Flexibility of short-strand RNA in aqueous solution as revealed by molecular dynamics simulation: are A′-RNA and A-RNA distinct conformational structures?

Defang Ouyang, Hong Zhang, Dirk-Peter Herten, Harendra S. Parekh, Sean C. Smith

Research output: Contribution to journalArticle

Abstract

We use molecular dynamics simulations to compare the conformational structure and dynamics of a 21-base pair RNA sequence initially constructed according to the canonical A-RNA and A'-RNA forms in the presence of counterions and explicit water. Our study aims to add a dynamical perspective to the solid-state structural information that has been derived from X-ray data for these two characteristic forms of RNA. Analysis of the three main structural descriptors commonly used to differentiate between the two forms of RNA namely major groove width, inclination and the number of base pairs in a helical twist over a 30 ns simulation period reveals a flexible structure in aqueous solution with fluctuations in the values of these structural parameters encompassing the range between the two crystal forms and more. This provides evidence to suggest that the identification of distinct A-RNA and A'-RNA structures, while relevant in the crystalline form, may not be generally relevant in the context of RNA in the aqueous phase. The apparent structural flexibility observed in our simulations is likely to bear ramifications for the interactions of RNA with biological molecules (e.g. proteins) and non-biological molecules (e.g. non-viral gene delivery vectors).
Original languageEnglish
Pages (from-to)1054-1061
Number of pages8
JournalAustralian Journal of Chemistry
Volume62
Issue number9
DOIs
Publication statusPublished - 17 Sep 2009

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Molecular dynamics
RNA
Computer simulation
Molecules
Flexible structures
Genes
Crystalline materials
X rays
Crystals
Water
Proteins

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Ouyang, Defang ; Zhang, Hong ; Herten, Dirk-Peter ; Parekh, Harendra S. ; Smith, Sean C. / Flexibility of short-strand RNA in aqueous solution as revealed by molecular dynamics simulation : are A′-RNA and A-RNA distinct conformational structures?. In: Australian Journal of Chemistry. 2009 ; Vol. 62, No. 9. pp. 1054-1061.
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abstract = "We use molecular dynamics simulations to compare the conformational structure and dynamics of a 21-base pair RNA sequence initially constructed according to the canonical A-RNA and A'-RNA forms in the presence of counterions and explicit water. Our study aims to add a dynamical perspective to the solid-state structural information that has been derived from X-ray data for these two characteristic forms of RNA. Analysis of the three main structural descriptors commonly used to differentiate between the two forms of RNA namely major groove width, inclination and the number of base pairs in a helical twist over a 30 ns simulation period reveals a flexible structure in aqueous solution with fluctuations in the values of these structural parameters encompassing the range between the two crystal forms and more. This provides evidence to suggest that the identification of distinct A-RNA and A'-RNA structures, while relevant in the crystalline form, may not be generally relevant in the context of RNA in the aqueous phase. The apparent structural flexibility observed in our simulations is likely to bear ramifications for the interactions of RNA with biological molecules (e.g. proteins) and non-biological molecules (e.g. non-viral gene delivery vectors).",
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Flexibility of short-strand RNA in aqueous solution as revealed by molecular dynamics simulation : are A′-RNA and A-RNA distinct conformational structures? / Ouyang, Defang; Zhang, Hong; Herten, Dirk-Peter; Parekh, Harendra S.; Smith, Sean C.

In: Australian Journal of Chemistry, Vol. 62, No. 9, 17.09.2009, p. 1054-1061.

Research output: Contribution to journalArticle

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