A direct ab initio molecular dynamics (MD) study on the repair reactions of stacked thymine dimer

DNA repair reactions of the thymine dimer (T) 2 following the hole capture have been investigated by means of direct ab initio molecular dynamics (MD) method in order to elucidate the mechanism of repair processes of thymine dimer interacting with a photo-enzyme. The thymine dimer has two C–C single bonds between thymine rings at neutral state expressed by (T T). After the hole capture of (T T), one of the C–C bonds was preferentially broken, while the structure of (T T) + was spontaneously changed to an intermediate having a C–C single bond expressed by (T–T) + . Time scale of the C–C bond breaking and formation of the intermediate was estimated to be 60–180 fs. The mechanism of repair reactions of the thymine dimer was discussed on the basis of theoretical results.