Benzo{a}pyrene is a potent mutagen/carcinogen that is metabolically activated inside cells, including to its (+)-anti-7,8-diol-9,10- epoxide [(+)-anti-B[a]PDE, which gives DNA adducts, principally a N2-dG. We showed that (+)-anti-B[a]PDE able to induce such a diverse array of mutations? Base substitution mutations predominate, and principally occur at G:C base pairs, where GC->TA, GC->AT and GC->CG are all significant (57%, 23%, 20%, respectively). We have done molecular biological/mutagenesis work to show that (+)-trans-antiB[a]P-n2-Gus is capable of inducing a preponderance of G->T mutations (> approximately 95 percent) in 5'-TGC sequences, or a preponderance of G->A mutations (->approximately 95 percent) in a 5'-AGA sequence. This raises the question: how can a single entity [i.e., (+)-trans-anti-B[a]P-N2-Gua] induce a different pattern of mutations depending on sequence context? Our working hypothesis has been that adduct mutational complexity is due to adduct conformational complexity, and that adduct conformation and, thereby, mutation is controlled by various factors, notably, DNA sequence context. To study adduct conformation, we did molecular modeling, and found that, based on first principles, (=)-trans-anti-B[a]P-N2-Gua can adopt at least 16 conformations. This is a large number, and probably all are not relevant to base substitutions mutagenesis, we have used a combination of common sense and the results of our molecular mechanical calculations to conclude that three conformations are most likely to be relevant to mutagenesis. Furthermore, we noticed a correlation. In a sequence where G->T mutations predominated (5'-TGC) a base displaced conformation of (+)-trans-anti-B[a]P-N2-Gua with the dG moiety in the major groove (Gma5) was calculated to be lower in energy. In two sequences where we observed G->A mutations were found more equally (5'-CGG, 5'-GGG) Gma5 and Gmi3 were calculated to be more similar in energy. This correlation suggests the hypothesis that Gma5 is the conformation responsible for G->T mutations and Gmi3 is responsible for G->A mutations. We are pursuing this hypothesis in molecular biological/mutagenesis studies (funded separately). Herein we propose three specific aims to pursue this hypothesis using molecular modeling and computational chemical techniques.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Research Project (R01)
Project #
5R01CA050432-08
Application #
6172221
Study Section
Special Emphasis Panel (ZRG1-ET-1 (02))
Program Officer
Okano, Paul
Project Start
1989-12-01
Project End
2002-08-31
Budget Start
2000-09-01
Budget End
2001-08-31
Support Year
8
Fiscal Year
2000
Total Cost
$239,369
Indirect Cost
Name
Boston University
Department
Biology
Type
Schools of Arts and Sciences
DUNS #
042250712
City
Boston
State
MA
Country
United States
Zip Code
02215
Kalam, M Abul; Haraguchi, Kazuhiro; Chandani, Sushil et al. (2006) Genetic effects of oxidative DNA damages: comparative mutagenesis of the imidazole ring-opened formamidopyrimidines (Fapy lesions) and 8-oxo-purines in simian kidney cells. Nucleic Acids Res 34:2305-15
Lee, Chiu Hong; Chandani, Sushil; Loechler, Edward L (2006) Homology modeling of four Y-family, lesion-bypass DNA polymerases: the case that E. coli Pol IV and human Pol kappa are orthologs, and E. coli Pol V and human Pol eta are orthologs. J Mol Graph Model 25:87-102
Chandani, Sushil; Lee, Chiu Hong; Loechler, Edward L (2005) Free-energy perturbation methods to study structure and energetics of DNA adducts: results for the major N2-dG adduct of benzo[a]pyrene in two conformations and different sequence contexts. Chem Res Toxicol 18:1108-23
Nagalingam, Arumugam; Seo, Kwang-Young; Loechler, Edward L (2005) Mutagenesis studies of the major benzo[a]pyrene N2-dG adduct in a 5'-TG versus a 5'-UG sequence: removal of the methyl group causes a modest decrease in the [G->T/G->A] mutational ratio. Mutagenesis 20:105-10
Yin, Jun; Seo, Kwang Young; Loechler, Edward L (2004) A role for DNA polymerase V in G --> T mutations from the major benzo[a]pyrene N2-dG adduct when studied in a 5'-TGT sequence in E. coli. DNA Repair (Amst) 3:323-34
Lee, Chiu Hong; Loechler, Edward L (2003) Molecular modeling of the major benzo[a]pyrene N2-dG adduct in cases where mutagenesis results are known in double stranded DNA. Mutat Res 529:59-76
Lee, Chiu Hong; Chandani, Sushil; Loechler, Edward L (2002) Molecular modeling of four stereoisomers of the major B[a]PDE adduct (at N(2)-dG) in five cases where the structure is known from NMR studies: molecular modeling is consistent with NMR results. Chem Res Toxicol 15:1429-44
Kozack, R; Seo, K Y; Jelinsky, S A et al. (2000) Toward an understanding of the role of DNA adduct conformation in defining mutagenic mechanism based on studies of the major adduct (formed at N(2)-dG) of the potent environmental carcinogen, benzo[a]pyrene. Mutat Res 450:41-59
Kozack, R E; Shukla, R; Loechler, E L (1999) A hypothesis for what conformation of the major adduct of (+)-anti-B[a]PDE (N2-dG) causes G-->T versus G-->A mutations based upon a correlation between mutagenesis and molecular modeling results. Carcinogenesis 20:95-102
Kozack, R E; Loechler, E L (1999) Molecular modeling of the major adduct of (+)-anti-B[a]PDE (N2-dG) in the eight conformations and the five DNA sequences most relevant to base substitution mutagenesis. Carcinogenesis 20:85-94

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