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Understanding the structural and dynamic consequences of DNA epigenetic modifications: Computational insights into cytosine methylation and hydroxymethylation

Carvalho, Alexandra T. P., Gouveia, Leonor, Kanna, Charan Raju, Wärmländer, Sebastian K T S, Platts, James Alexis and Kamerlin, Shina Caroline Lynn 2015. Understanding the structural and dynamic consequences of DNA epigenetic modifications: Computational insights into cytosine methylation and hydroxymethylation. Epigenetics 9 (12) , pp. 1604-1612. 10.4161/15592294.2014.988043

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We report a series of molecular dynamics (MD) simulations of up to a microsecond combined simulation time designed to probe epigenetically modified DNA sequences. More specifically, by monitoring the effects of methylation and hydroxymethylation of cytosine in different DNA sequences, we show, for the first time, that DNA epigenetic modifications change the molecule's dynamical landscape, increasing the propensity of DNA toward different values of twist and/or roll/tilt angles (in relation to the unmodified DNA) at the modification sites. Moreover, both the extent and position of different modifications have significant effects on the amount of structural variation observed. We propose that these conformational differences, which are dependent on the sequence environment, can provide specificity for protein binding.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Chemistry
Advanced Research Computing @ Cardiff (ARCCA)
Subjects: Q Science > QD Chemistry
Uncontrolled Keywords: DNA methylation, epigenetics, indirect readout, molecular dynamics, recognition, AFM, Atomic Force Microscopy, DDD, Dickerson-Drew Dodecamer, DFT, Density Functional Theory, DNA, Deoxyribonucleic Acid, DNMT, DNA Methyltransferase, LINEs, Long Interspred Transposable Elements, MD, Molecular Dynamics, MeCP, Methylated CpG-binding proteins, MM, Molecular Mechanics, PBC, Periodic Boundary Conditions, QM, Quantum Mechanics, RDF, Radial Distribution Functions, RESP, Restrained Electrostatic Potentials Model, SINEs, Short Interspred Transposable Elements, SPME, Smooth Particle-Mesh Ewald, TET, Translocation Proteins, WT, Wild Type
Additional Information: This is an Open Access article distributed under the terms of the Creative Commons Attribution-Non-Commercial License (, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. The moral rights of the named author(s) have been asserted.
Publisher: Taylor & Francis: STM, Behavioural Science and Public Health Titles
ISSN: 1559-2294
Date of First Compliant Deposit: 30 March 2016
Date of Acceptance: 6 November 2014
Last Modified: 12 Aug 2019 14:45

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