Computer simulation studies of the fidelity of DNA polymerases.
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 beta and T7, and the mechanism and energetics of the polymerization reaction catalyzed by T7 DNA polymerase.
Florián
Jan
J
Department of Chemistry, University of Southern California, Los Angeles, CA 90089-1062, USA.
Goodman
Myron F
MF
Warshel
Arieh
A
D003198:Computer Simulation; D019951:DNA Polymerase beta / Q000737:chemistry; D004261:DNA Replication; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry*; D008958:Models, Molecular; D013329:Structure-Activity Relationship; D013816:Thermodynamics
C034970:bacteriophage T7 induced DNA polymerase; D019951:DNA Polymerase beta; D004259:DNA-Directed DNA Polymerase