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

Nucleic Acids Res. 2004 Aug 3;32(13):4044-54. doi: 10.1093/nar/gkh736. Print 2004.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Pairing
  • Base Sequence
  • Cytidine / chemistry
  • Models, Molecular*
  • Molecular Structure
  • Nuclear Magnetic Resonance, Biomolecular
  • Nucleic Acid Conformation
  • Oligoribonucleotides / chemistry*
  • Phosphorus / chemistry
  • Protons
  • RNA, Double-Stranded / chemistry*
  • Sodium Chloride / chemistry

Substances

  • Oligoribonucleotides
  • Protons
  • RNA, Double-Stranded
  • tri(cytidylic acid-guanidylic acid)
  • Phosphorus
  • Sodium Chloride
  • Cytidine

Associated data

  • PDB/1T4X