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Nucleic Acids Research 2005 33(6):1749-1759; doi:10.1093/nar/gki318
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Published online 23 March 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

Solution structure of a modified 2',5'-linked RNA hairpin involved in an equilibrium with duplex

Miha Plevnik, Zofia Gdaniec1 and Janez Plavec*

Slovenian NMR Center, National Institute of Chemistry Hajdrihova 19, PO Box, 660, SI-1001 Ljubljana, Slovenia 1Institute of Bioorganic Chemistry, Polish Academy of Sciences Noskowskiego 12/14, 61-704 Poznan, Poland

*To whom correspondence should be addressed. Tel: +386 1 47 60 353; Fax: +386 1 47 60 300; Email: janez.plavec{at}ki.si

Received December 21, 2004. Revised February 2, 2005. Accepted March 2, 2005.

The isomerization of phosphodiester functionality of nucleic acids from 3',5'- to a less common 2',5'-linkage influences the complex interplay of stereoelectronic effects that drive pseudorotational equilibrium of sugar rings and thus affect the conformational propensities for compact or more extended structures. The present study highlights the subtle balance of non-covalent forces at play in structural equilibrium of 2',5'-linked RNA analogue, 3'-O-(2-methoxyethyl) substituted dodecamer *CG*CGAA*U*U*CG*CG, 3'-MOE-2',5'-RNA, where all cytosines and uracils are methylated at C5. The NMR and UV spectroscopic studies have shown that 3'-MOE-2',5'-RNA adopts both hairpin and duplex secondary structures, which are involved in a dynamic exchange that is slow on the NMR timescale and exhibits strand and salt concentration as well as pH dependence. Unusual effect of pH over a narrow physiological range is observed for imino proton resonances with exchange broadening observed at lower pH and relatively sharp lines observed at higher pH. The solution structure of 3'-MOE-2',5'-RNA hairpin displays a unique and well-defined loop, which is stabilized by Watson–Crick A5·*U8 base pair and by n -> {pi}* stacking interactions of O4' lone-pair electrons of A6 and *U8 with aromatic rings of A5 and *U7, respectively. In contrast, the stem region of 3'-MOE-2',5'-RNA hairpin is more flexible. Our data highlight the important feature of backbone modifications that can have pronounced effects on interstrand association of nucleic acids.

Protein Data Bank accession ID 1XV6


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