DNA strand break; Structural and electrostatic properties studied by molecular dynamics simulation

Kotulic Bunta, J.*; Laaksonen, A.*; Pinak, M.; Nemoto, Toshiyuki*

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.