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. (C) 2008 Elsevier B.V. All rights reserved.