Spectroscopic and Theoretical Insights into Sequence Effects of Aminofluorene-Induced Conformational Heterogeneity and Nucleotide Excision Repair
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- 作者：Srinivasa Rao Meneni ; Steven M. Shell ; Lan Gao ; Petr Jurecka ; Wang Lee ; Jiri Sponer ; Yue Zou ; M. Paul Chiarelli ; Bongsup P. Cho
- 刊名：Biochemistry
- 出版年：2007
- 出版时间：October 9, 2007
- 年：2007
- 卷：46
- 期：40
- 页码：11263 - 11278
- 全文大小：601K
- 年卷期：v.46,no.40(October 9, 2007)
- ISSN：1520-4995
文摘
A systematic spectroscopic and computational study was conducted in order to probe theinfluence of base sequences on stacked (S) versus B-type (B) conformational heterogeneity induced bythe major dG adduct derived from the model carcinogen 7-fluoro-2-aminofluorene (FAF). We preparedand characterized eight 12-mer DNA duplexes (-AG*N- series, d[CTTCTAG*NCCTC]; -CG*N- series,d[CTTCTCG*NCCTC]), in which the central guanines (G*) were site-specifically modified with FAFwith varying flanking bases (N = G, A, C, T). S/B heterogeneity was examined by CD, UV, and dynamic19F NMR spectroscopy. All the modified duplexes studied followed a typical dynamic exchange betweenthe S and B conformers in a sequence dependent manner. Specifically, purine bases at the 3'-flanking sitepromoted the S conformation (G > A > C > T). Simulation analysis showed that the S/B energy barrierswere in the 14-16 kcal/mol range. The correlation times ( = 1/) were found to be in the millisecondrange at 20 C. The van der Waals energy force field calculations indicated the importance of the stackinginteraction between the carcinogen and neighboring base pairs. Quantum mechanics calculations showedthe existence of correlations between the total interaction energies (including electrostatic and solvationeffects) and the S/B population ratios. The S/B equilibrium seems to modulate the efficiency of Escherichiacoli UvrABC-based nucleotide excision repair in a conformation-specific manner: i.e., greater repairsusceptibility for the S over B conformation and for the -AG*N- over the -CG*N- series. The resultsindicate a novel structure-function relationship, which provides insights into how bulky DNA adductsare accommodated by UvrABC proteins.