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Title: A multiscale analysis of DNA phase separation : from atomistic to mesoscale level
Authors: Sun, Tiedong
Mirzoev, Alexander
Lyubartsev, Alexander P.
Minhas, Vishal
Korolev, Nikolay
Nordenskiöld, Lars
Keywords: DNA
Science::Biological sciences
Issue Date: 2019
Source: Sun, T., Mirzoev, A., Minhas, V., Korolev, N., Lyubartsev, A. P., & Nordenskiöld, L. (2019). A multiscale analysis of DNA phase separation : from atomistic to mesoscale level. Nucleic Acids Research, 47(11), 5550-5562. doi:10.1093/nar/gkz377
Series/Report no.: Nucleic Acids Research
Abstract: DNA condensation and phase separation is of utmost importance for DNA packing in vivo with important applications in medicine, biotechnology and polymer physics. The presence of hexagonally ordered DNA is observed in virus capsids, sperm heads and in dinoflagellates. Rigorous modelling of this process in all-atom MD simulations is presently difficult to achieve due to size and time scale limitations. We used a hierarchical approach for systematic multiscale coarse-grained (CG) simulations of DNA phase separation induced by the three-valent cobalt(III)-hexammine (CoHex3+). Solvent-mediated effective potentials for a CG model of DNA were extracted from all-atom MD simulations. Simulations of several hundred 100-bp-long CG DNA oligonucleotides in the presence of explicit CoHex3+ ions demonstrated aggregation to a liquid crystalline hexagonally ordered phase. Following further coarse-graining and extraction of effective potentials, we conducted modelling at mesoscale level. In agreement with electron microscopy observations, simulations of an 10.2-kb-long DNA molecule showed phase separation to either a toroid or a fibre with distinct hexagonal DNA packing. The mechanism of toroid formation is analysed in detail. The approach used here is based only on the underlying all-atom force field and uses no adjustable parameters and may be generalised to modelling chromatin up to chromosome size.
ISSN: 0305-1048
DOI: 10.1093/nar/gkz377
Rights: © 2019 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (, which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact
Fulltext Permission: open
Fulltext Availability: With Fulltext
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