Prediction of Thymine Dimerization Yields from Molecular Dynamics Simulations
Yu Kay Law 1, Javad Azadi 1, Carlos E. Crespo-Hernandez 1, Eric Olmon 1 and Bern Kohler 1*
1 The Ohio State University
* To whom correspondence should be addressed. E-mail: kohler{at}chemistry.ohio-state.edu.
Submitted on July 31, 2007
Revised on September 26, 2007
Accepted on 6 December 2007
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Abstract |
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It was recently shown that thymine dimers in the all-thymine oligonucleotide (dT)18 are fully formed in less than 1 picosecond after UV excitation (W. J. Schreier et al.. 2007. Science. 315:625). The speed and the low quantum yield of this reaction suggest that only a small fraction of the conformers of this structurally disordered oligonucleotide are in a position to react at the instant of photon absorption. In this work, we explore the hypothesis that conventional molecular dynamics simulations can be used to predict the yield of cyclobutane pyrimidine dimers in DNA. Conformations obtained from simulations of thymidylyl-(3'-5')-thymidine in various co-solvents were classified as dimerizable or nondimerizable depending on the distance between the C5-C6 double bonds of the adjacent thymine bases and the torsion angle between them. The quantum yield of cyclobutane pyrimidine dimer (CPD) formation was calculated as the number of dimerizable conformations divided by the total number of conformations. The experimental quantum yields measured in the different solvents were satisfactorily reproduced using physically reasonable values for the two parameters. The mean dimerizable structure computed by averaging all of the dimerizable cis-syn conformations is structurally similar to the actual cis-syn dimer. Compared to the canonical B-form TT step, the most important structural property of a dimerizable conformation is its reduced helical twist angle of 22°.
Key Words:
CPD, Molecular Dynamics, Thymine dimer, UV photodamage, quantum yield
