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Base flipping in DNA: Pathways and energetics studied with molecular dynamic simulations
journal contribution
posted on 2023-06-08, 08:51 authored by Peter Varnai, Richard LaveryCarrying out chemistry on the bases of DNA, necessary for biological processes such as methylation or repair, requires flipping the base into an accessible position. In this work, molecular dynamics simulations are used to generate a free energy profile for flipping a cytosine base out of its helical stack in double-stranded DNA. The results shed light on the mechanics of this process by comparing routes for base flipping via the minor and major grooves.
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Publication status
- Published
Journal
Journal of the American Chemical SocietyISSN
0002-7863Publisher
ACS PublicationsExternal DOI
Issue
25Volume
124Page range
7272-7273Pages
2.0Department affiliated with
- Chemistry Publications
Notes
PV did most of the work and is principle author. First free energy description of a base flipping process in DNA, showing for the first time that flipping through minor groove is feasible. The energetics indicate spontaneous flipping before enzyme binding not a probable mechanism, cited 32 times.Full text available
- No
Peer reviewed?
- Yes
Legacy Posted Date
2012-02-06Usage metrics
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