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J Phys Chem Lett. 2016 Nov 3;7(21):4391-4397. Epub 2016 Oct 25.

Quantum Mechanics/Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer.

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Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid , ES-28049 Madrid, Spain.
Molecular Modelling Group, Center of Molecular Biology Severo Ochoa (CSIC-UAM) , ES-28049 Madrid, Spain.
Departamento de Biotecnología, Universidad Francisco de Vitoria , ctra. Pozuelo-Majadahonda, km 1,800, 28223 Pozuelo de Alarcón, Madrid, Spain.
Department of Physics, West Virginia University , Morgantown, West Virginia 26506-6315, United States.


The absorption of ultraviolet radiation by DNA may result in harmful genetic lesions that affect DNA replication and transcription, ultimately causing mutations, cancer, and/or cell death. We analyze the most abundant photochemical reaction in DNA, the cyclobutane thymine dimer, using hybrid quantum mechanics/molecular mechanics (QM/MM) techniques and QM/MM nonadiabatic molecular dynamics. We find that, due to its double helix structure, DNA presents a free energy barrier between nonreactive and reactive conformations leading to the photolesion. Moreover, our nonadiabatic simulations show that most of the photoexcited reactive conformations return to standard B-DNA conformations after an ultrafast nonradiative decay to the ground state. This work highlights the importance of dynamical effects (free energy, excited-state dynamics) for the study of photochemical reactions in biological systems.

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