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Computer simulation studies of the fidelity of DNA polymerases
Author(s) -
Florián Jan,
Goodman Myron F.,
Warshel Arieh
Publication year - 2003
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.10244
Subject(s) - chemistry , dna polymerase , polymerase , base pair , free energy perturbation , dna , fidelity , dna replication , biophysics , computational chemistry , molecular dynamics , biochemistry , computer science , biology , telecommunications
Computer simulations can provide in principle quantitative correlation between the structures of DNA polymerases and the replication fidelity. This paper describes our progress in this direction. Using several theoretical approaches, including the free energy perturbation (FEP), linear response approximation (LRA), and the empirical valence bond (EVB) methods, we examined the stability of several mismatched base pairs in DNA duplex in aqueous solution, the contribution of binding energy to the fidelity of DNA polymerases β and T7, and the mechanism and energetics of the polymerization reaction catalyzed by T7 DNA polymerase. © 2003 Wiley Periodicals, Inc. Biopolymers 68: 286–299, 2003