Next Article in Journal
Inhibition of TRPM7 Channels Reduces Degranulation and Release of Cytokines in Rat Bone Marrow-Derived Mast Cells
Next Article in Special Issue
Making the Bend: DNA Tertiary Structure and Protein-DNA Interactions
Previous Article in Journal
TupA: A Tungstate Binding Protein in the Periplasm of Desulfovibrio alaskensis G20
Previous Article in Special Issue
Comparisons of Non-Gaussian Statistical Models in DNA Methylation Analysis
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

,
 and *
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)
View Full-Text   |   Download PDF [1865 KB, uploaded 3 July 2014]   |   Browse Figures
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 DNA damage; base flip; molecular dynamics simulations; DNA recognition
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.

Export to BibTeX |
EndNote


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.


Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert