title: Kinetics and thermodynamics of exonuclease-deficient DNA polymerases.
abstract: A kinetic theory is developed for exonuclease-deficient DNA polymerases, based on the experimental observation that the rates depend not only on the newly incorporated nucleotide, but also on the previous one, leading to the growth of Markovian DNA sequences from a Bernoullian template. The dependencies on nucleotide concentrations and template sequence are explicitly taken into account. In this framework, the kinetic and thermodynamic properties of DNA replication, in particular, the mean growth velocity, the error probability, and the entropy production are calculated analytically in terms of the rate constants and the concentrations. Theory is compared with numerical simulations for the DNA polymerases of T7 viruses and human mitochondria.
authors.affiliation: Center for Nonlinear Phenomena and Complex Systems, Université Libre de Bruxelles, Code Postal 231, Campus Plaine, B-1050 Brussels, Belgium.
authors.forename: Pierre
authors.initials: P
authors.lastname: Gaspard
mesh_terms: D017123:Bacteriophage T7 / Q000201:enzymology; D004259:DNA-Directed DNA Polymerase / Q000378:metabolism*; D006801:Humans; D007700:Kinetics; D008390:Markov Chains; D008928:Mitochondria / Q000201:enzymology; D008954:Models, Biological; D011336:Probability; D013816:Thermodynamics
chemical_list: D004259:DNA-Directed DNA Polymerase