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Theoretical Biology and Medical Modelling

, 8:22

First Online: 24 June 2011Received: 22 March 2011Accepted: 24 June 2011DOI: 10.1186-1742-4682-8-22

Cite this article as: Xie, P. Theor Biol Med Model 2011 8: 22. doi:10.1186-1742-4682-8-22

Abstract

Y-family DNA polymerases are characterized by low-fidelity synthesis on undamaged DNA and ability to catalyze translesion synthesis over the damaged DNA. Their translocation along the DNA template is an important event during processive DNA synthesis. In this work we present a Brownian ratchet model for this translocation, where the directed translocation is rectified by the nucleotide binding to the polymerase. Using the model, different features of the available structures for Dpo4, Dbh and polymerase ι in binary and ternary forms can be easily explained. Other dynamic properties of the Y-family polymerases such as the fast translocation event upon dNTP binding for Dpo4 and the considerable variations of the processivity among the polymerases can also be well explained by using the model. In addition, some predicted results of the DNA synthesis rate versus the external force acting on Dpo4 and Dbh polymerases are presented. Moreover, we compare the effect of the external force on the DNA synthesis rate of the Y-family polymerase with that of the replicative DNA polymerase.

Electronic supplementary materialThe online version of this article doi:10.1186-1742-4682-8-22 contains supplementary material, which is available to authorized users.

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Autor: Ping Xie

Fuente: https://link.springer.com/







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