title: Kinetic selection vs. free energy of DNA base pairing in control of polymerase fidelity.
abstract: What is the free energy source enabling high-fidelity DNA polymerases (pols) to favor incorporation of correct over incorrect base pairs by 10(3)- to 10(4)-fold, corresponding to free energy differences of ΔΔGinc∼ 5.5-7 kcal/mol? Standard ΔΔG° values (∼0.3 kcal/mol) calculated from melting temperature measurements comparing matched vs. mismatched base pairs at duplex DNA termini are far too low to explain pol accuracy. Earlier analyses suggested that pol active-site steric constraints can amplify DNA free energy differences at the transition state (kinetic selection). A recent paper [Olson et al. (2013)J Am Chem Soc135:1205-1208] used Vent pol to catalyze incorporations in the presence of inorganic pyrophosphate intended to equilibrate forward (polymerization) and backward (pyrophosphorolysis) reactions. A steady-state leveling off of incorporation profiles at long reaction times was interpreted as reaching equilibrium between polymerization and pyrophosphorolysis, yielding apparent ΔG° = -RTlnKeq, indicating ΔΔG° of 3.5-7 kcal/mol, sufficient to account for pol accuracy without need of kinetic selection. Here we perform experiments to measure and account for pyrophosphorolysis explicitly. We show that forward and reverse reactions attain steady states far from equilibrium for wrong incorporations such as G opposite T. Therefore,[Formula: see text]values obtained from such steady-state evaluations ofKeqare not dependent on DNA properties alone, but depend largely on constraints imposed on right and wrong substrates in the polymerase active site.
authors.affiliation: Department of Biological Sciences, Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089;
authors.forename: Keriann
authors.initials: K
authors.lastname: Oertell
authors.affiliation: Department of Chemistry, Stanford University, Stanford, CA 94305.
authors.forename: Emily M
authors.initials: EM
authors.lastname: Harcourt
authors.affiliation: Department of Chemistry, Stanford University, Stanford, CA 94305.
authors.forename: Michael G
authors.initials: MG
authors.lastname: Mohsen
authors.affiliation: Department of Biological Sciences, Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089;
authors.forename: John
authors.initials: J
authors.lastname: Petruska
authors.affiliation: Department of Chemistry, Stanford University, Stanford, CA 94305.
authors.forename: Eric T
authors.initials: ET
authors.lastname: Kool
authors.affiliation: Department of Biological Sciences, Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089; mgoodman@usc.edu.
authors.forename: Myron F
authors.initials: MF
authors.lastname: Goodman
mesh_terms: D020029:Base Pairing; D004247:DNA / Q000737:chemistry*; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry*; D007700:Kinetics; D008956:Models, Chemical; D013816:Thermodynamics
chemical_list: D004247:DNA; C072146:Pfu DNA polymerase; D004259:DNA-Directed DNA Polymerase
keywords: DNA replication fidelity; Vent; polymerase; thermodynamics