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Nucleic Acids Research, 2003, Vol. 31, No. 24 7131-7140
© 2003 Oxford University Press

Article

Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening

Yongping Pan and Alexander D. MacKerell Jr*

Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA

*To whom correspondence should be addressed. Tel: +1 410 706 7442; Fax: +1 410 706 5017; Email: amackere{at}rx.umaryland.edu

DNA and RNA are known to have different structural properties. In the present study, molecular dynamics (MD) simulations on a series of RNA and DNA duplexes indicate differential structural flexibility for the two classes of oligonucleotides. In duplex RNA, multiple base pairs experienced local opening events into the major groove on the nanosecond time scale, while such events were not observed in the DNA simulations. Three factors are indicated to be responsible for the base opening events in RNA: solvent–base interactions, 2'OH(n)–O4'(n+1) intra-strand hydrogen bonding, and enhanced rigid body motion of RNA at the nucleoside level. Water molecules in the major groove of RNA contribute to initiation of base pair opening. Stabilization of the base pair open state is due to a ‘conformational switch’ comprised of 2'OH(n)–O4'(n+1) hydrogen bonding and a rigid body motion of the nucleoside moiety in RNA. This rigid body motion is associated with decreased flexibility of the glycosyl linkage and sugar moieties in A-form structures. The observed opening rates in RNA are consistent with the imino proton exchange experiments for AU base pairs, although not for GC base pairs, while structural and flexibility changes associated with the proposed conformational switch are consistent with survey data of RNA and DNA crystal structures. The possible relevance of base pair opening events in RNA to its many biological functions is discussed.


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