Issue 5, 2018

Origins of biological function in DNA and RNA hairpin loop motifs from replica exchange molecular dynamics simulation

Abstract

Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) have remarkably similar chemical structures, but despite this, they play significantly different roles in modern biology. In this article, we explore the possible conformations of DNA and RNA hairpins to better understand the fundamental differences in structure formation and stability. We use large parallel temperature replica exchange molecular dynamics ensembles to sample the full conformational landscape of these hairpin molecules so that we can identify the stable structures formed by the hairpin sequence. Our simulations show RNA adopts a narrower distribution of folded structures compared to DNA at room temperature, which forms both hairpins and many unfolded conformations. RNA is capable of forming twice as many hydrogen bonds than DNA which results in a higher melting temperature. We see that local chemical differences lead to emergent molecular properties such as increased persistence length in RNA that is weakly temperature dependant. These discoveries provide fundamental insight into how RNA forms complex folded tertiary structures which confer enzymatic-like function in ribozymes, whereas DNA retains structural motifs in order to facilitate function such as translation of sequence.

Graphical abstract: Origins of biological function in DNA and RNA hairpin loop motifs from replica exchange molecular dynamics simulation

Supplementary files

Article information

Article type
Paper
Submitted
16 sep 2017
Accepted
26 okt 2017
First published
03 jan 2018
This article is Open Access
Creative Commons BY license

Phys. Chem. Chem. Phys., 2018,20, 2990-3001

Origins of biological function in DNA and RNA hairpin loop motifs from replica exchange molecular dynamics simulation

J. B. Swadling, K. Ishii, T. Tahara and A. Kitao, Phys. Chem. Chem. Phys., 2018, 20, 2990 DOI: 10.1039/C7CP06355E

This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. You can use material from this article in other publications without requesting further permissions from the RSC, provided that the correct acknowledgement is given.

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