Sutthibutpong, Thana, Noy, Agnes orcid.org/0000-0003-0673-8949 and Harris, Sarah A. (2016) Atomistic Molecular Dynamics Simulations of DNA Minicircle Topoisomers: A Practical Guide to Setup, Performance and Analysis. In: Chromosome Architecture. Methods in Molecular Biology . Springer , pp. 195-219.
Abstract
While DNA supercoiling is ubiquitous in vivo, the structure of supercoiled DNA is more challenging to study experimentally than simple linear sequences because the DNA must have a closed topology in order to sustain superhelical stress. DNA minicircles, which are closed circular double-stranded DNA sequences typically containing between 60 and 500 base pairs, have proven to be useful biochemical tools for the study of supercoiled DNA mechanics. We present detailed protocols for constructing models of DNA minicircles in silico, for performing atomistic molecular dynamics (MD) simulations of supercoiled minicircle DNA, and for analyzing the results of the calculations. These simulations are computationally challenging due to the large system sizes. However, improvements in parallel computing software and hardware promise access to improve conformational sampling and simulation timescales. Given the concurrent improvements in the resolution of experimental techniques such as atomic force microscopy (AFM) and cryo-electron microscopy, the study of DNA minicircles will provide a more complete understanding of both the structure and the mechanics of supercoiled DNA.
Metadata
Item Type: | Book Section |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | Embargo period: 12 months |
Dates: |
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Institution: | The University of York |
Academic Units: | The University of York > Faculty of Sciences (York) > Physics (York) |
Depositing User: | Pure (York) |
Date Deposited: | 07 Oct 2022 12:20 |
Last Modified: | 28 Dec 2024 00:17 |
Published Version: | https://doi.org/10.1007/978-1-4939-3631-1_15 |
Status: | Published |
Publisher: | Springer |
Series Name: | Methods in Molecular Biology |
Identification Number: | 10.1007/978-1-4939-3631-1_15 |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:191839 |