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

Structures of r(CGCGCG)(2) and 2'-O-Me(CGCGCG)(2) have been determined by NMR spectroscopy under low salt conditions. All protons and phosph orus nuclei resonances have been assigned. Signals of H5'/5 '' have be en assigned stereospecifically. All (3)J(H,H) and (3)J(P,H) coupling c onstants have been measured. The structures were determined and refine d using an iterative relaxation matrix procedure (IRMA) and the restra ined 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 step s of both duplexes, the planes of the inter-strand cytosines are not p arallel while guanines are almost parallel. For the GC steps this patt ern is reversed. The 2'-O-methyl groups are spatially close to the 5'- hydrogens of neighbouring residues from the 3'-side and are directed t owards the minor groove of 2'-O-Me(CGCGCG)(2) forming a hydrophobic la yer. Solution structures of both duplexes are similar; the effect of 2 '-O-methylation on the parent RNA structure is small. This suggests th at intrinsic properties imposed by alternating CG base pairs govern th e overall conformation of both duplexes.