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

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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

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Publication details

The article was received on 16 Sep 2017, accepted on 26 Oct 2017 and first published on 03 Jan 2018


Article type: Paper
DOI: 10.1039/C7CP06355E
Citation: Phys. Chem. Chem. Phys., 2018, Advance Article
  • Open access: Creative Commons BY license
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    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, Advance Article , DOI: 10.1039/C7CP06355E

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