Int. J. Mol. Sci. 2014, 15(7), 11799-11816; doi:10.3390/ijms150711799
Article

Base Flip in DNA Studied by Molecular Dynamics Simulationsof Differently-Oxidized Forms of Methyl-Cytosine

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Received: 30 May 2014; in revised form: 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)
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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.
Keywords: DNA damage; base flip; molecular dynamics simulations; DNA recognition
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MDPI and ACS Style

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.

AMA Style

Helabad MB, Kanaan N, Imhof P. Base Flip in DNA Studied by Molecular Dynamics Simulationsof Differently-Oxidized Forms of Methyl-Cytosine. International Journal of Molecular Sciences. 2014; 15(7):11799-11816.

Chicago/Turabian Style

Helabad, Mahdi B.; Kanaan, Natalia; Imhof, Petra. 2014. "Base Flip in DNA Studied by Molecular Dynamics Simulationsof Differently-Oxidized Forms of Methyl-Cytosine." Int. J. Mol. Sci. 15, no. 7: 11799-11816.

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