A general theory of kinetics and thermodynamics of steady-state copolymerization

Shu, Yeqiang; Song, Yongshun; Ou-Yang, Zhong-Cun; Li, Ming

doi:10.1088/0953-8984/27/23/235105

Cited by 15 publications

(33 citation statements)

References 26 publications

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“…Following the same logic of Ref. 29, we use P s Xn···X 1 to denote the occurrence probability of the terminal sequence X n · · · X 1 in the synthetic (polymerase) site, P e Xn···X 1 to denote the occurrence probability of X n · · · X 1 in the exonuclease site, X i = A, B. N Xn···X 2 X 1 is defined as the total number of sequence X n · · · X 2 X 1 appearing in the primer chain.…”

Section: A First-order Proofreading Modelmentioning

confidence: 99%

“…This method has already been used for higher-order copolymerization by us (see the supplementary of Ref. 29) and can be readily extended to the exonuclease proofreading schemes.…”

Section: The Fidelity Problem Of Dna Replication By Dnapmentioning

confidence: 99%

“…The Galas-Branscomb models like FIG. 1(b1) or (b2), however, are seemingly reversible, and the corresponding kinetic equations are always unclosed and hierarchically coupled, which is hard to solve.Fortunately, a general rigorous treatment for such problems has been established recently by us29 , and this method can be directly applied to Model II (some important results are given in Appendix C). For Model Ilike FIG.…”

mentioning

confidence: 99%

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Proofreading of DNA polymerase: a new kinetic model with higher-order terminal effects

Song

Shu

Zhou

et al. 2016

J. Phys.: Condens. Matter

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The fidelity of DNA replication by DNA polymerase (DNAP) has long been an important issue in biology. While numerous experiments have revealed details of the molecular structure and working mechanism of DNAP which consists of both a polymerase site and an exonuclease (proofreading) site, there were quite a few theoretical studies on the fidelity issue. The first model which explicitly considered both sites was proposed in the 1970s and the basic idea was widely accepted by later models. However, all these models did not systematically investigate the dominant factor on DNAP fidelity, i.e. the higher-order terminal effects through which the polymerization pathway and the proofreading pathway coordinate to achieve high fidelity. In this paper, we propose a new and comprehensive kinetic model of DNAP based on some recent experimental observations, which includes previous models as special cases. We present a rigorous and unified treatment of the corresponding steady-state kinetic equations of any-order terminal effects, and derive analytical expressions for fidelity in terms of kinetic parameters under bio-relevant conditions. These expressions offer new insights on how the higher-order terminal effects contribute substantially to the fidelity in an order-by-order way, and also show that the polymerization-and-proofreading mechanism is dominated only by very few key parameters. We then apply these results to calculate the fidelity of some real DNAPs, which are in good agreements with previous intuitive estimates given by experimentalists.

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Section: A First-order Proofreading Modelmentioning

confidence: 99%

“…This method has already been used for higher-order copolymerization by us (see the supplementary of Ref. 29) and can be readily extended to the exonuclease proofreading schemes.…”

Section: The Fidelity Problem Of Dna Replication By Dnapmentioning

confidence: 99%

mentioning

confidence: 99%

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Proofreading of DNA polymerase: a new kinetic model with higher-order terminal effects

Song

Shu

Zhou

et al. 2016

J. Phys.: Condens. Matter

Self Cite

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“…As suggested by previous work [21,22] devoted to the k = 0 and k = 1 cases, k th -order Markov chains are generated if the kinetics depends on k lastly incorporated monomeric units [23]. In the present paper, the analytical method previously developed in Ref.…”

mentioning

confidence: 93%

Growth and Dissolution of Macromolecular Markov Chains

Gaspard

2016

J Stat Phys

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The kinetics and thermodynamics of free living copolymerization are studied for processes with rates depending on k monomeric units of the macromolecular chain behind the unit that is attached or detached. In this case, the sequence of monomeric units in the growing copolymer is a k th -order Markov chain. In the regime of steady growth, the statistical properties of the sequence are determined analytically in terms of the attachment and detachment rates. In this way, the mean growth velocity as well as the thermodynamic entropy production and the sequence disorder can be calculated systematically. These different properties are also investigated in the regime of depolymerization where the macromolecular chain is dissolved by the surrounding solution. In this regime, the entropy production is shown to satisfy Landauer's principle.

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“…These considerations have been addressed in recent kinetic formalisms of growth velocity and fidelity during the real, non-equilibrium process, these models including nearest neighbor and higher-order effects 35–38 . In addition, within the context of information theory and thermodynamics of DNA replication, it has been recently shown that to keep the fidelity within a given tolerance, average consumed energy E must increase with the reliability of the incorporated nucleotide according the next relation 33 (see Methods):where p error is the sequence-independent probability of error per incorporated nucleotide (or error rate) in the absence of exonucleolytic proofreading and β = 1/ kT .…”

Section: Discussionmentioning

confidence: 99%

A DNA-centered explanation of the DNA polymerase translocation mechanism

Arias-González

2017

Sci Rep

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DNA polymerase couples chemical energy to translocation along a DNA template with a specific directionality while it replicates genetic information. According to single-molecule manipulation experiments, the polymerase-DNA complex can work against loads greater than 50 pN. It is not known, on the one hand, how chemical energy is transduced into mechanical motion, accounting for such large forces on sub-nanometer steps, and, on the other hand, how energy consumption in fidelity maintenance integrates in this non-equilibrium cycle. Here, we propose a translocation mechanism that points to the flexibility of the DNA, including its overstretching transition, as the principal responsible for the DNA polymerase ratcheting motion. By using thermodynamic analyses, we then find that an external load hardly affects the fidelity of the copying process and, consequently, that translocation and fidelity maintenance are loosely coupled processes. The proposed translocation mechanism is compatible with single-molecule experiments, structural data and stereochemical details of the DNA-protein complex that is formed during replication, and may be extended to RNA transcription.

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A general theory of kinetics and thermodynamics of steady-state copolymerization

Cited by 15 publications

References 26 publications

Proofreading of DNA polymerase: a new kinetic model with higher-order terminal effects

Proofreading of DNA polymerase: a new kinetic model with higher-order terminal effects

Growth and Dissolution of Macromolecular Markov Chains

A DNA-centered explanation of the DNA polymerase translocation mechanism

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