Femtosecond Stimulated Raman Spectroscopy of the Cyclobutane Thymine Dimer Repair Mechanism: A Computational Study
journal contributionposted on 17.12.2015, 05:22 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 CC bond splitting, still remains an open question. In a simulation study, we demonstrate how the time evolution of characteristic marker bands (CO and CC/CC 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 C5C5′ splitting and a main barrier for the C6C6′ splitting, and identify the appearance of two C5C6 stretch vibrations due to the C6C6′ 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.
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dispersive line shapesvibrationphotoreactivation processcyclobutane thymine dimerenergy surfaceComputational StudyCyclobutane thymine dimerspectroscopic signaturemarker bandsRaman spectroscopytime evolutionbarrierFemtosecond Stimulated Raman Spectroscopybond splitting mechanismFSRS signalsthymine dinucleotideUV sunlightDNADFTsequential mechanismintradimersimulation studyCyclobutane Thymine Dimer Repair Mechanism