Molecular dynamics simulation studies of radiation damaged DNA molecules and repair enzymes

Pinak, M.

Molecular dynamics (MD) studies on several radiation damages to DNA - thymine dimer, thymine glycol8-oxoguanine and their recognition by repair enzymes are introduced in order to describe on the stepwise description of molecular process observed at radiation lesion sites. In all cases the significant structural changes in the DNA double helical structure were observed: (a) the breaking of hydrogen bonds network between complementary bases and resulting opening of the double helix (8-oxoguanine); (b) the sharp bending of the DNA helix centered at the lesion site (thymine dimer, thymine glycol); and (c) the flipping-out base on the strand complementary to the lesion (8-oxoguanine). The specific values of electrostatic interaction energy were found at the lesion sites (thymine dimmer: -10kcal/mol, thymine glycol: -26kcal/mol, 8-oxoguanine: -48kcal/mol).