Order and interactions in DNA arrays: Multiscale molecular dynamics simulation

Abstract While densely packed DNA arrays are known to exhibit hexagonal and orthorhombic local packings, the detailed mechanism governing the associated phase transition remains rather elusive. Furthermore, at high densities the atomistic resolution is paramount to properly account for fine details,...

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Autores principales:	Julija Zavadlav, Rudolf Podgornik, Matej Praprotnik
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/bfa4dbbcdd5b4028a862969c028edb94
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spelling	oai:doaj.org-article:bfa4dbbcdd5b4028a862969c028edb942021-12-02T15:05:51ZOrder and interactions in DNA arrays: Multiscale molecular dynamics simulation10.1038/s41598-017-05109-22045-2322https://doaj.org/article/bfa4dbbcdd5b4028a862969c028edb942017-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-05109-2https://doaj.org/toc/2045-2322Abstract While densely packed DNA arrays are known to exhibit hexagonal and orthorhombic local packings, the detailed mechanism governing the associated phase transition remains rather elusive. Furthermore, at high densities the atomistic resolution is paramount to properly account for fine details, encompassing the DNA molecular order, the contingent ordering of counterions and the induced molecular ordering of the bathing solvent, bringing together electrostatic, steric, thermal and direct hydrogen-bonding interactions, resulting in the observed osmotic equation of state. We perform a multiscale simulation of dense DNA arrays by enclosing a set of 16 atomistically resolved DNA molecules within a semi-permeable membrane, allowing the passage of water and salt ions, and thus mimicking the behavior of DNA arrays subjected to external osmotic stress in a bathing solution of monovalent salt and multivalent counterions. By varying the DNA density, local packing symmetry, and counterion type, we obtain osmotic equation of state together with the hexagonal-orthorhombic phase transition, and full structural characterization of the DNA subphase in terms of its positional and angular orientational fluctuations, counterion distributions, and the solvent local dielectric response profile with its order parameters that allow us to identify the hydration force as the primary interaction mechanism at high DNA densities.Julija ZavadlavRudolf PodgornikMatej PraprotnikNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-11 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Julija Zavadlav Rudolf Podgornik Matej Praprotnik Order and interactions in DNA arrays: Multiscale molecular dynamics simulation
description	Abstract While densely packed DNA arrays are known to exhibit hexagonal and orthorhombic local packings, the detailed mechanism governing the associated phase transition remains rather elusive. Furthermore, at high densities the atomistic resolution is paramount to properly account for fine details, encompassing the DNA molecular order, the contingent ordering of counterions and the induced molecular ordering of the bathing solvent, bringing together electrostatic, steric, thermal and direct hydrogen-bonding interactions, resulting in the observed osmotic equation of state. We perform a multiscale simulation of dense DNA arrays by enclosing a set of 16 atomistically resolved DNA molecules within a semi-permeable membrane, allowing the passage of water and salt ions, and thus mimicking the behavior of DNA arrays subjected to external osmotic stress in a bathing solution of monovalent salt and multivalent counterions. By varying the DNA density, local packing symmetry, and counterion type, we obtain osmotic equation of state together with the hexagonal-orthorhombic phase transition, and full structural characterization of the DNA subphase in terms of its positional and angular orientational fluctuations, counterion distributions, and the solvent local dielectric response profile with its order parameters that allow us to identify the hydration force as the primary interaction mechanism at high DNA densities.
format	article
author	Julija Zavadlav Rudolf Podgornik Matej Praprotnik
author_facet	Julija Zavadlav Rudolf Podgornik Matej Praprotnik
author_sort	Julija Zavadlav
title	Order and interactions in DNA arrays: Multiscale molecular dynamics simulation
title_short	Order and interactions in DNA arrays: Multiscale molecular dynamics simulation
title_full	Order and interactions in DNA arrays: Multiscale molecular dynamics simulation
title_fullStr	Order and interactions in DNA arrays: Multiscale molecular dynamics simulation
title_full_unstemmed	Order and interactions in DNA arrays: Multiscale molecular dynamics simulation
title_sort	order and interactions in dna arrays: multiscale molecular dynamics simulation
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/bfa4dbbcdd5b4028a862969c028edb94
work_keys_str_mv	AT julijazavadlav orderandinteractionsindnaarraysmultiscalemoleculardynamicssimulation AT rudolfpodgornik orderandinteractionsindnaarraysmultiscalemoleculardynamicssimulation AT matejpraprotnik orderandinteractionsindnaarraysmultiscalemoleculardynamicssimulation
_version_	1718388668395159552

Order and interactions in DNA arrays: Multiscale molecular dynamics simulation

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