Influence of DNA Conformation and Repair Enzyme on Guanine and 8-Oxoguanine Base Flipping

Abstract

8-oxoguanine (8oxoG) is an abundant product of oxidative damage in DNA and if not repaired can result in mutations upon DNA replication. It is removed by repair glycosylases (e.g. MutM-glycosylase in bacteria) after flipping out the damaged base towards an extra-helical conformation into the repair enzyme active site. The exact mechanism how the repair enzyme identifies a damaged site within a large surplus of undamaged DNA is not fully understood. Binding of a repair enzyme results also in significant DNA deformation such as bending and minor groove opening. Looping out nucleotides from an intra-helical base paired conformation is energetically costly and it is not clear how the presence of a repair enzyme or the deformation of DNA may facilitate the looping out process. In this study we use Molecular Dynamics free energy simulations to evaluate the effects of DNA deformation and enzyme binding on the DNA base flipping process. The simulations indicate distinct free energy profiles for flipping 8oxoG or guanine and resulted in an overall calculated free energy for the flipping process in accordance with experimental imino proton exchange from Nuclear Magnetic Resonance spectroscopy. Distortion of the DNA towards a conformation as observed in complex with the repair enzyme lowered the free energy barrier and penalty for the flipping process. The result indicates that the DNA deformation induced by the repair enzyme binding has a significant influence on the flipping process. The additional effect of protein-DNA contacts on the calculated free energy for the flipping process will also be presented.