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Nucleic Acids Research 2004 32(13):4044-4054; doi:10.1093/nar/gkh736
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Published online 3 August 2004

Nucleic Acids Research, Vol. 32 No. 13 © Oxford University Press 2004; all rights reserved

High salt solution structure of a left-handed RNA double helix

Mariusz Popenda, Jan Milecki1 and Ryszard W. Adamiak*

Laboratory of Structural Chemistry of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12-14, 61-704 Poznan, Poland and 1 Faculty of Chemistry, Adam Mickiewicz University, Poznan, Poland

* To whom correspondence should be addressed. Tel: +48 61 8528503; Fax: +48 61 8520532; Email: adamiakr{at}ibch.poznan.pl
This paper is dedicated to Professor Wolfram Saenger on the occasion of his 65th birthday and in recognition of his outstanding contribution to knowledge of the nucleic acid structure.

Received May 20, 2004; Revised June 24, 2004; Accepted July 13, 2004

Right-handed RNA duplexes of (CG)n sequence undergo salt-induced helicity reversal, forming left-handed RNA double helices (Z-RNA). In contrast to the thoroughly studied Z-DNA, no Z-RNA structure of natural origin is known. Here we report the NMR structure of a half-turn, left-handed RNA helix (CGCGCG)2 determined in 6 M NaClO4. This is the first nucleic acid motif determined at such high salt. Sequential assignments of non-exchangeable proton resonances of the Z-form were based on the hitherto unreported NOE connectivity path [H6(n)-H5'/H5''(n)-H8(n+1)-H1'(n+1)-H6(n+2)] found for left-handed helices. Z-RNA structure shows several conformational features significantly different from Z-DNA. Intra-strand but no inter-strand base stacking was observed for both CpG and GpC steps. Helical twist angles for CpG steps have small positive values (4–7°), whereas GpC steps have large negative values (–61°). In the full-turn model of Z-RNA (12.4 bp per turn), base pairs are much closer to the helix axis than in Z-DNA, thus both the very deep, narrow minor groove with buried cytidine 2'-OH groups, and the major groove are well defined. The 2'-OH group of cytidines plays a crucial role in the Z-RNA structure and its formation; 2'-O-methylation of cytidine, but not of guanosine residues prohibits A to Z helicity reversal.


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