title: Femtosecond stimulated Raman spectroscopy of the cyclobutane thymine dimer repair mechanism: a computational study.
abstract: 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.
authors.affiliation: Department of Chemistry, 1102 Natural Sciences II, University of California , Irvine, California 92697-2025, United States.
authors.forename: Hideo
authors.initials: H
authors.lastname: Ando
authors.forename: Benjamin P
authors.initials: BP
authors.lastname: Fingerhut
authors.forename: Konstantin E
authors.initials: KE
authors.lastname: Dorfman
authors.forename: Jason D
authors.initials: JD
authors.lastname: Biggs
authors.forename: Shaul
authors.initials: S
authors.lastname: Mukamel
mesh_terms: D004260:DNA Repair; D005609:Free Radicals / Q000737:chemistry; D008958:Models, Molecular; D008968:Molecular Conformation; D011740:Pyrimidine Dimers / Q000737:chemistry* / Q000378:metabolism; D011789:Quantum Theory; D013059:Spectrum Analysis, Raman; D013816:Thermodynamics; D013997:Time Factors
chemical_list: D005609:Free Radicals; D011740:Pyrimidine Dimers