Biophys J, April 2001, p. 1957-1966, Vol. 80, No. 4

Solution Structure of the SL1 RNA of the M1 Double-Stranded RNA Virus of Saccharomyces cerevisiae

Jun-Seok Yoo,^* Hae-Kap Cheong,^* Bong Jin Lee, Yang-Bae Kim, and Chaejoon Cheong^*

 ^*Magnetic Resonance Team, Korea Basic Science Institute, Taejon 305-333, and  Department of Pharmacy, Seoul National University, Seoul 151-742, Korea

The 20-nucleotide SL1 VBS RNA, 5'-GGAGACGC[GAUUC]GCGCUCC (bulged 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 structure was determined by NMR spectroscopy. Structure calculations gave a precisely defined structure, with an average pairwise root mean square deviation (RMSD) of 1.28 Å for the entire molecule, 0.57 Å for the loop region (C8-G14), and 0.46 Å for the bulge region (G4-G7, C15-C17). Base stacking continues for three nucleotides on the 5' side of the loop. The final structure contains a single hydrogen bond involving the guanine imino proton and the carbonyl O₂ of the cytosine between the nucleotides on the 5' and 3' ends of the loop, although they do not form a Watson-Crick base pair. All three pyrimidine bases in the loop point toward the major groove, 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 loop regions may allow the SL1 VBS RNA to interact with Cap-Pol protein without drastically changing its own conformation.

Biophys J, April 2001, p. 1957-1966, Vol. 80, No. 4
© 2001 by the Biophysical Society   0006-3495/01/04/1957/10  $2.00