BASE-PAIRINGS WITHIN THE RNA PSEUDOKNOT ASSOCIATED WITH THE SIMIAN RETROVIRUS-1 GAG-PRO FRAMESHIFT SITE

Frameshift and readthrough sites within retroviral messenger RNAs are often followed by nucleotide sequences that have the potential to form pseudoknot structures. In the work presented here, NMR methods were u sed to characterize the base-pairings and structural features of the R NA pseudoknot downstream of the gag-pro frameshift site of simian retr ovirus type-1 (SRV-1) and a functional mutant of the SRV-1 pseudoknot. Evidence is presented that these pseudoknots contain two A-form helic al stems of six base-pairs each, connected by two loops, in a classic PI-type pseudoknot topology. A particularly interesting feature is tha t the shorter of the two connecting loops, loop 1, consists of only a single adenosine nucleotide that spans the major groove of stem 2. In this respect, the frameshift-associated pseudoknots are structurally s imilar to the pseudoknot within the gene 32 mRNA of bacteriophage T2, previously characterized by NMR methods. Despite having similar nucleo tide sequences, the solvent exchange rates of the imino protons at the junction of the helical stems in the wild-type and mutant frameshifti ng pseudoknots differ from each other and from the bacteriophage T2 ps eudoknot. The implications of this finding are discussed. (C) 1997 Aca demic Press Limited.