NMR STRUCTURE OF A CLASSICAL PSEUDOKNOT - INTERPLAY OF SINGLE-STRANDED-RNA AND DOUBLE-STRANDED-RNA

Pseudoknot formation folds the 3' ends of many plant viral genomic RNA s into structures that resemble transfer RNA in global folding and in their reactivity to transfer RNA-specific proteins. The solution struc ture of the pseudoknotted T arm and acceptor arm of the transfer RNA-l ike structure of turnip yellow mosaic virus (TYMV) was determined by n uclear magnetic resonance (NMR) spectroscopy. The molecule is stabiliz ed by the hairpin formed by the 5' end of the RNA, and by the intricat e interactions related to the loops of the pseudoknot. Loop 1 spans th e major groove of the helix with only two of its four nucleotides. Loo p 2, which crosses the minor groove, interacts closely with its opposi ng helix, in particular through hydrogen bonds with a highly conserved adenine. The structure resulting from this interaction between the mi nor groove and single-stranded RNA at helical junctions displays inter nal mobility, which may be a general feature of RNA pseudoknots that r egulates their interaction with proteins or other RNA molecules.