HIV-1 genome dimerization: Formation kinetics and thermal stability of dimeric HIV-1(Lai) RNAs are not improved by the 1-232 and 296-790 regions flanking the kissing-loop domain

The genome of all retroviruses consists of two identical RNAs noncovalently linked near their 5' end. Dimerization of genomic RNA is thought to modulate several steps in the retroviral life cycle, such as recombination, translation, and encapsidation. The kissing-loop model of HIV-1 genome dimerization posits that the 233-285 region of the HIV-1 genome, by forming a hairpin and initiating dimerization through a loop-loop interaction, is at least the core dimerization domain of HIV-1 RNA. This region is called the kissing-loop domain. In addition, it can be argued that sequences within the 296-401 region [Paillart et al. (1994) J. Biol. Chem. 269, 27486-27493] or 5' of the primer binding site [Laughrea & Jette (1996) Biochemistry 35, 1589-1598] might play some role in the dimerization process, Accordingly, we have studied the effect of regions 1-232 and 296-790 on the dimerization kinetics and thermal stability of HIV-1(Lai) RNAs containing the kissing-loop domain (HIV-1(Lai) is a typical representative of North American and European HIV-1 viruses). Experiments conducted at high and low ionic strength indicate that these regions have no strongly positive effect on the dimerization process, Our experiments also indicate that the kissing-loop domain of HIV-1(Lai) has an apparent dissociation temperature 13 degrees C higher than that of the HIV-1(Mal) kissing-loop domain (HIV-1(Mal) is a Central African virus whose kissing-loop domain has a ''weak'' GUGCAC autocomplementary sequence). Because the 296-401 region of HIV-1(Mal) RNA stabilizes dimeric RNAs by less than or equal to 12 CC (Paillart et al,, 1994), we infer that the contributions of sequences downstream of U295 are (at best) concealed in HIV-1(Lai) and in most American and European HIV-1 viruses, i.e., in viruses whose kissing-loop domain is characterized by a ''strong'' GCGCGC autocomplementary sequence.