Structural and kinetic study of N7-methyl, N7-benzyl and C8-chloro guanine lesions using human DNA polymerase β
DNA bases are constantly under the damages from both outside and inside, bringing possible mutagenic changes. To elucidate the detailed mechanisms, structural method of X-ray crystallography and steady state kinetics together with other necessary means are used in human DNA polymerase β (polβ) model to study the N7-methyl (N7meG), N7-benzyl (N7bnG) and C8-chloro (8ClG) guanine lesions. The results show that polβ will maintain the DNA fidelity by deterring dTTP insertion across N7meG lesion. But dCTP insertion is also severely slowed down. For the N7meG post-insertion base pairs, surprisingly unlike others, N7meG:dT base pair shows stabilizing effect on the DNA duplex, as indicated by the structure and thermodynamic parameters. When N7 substitution is replaced by bulky and flexible group to form N7bnG, correct insertion of dCTP shows metal ion dependence. And the previously minimal insertion of dTTP can be seen with increased efficiency. Both of which are also contributed by the flexibility and hydrophobic interactions made by benzyl group. For 8ClG lesion, it shows Watson-Crick base pair for incoming dCTP, Hoogsteen base pair for incoming dGTP, similar to 8BrG in the polβ model. However, from the structural comparison, 8ClG seems to be more mutagenic than 8BrG. Additionally, it can have some dATP and dTTP insertions, although they are in less extent both structurally and kinetically.