Thymine glycol and 8-oxoguanine lesioned DNA-structural and energetical changes as onset of enzymatic recognition and repair; Large scale MD simulations of biomolecules

Pinak, M.; Nemoto, Toshiyuki*

The molecular dynamics (MD) studies of oxidative lesions on DNA molecules are presented with respect to the proper recognition of lesions by their respective repair enzymes. The recognition of lesion and the formation of stable DNA-enzyme complex are necessary conditions for the onset of the enzymatic repair process. Two DNA lesions, thymine glycol and 8-oxoguanine were subjected to the MD simulations for several hundreds picoseconds using MD simulation codes AMBER 5.0 and AMBER 7.0. Amber was changed and partly vectorized to be able to handle this large systems. Simulations were performed on FUJITSU VPP5000/64 vector/parallel type, the HITACHI SR8000 and FUJITSU PRIMEPOWER parallel types supercomputers.