Photolyase is an enzyme that catalyzes photorepair of thymine dimers in UV damaged DNA by electron-transfer reaction. We docked a thymine dimer to photolyase catalytic site, using crystal structure coordinates of the substrate-free enzyme from Escherichia coli, studied molecular dynamics of the system, and calculated the electron-transfer matrix element between the lowest unoccupied molecular orbitals of flavin and the dimer. We find that the rms transfer matrix element along the dynamic trajectory is about 6 cm(-1) which is consistent with the experimentally determined rate of transfer. In the average configuration the docked thymine dimer is sitting deep in the catalytic site, and approaches the adenine of FAD with the C4=O4 carbonyl groups. The average distance between the flavin and the base pair is less than 3 A. The electron-transfer mechanism utilizes the unusual conformation of FAD in photolyases, in which the isoalloxazine ring of the flavin and the adenine are in close proximity, and the peculiar features of the docked orientation of the dimer. The calculations show that despite the short distance between the donor and acceptor complexes, the electron-transfer mechanism between the flavin and the thymine bases is not direct, but indirect, with the adenine acting as an intermediate.