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

Ravi Radhakrishnan, Tamar Schlick

Research output: Contribution to journalArticlepeer-review

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 β'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 leads to primer extension, the enzyme remains open longer, has a more transient closed state, and forms product more slowly when an incorrect nucleotide is present. Our results also suggest that the rate-limiting step in pol β's conformational closing is not identical to that for overall nucleotide insertion and that the rate-limiting step in the overall nucleotide incorporation process for matched as well as mismatched systems occurs after the closing conformational change.

Original languageEnglish (US)
Pages (from-to)13245-13252
Number of pages8
JournalJournal of the American Chemical Society
Volume127
Issue number38
DOIs
StatePublished - Sep 28 2005

ASJC Scopus subject areas

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry

Fingerprint Dive into the research topics of 'Fidelity discrimination in DNA polymerase β: Differing closing profiles for a mismatched (G:A) versus matched (G:C) base pair'. Together they form a unique fingerprint.

Cite this