Conformational analysis of genotoxic benzo[a]pyrene- 7,8-dione-duplex DNA adducts using a molecular dynamics method

Journal of Biomolecular Structure & Dynamics
Biao JinSeog K Kim

Abstract

Benzo[a]pyrene-7,8-quinone (BPQ), a metabolite of the wide spread carcinogen benzo[a]pyrene, has been known to form adducts with DNA bases, namely guanine and adenine. The adducts include stereoisomers of the eight BPQ-G(1,2) and products of the formation of the cyclic five-member ring between BPQ and the G base. The stereochemical characteristics, structural properties, and thermodynamic aspects of the formation of the BPQ-G modified duplexes were investigated in this work using molecular modeling and a molecular dynamics (MD) simulation technique. Three conformations for the BPQ- oligonucleotides adduct showed the most favorable free energy (DeltaG). The molecular plane of the BPQ is nearly perpendicular to the DNA base plane for all three stable adducts. In two adducts, BPQ is located in the minor groove with either anti or syn conformations around the glycosidic bond. One of adducts in which BPQ locates into the major groove with the anti conformation around the glycosidic bond was also energetically possible. The resulting detailed structures of the three conceivable BPQ-oligonucleotide adducts are elucidated in this work.

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Citations

Oct 6, 2010·Journal of Biomolecular Structure & Dynamics·Hyun Mee LeeSeog K Kim
Feb 8, 2011·Journal of Biomolecular Structure & Dynamics·Elif Ozkirimli Olmez, Burak Alakent
Feb 8, 2011·Journal of Biomolecular Structure & Dynamics·Xianjin XuCunxin Wang
Feb 8, 2011·Journal of Biomolecular Structure & Dynamics·Zheng-Li ZhouYih Ho
Feb 8, 2011·Journal of Biomolecular Structure & Dynamics·Tung-Ti ChangCalvin Yu-Chian Chen
Feb 8, 2011·Journal of Biomolecular Structure & Dynamics·Evandro P SemighiniCarlos H T P Silva
Jan 27, 2015·Journal of Biomolecular Structure & Dynamics·Sun Hee JeonHyun Mee Lee
Aug 31, 2011·Journal of Biomolecular Structure & Dynamics·Aline A OliveiraTanos C C França
Aug 31, 2011·Journal of Biomolecular Structure & Dynamics·Esmaeil BehmardSamad Jahandideh
Jan 3, 2012·Journal of Biomolecular Structure & Dynamics·Sundarapandian ThangapandianKeun Woo Lee
Dec 15, 2010·Journal of Biomolecular Structure & Dynamics·Bornali ChakrabartiAsim K Bera
Jun 24, 2011·Journal of Biomolecular Structure & Dynamics·R SerikovM Zenkova
Apr 10, 2020·Food and Chemical Toxicology : an International Journal Published for the British Industrial Biological Research Association·Zhixiang WuJianping Hu
Sep 22, 2010·The Journal of Physical Chemistry. B·Andrea L MillenStacey D Wetmore
Sep 29, 2011·The Journal of Physical Chemistry. B·Andrea L MillenStacey D Wetmore

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