Js. Yoo et al., Solution structure of the SL1 RNA of the m1 double-stranded RNA virus of Saccharomyces cerevisiae, BIOPHYS J, 80(4), 2001, pp. 1957-1966
The 20-nucleotide SL1 VBS RNA, 5'-GGAG (A) under bar CGC[GAUUC]GCGCUCC (bul
ged A underlined and loop bases in brackets), plays a crucial role in viral
particle binding to the plus strand and packaging of the RNA. its structur
e was determined by NMR spectroscopy. Structure calculations gave a precise
ly defined structure, with an average pairwise root mean square deviation (
RMSD) of 1.28 Angstrom for the entire molecule, 0.57 Angstrom for the loop
region (C8-G14), and 0.46 Angstrom for the bulge region (G4-G7, C15-C17). B
ase stacking continues for three nucleotides on the 5' side of the loop. Th
e final structure contains a single hydrogen bond involving the guanine imi
no proton and the carbonyl O-2 of the cytosine between the nucleotides on t
he 5' and 3' ends of the loop, although they do not form a Watson-Crick bas
e pair. All three pyrimidine bases in the loop point toward the major groov
e, which implies that Cap-Pol protein may recognize the major groove of the
SL1 loop region. The bulged A5 residue is stacked in the stem, but nuclear
Overhauser enhancements (NOEs) suggest that A5 spends part of the time in
the bulged-out conformation. The rigid conformation of the upper stem and l
oop regions may allow the SL1 VBS RNA to interact with Cap-Pot protein with
out drastically changing its own conformation.