Nucleic Acids Research, Vol 25, Issue 22 4589-4598, Copyright © 1997 by Oxford University Press
M Popenda, E Biala, J Milecki and RW Adamiak
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.
ARTICLES
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
Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
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