QM/MM studies reveal pathways leading to the quenching of the formation of thymine dimer photoproduct by flanking bases

Physical Chemistry Chemical Physics : PCCP
Wook Lee, Spiridoula Matsika

Abstract

It is known that the formation of the photochemical product of thymine-thymine cyclobutane pyrimidine dimer (TT-CPD) formed upon UV excitation in DNA is significantly affected by the nature of the flanking bases, and that the oxidation potential of the flanking base correlates with the quenching of TT-CPD formation. However, the electronic details of this correlation have remained controversial. The quenching of thymine dimer formation exerted by flanking bases was suggested to be driven by both conformational and electronic effects. In the present study, we examine both of these effects using umbrella sampling and a quantum mechanical/molecular mechanical (QM/MM) approach for selected model systems. Our results demonstrate that a charge transfer (CT) state between the flanking base and the adjacent thymine base can provide a decay pathway for the population to escape from dimer formation, which eventually leads to the formation of an exciplex. The QM/MM vertical excitation energies also reveal that the oxidation potential of flanking bases correlates with the energy level of the CT state, thereby determining whether the CT state intersects with the state that can lead to dimer formation. The consistency between these results a...Continue Reading

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Citations

Oct 6, 2015·Photochemistry and Photobiology·Dimitra Markovitsi
Feb 26, 2016·The Journal of Physical Chemistry Letters·Vincent A SpataSpiridoula Matsika
Sep 1, 2015·The Science of the Total Environment·Hongliang ZhangMichael J Kleeman
Apr 22, 2016·The Journal of Physical Chemistry Letters·Michael EpshteinIlana Bar
Apr 15, 2016·The Journal of Physical Chemistry. B·Akos BanyaszDimitra Markovitsi
Sep 30, 2016·Journal of the American Chemical Society·Clemens RauerLeticia González
Apr 1, 2017·Journal of Chemical Theory and Computation·Changjian XieHua Guo
Jan 17, 2017·Physical Chemistry Chemical Physics : PCCP·Wook Lee, Spiridoula Matsika
Apr 7, 2018·Photochemical & Photobiological Sciences : Official Journal of the European Photochemistry Association and the European Society for Photobiology·Lara Martínez-Fernández, Roberto Improta
Mar 25, 2018·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Wook Lee, Spiridoula Matsika
Apr 27, 2019·Faraday Discussions·Wook Lee, Spiridoula Matsika
May 8, 2018·Chemical Science·Rafał SzablaAndrzej L Sobolewski
Sep 25, 2019·Physical Chemistry Chemical Physics : PCCP·Xiaoran ZouChun-Yang Zhang
Feb 10, 2021·Annual Review of Biophysics·Iker Ortiz de LuzuriagaAdrià Gil
Dec 22, 2020·Journal of Chemical Theory and Computation·Camilo ZuluagaSpiridoula Matsika

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