1PBM

STRUCTURE OF RIBONUCLEIC ACID, NMR, 1 STRUCTURE

Summary for 1PBM

• Entry DOI: 10.2210/pdb1pbm/pdb
• Related: 1PBL
• Descriptor: RNA (5'-R(*CP*GP*CP*GP*CP*G)-3') (1 entity in total)
• Functional Keywords: ribonucleic acid, rna duplex, rna
• Total number of polymer chains: 2
• Total formula weight: 3812.41

Authors

Popenda, M.,Biala, E.,Milecki, J.,Adamiak, R.W. (deposition date: 1996-08-05, release date: 1997-07-07, Last modification date: 2024-05-22)

Primary citation

Popenda, M.,Biala, E.,Milecki, J.,Adamiak, R.W.
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.
Nucleic Acids Res., 25:4589-4598, 1997

PubMed Abstract: 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 3JH,H and 3JP,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.

PubMed: 9358170
DOI: 10.1093/nar/25.22.4589

Experimental method

SOLUTION NMR