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Femtosecond Stimulated Raman Spectroscopy of the Cyclobutane Thymine Dimer Repair Mechanism: A Computational Study

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journal contribution
posted on 17.12.2015 by Hideo Ando, Benjamin P. Fingerhut, Konstantin E. Dorfman, Jason D. Biggs, Shaul Mukamel
Cyclobutane thymine dimer, one of the major lesions in DNA formed by exposure to UV sunlight, is repaired in a photoreactivation process, which is essential to maintain life. The molecular mechanism of the central step, i.e., intradimer CC bond splitting, still remains an open question. In a simulation study, we demonstrate how the time evolution of characteristic marker bands (CO and CC/CC stretch vibrations) of cyclobutane thymine dimer and thymine dinucleotide radical anion, thymidylyl(3′→5′)­thymidine, can be directly probed with femtosecond stimulated Raman spectroscopy (FSRS). We construct a DFT­(M05‑2X) potential energy surface with two minor barriers for the intradimer C5C5 splitting and a main barrier for the C6C6 splitting, and identify the appearance of two C5C6 stretch vibrations due to the C6C6 splitting as a spectroscopic signature of the underlying bond splitting mechanism. The sequential mechanism shows only absorptive features in the simulated FSRS signals, whereas the fast concerted mechanism shows characteristic dispersive line shapes.