KISSING-LOOP MODEL OF HIV-1 GENOME DIMERIZATION - HTV-1 RNAS CAN ASSUME ALTERNATIVE DIMERIC FORMS, AND ALL SEQUENCES UPSTREAM OR DOWNSTREAMOF HAIRPIN 248-271 ARE DISPENSABLE FOR DIMER FORMATION

The genome of all retroviruses consists of two identical RNAs noncoval ently linked near their 5' end. Dimerization of genomic RNA is thought to modulate several steps in the retroviral life cycle, such as recom bination, translation, and encapsidation. The kissing-loop model of HI V-1 genome dimerization [Laughrea, M., & Jette, L. (1994) Biochemistry 33, 13464-13474; Skripkin et al. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 4945-4949] posits that the 248-270 region of the HIV-1 genome, by forming a hairpin and initiating dimerization through a loop-loop int eraction, is the full. or at least the core dimerization domain of HIV -1 RNA. Here, we show by nested deletion analysis that the 3' boundary of the HIV-1 dimerization domain is immediately downstream of hairpin 248-270 and that the isolated region 248-271 dimerizes at least as re adily as longer RNAs. Among various HIV-1(Lai) RNA transcripts contain ing hairpin 248-270, all form two types of dimer, as is implicit in th e kissing-loop model. The high-stability dimer resists semidenaturing conditions and the low-stability dimer cannot, which is consistent wit h the model. At physiological temperatures, low-stability dimers are u sually formed, as if dimerization without nucleocapsid proteins corres ponded to loop-loop interaction without switching from intra- to inter strand hydrogen bonding. Our results show that the 3' DLS (a sequence immediately 3' from the 5' splice junction and originally thought to b e the dimerization domain of the HIV-I genome) and adjacent nucleotide s are not necessary for efficient dimerization of HIV-1(Lai) RNA at lo w and high ionic strength. Upstream of hairpin 248-270 exists another ''DLS-like'' sequence that we name 5' DLS: like the isolated 3' DLS, t he isolated 5' DLS forms an apparently nonphysiological structure that can become substantially dimeric at high ionic strength.