1T4X

The first left-handed RNA structure of (CGCGCG)2, Z-RNA, NMR, 12 structures, determined in high salt

Summary for 1T4X

• Entry DOI: 10.2210/pdb1t4x/pdb
• Descriptor: RNA (5'-R(*CP*GP*CP*GP*CP*G)-3') (1 entity in total)
• Functional Keywords: left-handed rna duplex, z-rna, rna
• Total number of polymer chains: 2
• Total formula weight: 3812.41

Authors

Popenda, M.,Milecki, J.,Adamiak, R.W. (deposition date: 2004-04-30, release date: 2004-08-03, Last modification date: 2024-05-22)

Primary citation

Popenda, M.,Milecki, J.,Adamiak, R.W.
High salt solution structure of a left-handed RNA double helix.
Nucleic Acids Res., 32:4044-4054, 2004

PubMed Abstract: 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 degrees), whereas GpC steps have large negative values (-61 degrees). 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.

PubMed: 15292450
DOI: 10.1093/nar/gkh736

Experimental method

SOLUTION NMR