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Li, Qiu-Shi; Shu, Yao-Gen; Ou-Yang, Zhong-Can; Li, Ming1
Kinetic assays of DNA polymerase fidelity: A theoretical perspective beyond Michaelis-Menten kinetics
Source PublicationPHYSICAL REVIEW E
Language英语
KeywordNUCLEOTIDE INCORPORATION CONFORMATIONAL-CHANGES SPONTANEOUS MUTATION TRANSLOCATION STEP MECHANISM REPLICATION EXONUCLEASE SELECTION DYNAMICS BINDING
AbstractThe high fidelity of DNA polymerase (DNAP) is critical for the faithful replication of DNA. There are several quantitative approaches to measure DNAP fidelity. Directly counting the error frequency in the replication products gives the true fidelity but it turns out very hard to implement in practice. Two biochemical kinetic approaches, the steady-state assay and the transient-state assay, were then suggested and widely adopted. In these assays, the error frequency is indirectly estimated by using kinetic theories combined with the measured apparent kinetic rates. However, whether it is equivalent to the true fidelity has never been clarified theoretically, and in particular there are different strategies using these assays to quantify the proofreading efficiency of DNAP but often lead to inconsistent results. In this paper, we make a comprehensive examination on the theoretical foundation of the two kinetic assays, based on the theory of DNAP fidelity recently proposed by us. Our studies show that while the conventional kinetic assays are generally valid to quantify the discrimination efficiency of DNAP, they are valid to quantify the proofreading efficiency of DNAP only when the kinetic parameters satisfy some constraints which will be given explicitly in this paper. These results may inspire more carefully-designed experiments to quantify DNAP fidelity.
2021
ISSN2470-0045
Volume104Issue:1Pages:14408
Cooperation Status国内
Subject AreaPhysics
MOST Discipline CataloguePhysics, Fluids & Plasmas ; Physics, Mathematical
DOI10.1103/PhysRevE.104.014408
Indexed BySCIE
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Document Type期刊论文
Identifierhttp://ir.itp.ac.cn/handle/311006/27375
CollectionSCI期刊论文
Affiliation1.[Li, Qiu-Shi
2.Univ Chinese Acad Sci, Sch Phys Sci, 19A Yuquan Rd, Beijing 101400, Peoples R China
3.Univ Chinese Acad Sci, Wenzhou Inst, 1 Jinlian Rd, Wenzhou 325000, Zhejiang, Peoples R China
4.Chinese Acad Sci, Inst Theoret Phys, Zhong Guan Cun East St 55,POB 2735, Beijing 100190, Peoples R China
Recommended Citation
GB/T 7714
Li, Qiu-Shi,Shu, Yao-Gen,Ou-Yang, Zhong-Can,et al. Kinetic assays of DNA polymerase fidelity: A theoretical perspective beyond Michaelis-Menten kinetics[J]. PHYSICAL REVIEW E,2021,104(1):14408.
APA Li, Qiu-Shi,Shu, Yao-Gen,Ou-Yang, Zhong-Can,&Li, Ming.(2021).Kinetic assays of DNA polymerase fidelity: A theoretical perspective beyond Michaelis-Menten kinetics.PHYSICAL REVIEW E,104(1),14408.
MLA Li, Qiu-Shi,et al."Kinetic assays of DNA polymerase fidelity: A theoretical perspective beyond Michaelis-Menten kinetics".PHYSICAL REVIEW E 104.1(2021):14408.
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