Solution structure of RNA duplexes containing alternating CG base pairs: NMR study of r(CGCGCG)2 and 2′-O-Me(CGCGCG)2 under low salt conditions

摘要

Structures of r(CGCGCG)₂ and 2′-O-Me(CGCGCG)₂ have been determined by NMR spectroscopy under low salt conditions. All protons and phosphorus nuclei resonances have been assigned. Signals of H5′/5″ have been assigned stereospecifically. All 3J_H,H and 3J_P,H coupling constants have been measured. The structures were determined and refined using an iterative relaxation matrix procedure (IRMA) and the restrained MD simulation. Both duplexes form half-turn, right-handed helices with several conformational features which deviate significantly from a canonical A-RNA structure. Duplexes are characterised as having C3′-endo sugar pucker, very low base-pair rise and high helical twist and inclination angles. Helices are overwound with 10 bp per turn. There is limited inter-strand guanine stacking for CG steps. Within CG steps of both duplexes, the planes of the inter-strand cytosines are not parallel while guanines are almost parallel. For the GC steps this pattern is reversed. The 2′-O-methyl groups are spatially close to the 5′-hydrogens of neighbouring residues from the 3′-side and are directed towards the minor groove of 2′-O-Me(CGCGCG)₂ forming a hydrophobic layer. Solution structures of both duplexes are similar; the effect of 2′-O-methylation on the parent RNA structure is small. This suggests that intrinsic properties imposed by alternating CG base pairs govern the overall conformation of both duplexes.