CONFORMATIONAL-ANALYSIS OF THE 5' LEADER AND THE GAG INITIATION SITE OF MO-MULV RNA AND ALLOSTERIC TRANSITIONS INDUCED BY DIMERIZATION

Dimerization of genomic RNA is a key step in the retroviral life cycle and has been postulated to be involved in the regulation of translati on, encapsidation and reverse transcription. Here, we have derived a s econdary structure model of nucleotides upstream from PSI and of the g ag initiation region of Mo-MuLV RNA in monomeric and dimeric forms, us ing chemical probing, sequence comparison and computer prediction. The 5' domain is extensively base-paired and interactions take place betw een U5 and 5' leader sequences. The U5-PBS subdomain can fold in two m utually exclusive conformations: a very stable and extended helical st ructure (E form) in which 17 of the 18 nucleotides of the PBS are pair ed, or an irregular three-branch structure (B form) in which 1 0 nucle otides of the PBS are paired. The dimeric RNA adopts the B conformatio n. The monomeric RNA can switch from the E to the B conformation by a thermal treatment. If the E to B transition is associated to dimerizat ion, it may facilitate annealing of the primer tRNA(Pro) to the PBS by lowering the free energy required for melting the PBS. Furthermore, d imerization induces allosteric rearrangements around the SD site and t he gag initiation region.