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 dependences 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 in terms of the rate constants and the concentrations are calculated analytically. Theory is compared with numerical simulations for the DNA polymerases of T7 viruses and human mitochondria.

Physical Review E (2016)

References in corpus (4)

• Stochastic kinetics of ribosomes: single motor properties and collective behavior
• Thermodynamics of accuracy in kinetic proofreading: Dissipation and efficiency trade-offs
• Kinetics and thermodynamics of first-order Markov chain copolymerization
• Kinetics and thermodynamics of DNA polymerases with exonuclease proofreading

Cited by in corpus (7)

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• Kinetics and thermodynamics of DNA polymerases with exonuclease proofreading
• Proofreading of DNA Polymerase: a new kinetic model with higher-order terminal effects
• The template-specific fidelity of DNA replication with high-order neighbor effects: a first-passage approach
• Template-directed growth of copolymers
• Kinetic discrimination of a polymerase in the presence of obstacles