Predicting Thymine Dimerization Yields from Molecular Dynamics Simulations
- Law, Yu Kay
- Azadi, Javad
- Crespo-Hernández, Carlos E.
- Olmon, Eric
- Kohler, Bern
DOIAbstract
AbstractIt was recently shown that thymine dimers in the all-thymine oligonucleotide (dT)18 are fully formed in <1ps after ultraviolet excitation. The speed and 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 cosolvents were classified as dimerizable or nondimerizable depending on the distance between the C5-C6 double bonds of the adjacent thymine ba...
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