Liquid crystal ordering of nucleic acids

Naskar, S and Saurabh, S and Jang, YH and Lansac, Y and Maiti, PK (2020) Liquid crystal ordering of nucleic acids. In: Soft Matter, 16 (3). pp. 634-641.

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Abstract

Several analytical calculations and computer simulations propose that cylindrical monodispersive rods having an aspect ratio (ratio of length to diameter) greater than 4 can exhibit liquid crystal (LC) ordering. But, recent experiments demonstrated the signature of LC ordering in systems of 4- to 20-base pair (bp) long nucleic acids (NAs) that do not satisfy the shape anisotropy criterion. Mechanisms of end-to-end adhesion and stacking have been proposed to explain this phenomenon. In this study, using all-atom molecular dynamics (MD) simulation, we explicitly verify the end-to-end stacking of double-stranded RNA (dsRNA) and demonstrate the LC ordering at the microscopic level. Using umbrella sampling (US) calculation, we quantify the potential of mean force (PMF) between two dsRNAs for various reaction coordinates (RCs) and compare our results with previously reported PMFs for double-stranded DNA (dsDNA). The PMF profiles demonstrate the anisotropic nature of inter-NA interaction. We find that, like dsDNA, dsRNA also prefers to stack on top of each other while repelling sideways, leading to the formation of supra-molecular-columns that undergo LC ordering at high NA volume fraction (�). We also demonstrate and quantify the nematic ordering of the RNAs using several hundred nanosecond-long MD simulations that remain almost invariant for different initial configurations and under different external physiological conditions.

Item Type:	Journal Article
Publication:	Soft Matter
Publisher:	Royal Society of Chemistry
Additional Information:	Copyright of this article belongs to Royal Society of Chemistry
Keywords:	Anisotropy; Aspect ratio; Liquid crystals; Molecular dynamics; Reaction kinetics; RNA, Analytical calculation; Double-stranded DNA (ds-DNA); Double-stranded RNA (dsRNA); Initial configuration; Molecular dynamics simulations; Physiological condition; Potential of mean force; Ratio of length to diameters, Bioinformatics
Department/Centre:	Division of Physical & Mathematical Sciences > Physics
Date Deposited:	18 Feb 2020 10:25
Last Modified:	18 Feb 2020 10:25
URI:	http://eprints.iisc.ac.in/id/eprint/64547

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