Abstract
The photo-induced cis-syn-cyclobutane pyrimidine (CPD) dimer is a frequent DNA lesion. In bacteria photolyases efficiently repair dimers employing a light-driven reaction after flipping out the CPD damage to the active site. How the repair enzyme identifies a damaged site and how the damage is flipped out without external energy is still unclear. Employing molecular dynamics free energy calculations, the CPD flipping process was systematically compared to flipping undamaged nucleotides in various DNA global states and bound to photolyase enzyme. The global DNA deformation alone (without protein) significantly reduces the flipping penalty and induces a partially looped out state of the damage but not undamaged nucleotides. Bound enzyme further lowers the penalty for CPD damage flipping with a lower free energy of the flipped nucleotides in the active site compared to intra-helical state (not for undamaged DNA). Both the reduced penalty and partial looping by global DNA deformation contribute to a significantly shorter mean first passage time for CPD flipping compared to regular nucleotides which increases the repair likelihood upon short time encounter between repair enzyme and DNA.
Highlights
Binds first transiently forming an encounter complex followed by the flipping process in the presence of the repair enzyme
Recent Molecular Dynamics (MD) simulations comparing regular B-DNA and a cyclobutane pyrimidine dimer (CPD) lesion in the same sequence context indicated distortions caused by the CPD damage and increased DNA flexibility[22,23,24] but during the simulations the damage remained intra-helical without any spontaneous flipping to a looped out state in 1 μs simulation time[22]
Looping out or flipping of the CPD lesion from an intra-helical to an extra-helical state is necessary to access the active site of a repair enzyme
Summary
Binds first transiently forming an encounter complex (with the damaged site still in an intra-helical conformation) followed by the flipping process in the presence of the repair enzyme. In order to characterize the transition from the intra-helical to the extra-helical conformation of a CPD lesion it is possible to calculate the free energy change along an appropriate reaction coordinate to describe the transition during MD simulations Such simulations have been used to study base pair opening in regular DNA26,27, mismatch opening[28,29] and the recognition of methylated or damaged DNA29–33. It includes unrestrained double stranded (ds)DNA in the absence of repair enzyme, DNA deformed to a structure that mimics the protein induced deformation (but again without repair enzyme) and employing DNA in complex with the photolyase repair enzyme. The results likely have implications for the recognition mechanism of other types of DNA damages since for most significant DNA deformations in complex with repair enzymes have been observed
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