studies will be extended to the N7 guanine adducts formed by the anthrapyrone antibiotics sapurimycin and DC-92B where the covalent adduct and intercalation sites are separated by two single bonds compared to a fused bicyclic linker in the food mycotoxin adducts. We will continue our efforts towards the characterization of cis-platin intrastrand crosslinks at the N7 of guanines in d(*G-*G), d(*A-*G) and d(*G-N-*G) steps in DNA duplexes in an attempt to identify the nature of the structural distortion at the 5'- coordinated purine site and the extent of propagation along the helix. Comparative studies will be undertaken on both cytidine and adenine positioned opposite the 5'-coordinated guanine in efforts to explain the propensity for transversion mutations at this site. We propose in the longer term to extend this research to platinum analogs and their N7 guanine adducts at the duplex level. These include chiral cis-platin intrastrand crosslinks, bis(platinum) complexes containing linked cis- platin units, interstrand crosslinks at (*dGdC).(*dG-dC) steps and linked platinum intercalator complexes. Overall, our research should contribute to the development of structure-mutagenesis relationships in chemical carcinogenesis.

National Institute of Health (NIH)
National Cancer Institute (NCI)
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Molecular and Cellular Biophysics Study Section (BBCA)
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Okano, Paul
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Sloan-Kettering Institute for Cancer Research
New York
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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

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