Fidelity discrimination in DNA polymerase beta: differing closing profiles for a mismatched (G:A) versus matched (G:C) base pair.

ABSTRACT: Understanding fidelity-the faithful replication or repair of DNA by polymerases-requires tracking of the structural and energetic changes involved, including the elusive transient intermediates, for nucleotide incorporation at the template/primer DNA junction. We report, using path sampling simulations and a reaction network model, strikingly different transition states in DNA polymerase beta's conformational closing for correct dCTP versus incorrect dATP incoming nucleotide opposite a template G. The cascade of transition states leads to differing active-site assembly processes toward the "two-metal-ion catalysis" geometry. We demonstrate that these context-specific pathways imply different selection processes: while active-site assembly occurs more rapidly with the correct nucleotide and

SUBMITTER: Radhakrishnan R 

PROVIDER: S-EPMC2625286 | biostudies-literature | 2005 Sep

REPOSITORIES: biostudies-literature