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Kotulic Bunta, J.*; Laaksonen, A.*; Pinak, M.; Nemoto, Toshiyuki*
Computational Biology and Chemistry, 30(2), p.112 - 119, 2006/04
Times Cited Count：3 Percentile：22.11(Biology)Due to their lethal consequences, single and double strand breaks are among the most important and dangerous DNA lesions. This work defines and analyzes a DNA with single strand break as a template study for future complex analyses of biologically serious double strand break damage and its enzymatic repair mechanisms. Besides a non-damaged DNA serving as a reference system, system with open valences of the atoms at the strand break ends as well as a system with filled valences was simulated. As for the results, the system with open valences is partly disrupted, and the system with filled valences is stabilized by forming new hydrogen bonds between two strand endings.
Pinak, M.
Computational Biology and Chemistry, 27(3), p.431 - 441, 2003/07
Times Cited Count：9 Percentile：45.7(Biology)One nanosecond molecular dynamics (MD) simulation was performed for two DNA segments each composed of 30 base pairs. The analysis of results was focused on the electrostatic energy that is supposed to be significant factor causing the disruption of DNA base stacking in DNA duplex and may also to serve as a signal toward the repair enzyme informing on the presence of the lesion. This electrostatic potential may signal presence of the lesion to the repair enzyme.
