Solvent Effects on the Suppression of Oxidative Decomposition of Guanines by Phenyl Group Attachment in Deoxyribonucleic Acid (DNA)
- Satoshi Yokojima ,
- Wataru Yanoi ,
- Norifumi Yoshiki ,
- Noriyuki Kurita ,
- Shigenori Tanaka ,
- Kazuhiko Nakatani , and
- Akira Okada
Abstract
A recent experimental report on the suppression of the oxidative decomposition of guanines in deoxyribonucleic acid (DNA) double helices due to the attachment of a phenyl group to a guanine [Nakatani, K.; Dohno, C.; Saito, I. J. Am. Chem. Soc.2002, 124, 6802] is examined by semiempirical Hartree−Fock (HF) molecular orbital (MO) calculations and ab initio HF MO calculations with the STO-3G basis set. Because of this attachment, the energy level of MO localized on the guanine shifts to lower energy in a vacuum, whereas it shifts to higher energy in water. This is mainly because the energy reduction of MO levels by the water solvent becomes smaller when the solvent molecules are excluded by the phenyl group. Consequently, a hole trap is enhanced at the phenylated guanine base in water. The observed suppression of the oxidative decomposition of guanines around the phenylated guanine is thus explained by considering the solvent effects. In addition, we have observed that energy shifts due to a benzyl group or a tert-butyl group are similar to those due to the phenyl group in our calculation.
†
JST.
‡
University of Tsukuba.
§
Toyohashi University of Technology.
⊥
Toshiba R&D Center.
‖
Kyoto University, PRESTO.
*
Author to whom correspondence should be addressed. E-mail address: [email protected]
Cited By
This article is cited by 5 publications.
- Satoshi Yokojima, Norifumi Yoshiki, Wataru Yanoi and Akira Okada. Solvent Effects on Ionization Potentials of Guanine Runs and Chemically Modified Guanine in Duplex DNA: Effect of Electrostatic Interaction and Its Reduction due to Solvent. The Journal of Physical Chemistry B 2009, 113 (51) , 16384-16392. https://doi.org/10.1021/jp9054582
- J. H. Wei, X. J. Liu, J. Berakdar, YiJing Yan. Pathways of polaron and bipolaron transport in DNA double strands. The Journal of Chemical Physics 2008, 128 (16) , 165101. https://doi.org/10.1063/1.2902279
- Alexander A. Voityuk. Quantum chemical modeling of charge transfer in DNA. 2006,,, 99-119. https://doi.org/10.1016/B978-044452220-7/50069-1
- . Modern Methods for Theoretical Physical Chemistry of Biopolymers. 2006,,https://doi.org/
- J. H. Wei, L. X. Wang, K. S. Chan, YiJing Yan. Trapping and hopping of bipolarons in DNA: Su-Schrieffer-Heeger model calculations. Physical Review B 2005, 72 (6) https://doi.org/10.1103/PhysRevB.72.064304