Numerous environmental and endogenous chemicals can initiate cancer. A slight change in structure may distinguish carcinogenic chemicals from harmless ones. The relation between chemical structure and cancer-causing potential will be investigated for polycyclic aromatic hydrocarbons (PAHs), a representative class of chemical carcinogens. On metabolic activation, PAHs react with DNA, causing mutations in tumor suppressors and oncogenes, which initiate cancer. This proposal focuses on human nucleotide excision repair (NER) of PAH-damaged DNA and the effect of PAH-modified templates on the replication process within polymerases. The overall hypotheses are: (i) The specific conformation of damaged DNA determines whether it is repaired, (ii) If repair fails, the DNA conformation within a polymerase determines whether blockage, normal, or mutagenic bypass occurs. It is hypothesized that differences in local polymerase structure, adduct topology, adduct stereochemistry, and local base sequence context govern the lesion treatment in NER and translesion synthesis. The method of determining structure employs molecular modeling to delineate structural, dynamic, and thermodynamic properties of DNA adducts.
In Specific Aim 1, variation of detailed structure with sequence for guanine and adenine adducts derived from the bay region PAH, benzo[a]pyrene and the fjord region PAHs benzo[c]phenanthrene and dibenzo[a,l]pyrene will be determined, in order to delineate structural and thermodynamic features governing NER.
In Specific Aim 2, we propose to delineate structural alterations in polymerase-primer-template-dNTP ternary complexes caused by a PAH adduct at the template. The focus is on error-prone lesion bypass polymerases, and replicative polymerases, to determine structural features leading to blockage, mutagenic bypass, or error free translesion synthesis. The long term goals are to define conformational details governing NER and translesion DNA synthesis to gain predictive power relating lesion structure with carcinogenic hazard. ? ?

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Research Project (R01)
Project #
5R01CA028038-28
Application #
7405453
Study Section
Cancer Etiology Study Section (CE)
Program Officer
Okano, Paul
Project Start
1981-04-01
Project End
2010-04-30
Budget Start
2008-05-01
Budget End
2009-04-30
Support Year
28
Fiscal Year
2008
Total Cost
$298,433
Indirect Cost
Name
New York University
Department
Biology
Type
Schools of Arts and Sciences
DUNS #
041968306
City
New York
State
NY
Country
United States
Zip Code
10012
Fu, Iwen; Cai, Yuqin; Geacintov, Nicholas E et al. (2017) Nucleosome Histone Tail Conformation and Dynamics: Impacts of Lysine Acetylation and a Nearby Minor Groove Benzo[a]pyrene-Derived Lesion. Biochemistry 56:1963-1973
Fu, Iwen; Cai, Yuqin; Zhang, Yingkai et al. (2016) Entrapment of a Histone Tail by a DNA Lesion in a Nucleosome Suggests the Lesion Impacts Epigenetic Marking: A Molecular Dynamics Study. Biochemistry 55:239-42
Cai, Yuqin; Kropachev, Konstantin; Terzidis, Michael A et al. (2015) Differences in the Access of Lesions to the Nucleotide Excision Repair Machinery in Nucleosomes. Biochemistry 54:4181-5
Liu, Zhi; Ding, Shuang; Kropachev, Konstantin et al. (2015) Resistance to Nucleotide Excision Repair of Bulky Guanine Adducts Opposite Abasic Sites in DNA Duplexes and Relationships between Structure and Function. PLoS One 10:e0137124
Mu, Hong; Geacintov, Nicholas E; Zhang, Yingkai et al. (2015) Recognition of Damaged DNA for Nucleotide Excision Repair: A Correlated Motion Mechanism with a Mismatched cis-syn Thymine Dimer Lesion. Biochemistry 54:5263-7
Cai, Yuqin; Geacintov, Nicholas E; Broyde, Suse (2014) Ribonucleotides as nucleotide excision repair substrates. DNA Repair (Amst) 13:55-60
Lior-Hoffmann, Lee; Ding, Shuang; Geacintov, Nicholas E et al. (2014) Structural and dynamic characterization of polymerase ?'s minor groove lesion processing reveals how adduct topology impacts fidelity. Biochemistry 53:5683-91
Rodríguez, Fabián A; Liu, Zhi; Lin, Chin H et al. (2014) Nuclear magnetic resonance studies of an N2-guanine adduct derived from the tumorigen dibenzo[a,l]pyrene in DNA: impact of adduct stereochemistry, size, and local DNA sequence on solution conformations. Biochemistry 53:1827-41
Kropachev, Konstantin; Ding, Shuang; Terzidis, Michael A et al. (2014) Structural basis for the recognition of diastereomeric 5',8-cyclo-2'-deoxypurine lesions by the human nucleotide excision repair system. Nucleic Acids Res 42:5020-32
Lee, Yuan-Cho; Cai, Yuqin; Mu, Hong et al. (2014) The relationships between XPC binding to conformationally diverse DNA adducts and their excision by the human NER system: is there a correlation? DNA Repair (Amst) 19:55-63

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