title: Dynamics and mechanism of UV-damaged DNA repair in indole-thymine dimer adduct: molecular origin of low repair quantum efficiency.
abstract: Many biomimetic chemical systems for repair of UV-damaged DNA showed very low repair efficiency, and the molecular origin is still unknown. Here, we report our systematic characterization of the repair dynamics of a model compound of indole-thymine dimer adduct in three solvents with different polarity. By resolving all elementary steps including three electron-transfer processes and two bond-breaking and bond-formation dynamics with femtosecond resolution, we observed the slow electron injection in 580 ps in water, 4 ns in acetonitrile, and 1.38 ns in dioxane, the fast back electron transfer without repair in 120, 150, and 180 ps, and the slow bond splitting in 550 ps, 1.9 ns, and 4.5 ns, respectively. The dimer bond cleavage is clearly accelerated by the solvent polarity. By comparing with the biological repair machine photolyase with a slow back electron transfer (2.4 ns) and a fast bond cleavage (90 ps), the low repair efficiency in the biomimetic system is mainly determined by the fast back electron transfer and slow bond breakage. We also found that the model system exists in a dynamic heterogeneous C-clamped conformation, leading to a stretched dynamic behavior. In water, we even identified another stacked form with ultrafast cyclic electron transfer, significantly reducing the repair efficiency. Thus, the comparison of the repair efficiency in different solvents is complicated and should be cautious, and only the dynamics by resolving all elementary steps can finally determine the total repair efficiency. Finally, we use the Marcus electron-transfer theory to analyze all electron-transfer reactions and rationalize all observed electron-transfer dynamics.
authors: Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States.
authors: Xunmin
authors: X
authors: Guo
authors: Zheyun
authors: Z
authors: Liu
authors: Qinhua
authors: Q
authors: Song
authors: Lijuan
authors: L
authors: Wang
authors: Dongping
authors: D
authors: Zhong
mesh_terms: D000097:Acetonitriles / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D004249:DNA Damage; D004260:DNA Repair; D004255:Deoxyribodipyrimidine Photo-Lyase / Q000737:chemistry; D004146:Dioxanes / Q000737:chemistry; D004583:Electrons; D007211:Indoles / Q000737:chemistry*; D008957:Models, Genetic; D008958:Models, Molecular; D011740:Pyrimidine Dimers / Q000737:chemistry*; D011789:Quantum Theory; D012997:Solvents / Q000737:chemistry; D013057:Spectrum Analysis; D014466:Ultraviolet Rays / Q000009:adverse effects*; D014867:Water / Q000737:chemistry
chemical_list: D000097:Acetonitriles; D004146:Dioxanes; D007211:Indoles; D011740:Pyrimidine Dimers; D012997:Solvents; D014867:Water; C030374:indole; D004247:DNA; D004255:Deoxyribodipyrimidine Photo-Lyase; C025223:1,4-dioxane; C032159:acetonitrile