Computational Study of the Force Dependence of Phosphoryl Transfer during DNA Synthesis by a High Fidelity Polymerase

Loading...
Thumbnail Image
Penn collection
Departmental Papers (BE)
Degree type
Discipline
Subject
Funder
Grant number
License
Copyright date
Distributor
Related resources
Author
Venkatramani, Ravindra
Contributor
Abstract

High fidelity polymerases are efficient catalysts of phosphodiester bond formation during DNA replication or repair. We interpret molecular dynamics simulations of a polymerase bound to its substrate DNA and incoming nucleotide using a quasiharmonic model to study the effect of external forces applied to the bound DNA on the kinetics of phosphoryl transfer. The origin of the force dependence is shown to be an intriguing coupling between slow, delocalized polymerase-DNA modes and fast catalytic site motions. Using noncognate DNA substrates we show that the force dependence is context specific.

Advisor
Date Range for Data Collection (Start Date)
Date Range for Data Collection (End Date)
Digital Object Identifier
Series name and number
Publication date
2008-02-29
Journal title
Volume number
Issue number
Publisher
Publisher DOI
Journal Issue
Comments
Copyright 2008 American Physical Society. Reprinted from Physical Review Letters, Volume 1008, Article 088102, February 2008, 4 pages.
Recommended citation
Collection