Int. J. Mol. Sci. 2014, 15(7), 11799-11816; https://doi.org/10.3390/ijms150711799
Base Flip in DNA Studied by Molecular Dynamics Simulationsof Differently-Oxidized Forms of Methyl-Cytosine
Institute of Theoretical Physics, Free University Berlin, Arnimallee 14, 14195 Berlin, Germany
†
These authors contributed equally to this work.
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Received: 30 May 2014 / Revised: 23 June 2014 / Accepted: 25 June 2014 / Published: 3 July 2014
(This article belongs to the Special Issue Identification and Roles of the Structure of DNA)
Abstract
Distortions in the DNA sequence, such as damage or mispairs, are specifically recognized and processed by DNA repair enzymes. Many repair proteins and, in particular, glycosylases flip the target base out of the DNA helix into the enzyme’s active site. Our molecular dynamics simulations of DNA with intact and damaged (oxidized) methyl-cytosine show that the probability of being flipped is similar for damaged and intact methyl-cytosine. However, the accessibility of the different 5-methyl groups allows direct discrimination of the oxidized forms. Hydrogen-bonded patterns that vary between methyl-cytosine forms carrying a carbonyl oxygen atom are likely to be detected by the repair enzymes and may thus help target site recognition. View Full-TextKeywords:
DNA damage; base flip; molecular dynamics simulations; DNA recognition
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Helabad, M.B.; Kanaan, N.; Imhof, P. Base Flip in DNA Studied by Molecular Dynamics Simulationsof Differently-Oxidized Forms of Methyl-Cytosine. Int. J. Mol. Sci. 2014, 15, 11799-11816.
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