Recent successes in coarse-grained modeling of DNA

Davit A. Potoyan, Alexey Savelyev, Garegin A. Papoian

Research output: Contribution to journalReview articlepeer-review

Abstract

The growing interest in the DNA-based mesoscale systems of biological and nonbiological nature has encouraged the computational molecular science community to develop coarse-grained (CG) representationsof the DNA that will be simple enough to permit exhaustive simulations in a reasonable amount of time, yet complex enough to capture the essential physics at play. In the recent years, there have been some major developments in the DNA coarse-graining area and several fairly sophisticated models are now available that faithfully reproduce key mechanical and chemical properties of the double- and single-stranded DNA. However, there are still many challenges, which limit the applicability of the present models, and much has to be done yet to develop more reliable schemes which would have a predictive power beyond the target domain of the intrinsic parametrization. A development of robust, controllable, and transferrable CG DNA force fields will provide an invaluable tool for gaining physical insights into the molecular nature of complex DNA-based nanoscale entities such as the chromatin, virus capsids, and DNA nanocomposites. In the present contribution, we provide an overview of the recent developments in the DNA coarse-graining field. Our aim is to review the existing CG models of the double-stranded DNA, where a small selection of models, which we believe provide avenues for promising future development, are discussed in some detail.

Original languageEnglish
Pages (from-to)69-83
Number of pages15
JournalWiley Interdisciplinary Reviews: Computational Molecular Science
Volume3
Issue number1
DOIs
StatePublished - Jan 2013

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