Atomistic Molecular Dynamics Simulations of DNA Minicircle Topoisomers: A Practical Guide to Setup, Performance and Analysis

Thana Sutthibutpong, Agnes Noy, Sarah A. Harris

Research output: Chapter in Book/Report/Conference proceedingChapter


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.
Original languageEnglish
Title of host publicationChromosome Architecture
Subtitle of host publicationMethods and Protocols
ISBN (Electronic)978-1-4939-3631-1
ISBN (Print)978-1-4939-3629-8
Publication statusPublished - 10 Jun 2016

Publication series

NameMethods in Molecular Biology

Bibliographical note

Embargo period: 12 months

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