| Abstract
| - The genome of all retroviruses consists of two identical RNAsnoncovalently linked near their5‘ end. Dimerization of genomic RNA is thought to modulate severalsteps in the retroviral life cycle,such as recombination, translation, and encapsidation. Thekissing-loop model of HIV-1 genomedimerization [Laughrea, M., & Jetté, L. (1994)Biochemistry 33, 13464−13474; Skripkin et al.(1994)Proc. Natl. Acad. Sci. U.S.A. 91, 4945−4949] posits thatthe 248−270 region of the HIV-1 genome, byforming a hairpin and initiating dimerization through a loop−loopinteraction, is the full or at least thecore dimerization domain of HIV-1 RNA. Here, we show by nesteddeletion analysis that the 3‘ boundaryof the HIV-1 dimerization domain is immediately downstream of hairpin248−270 and that the isolatedregion 248−271 dimerizes at least as readily as longer RNAs.Among various HIV-1Lai RNA transcriptscontaining hairpin 248−270, all form two types of dimer, as isimplicit in the kissing-loop model. Thehigh-stability dimer resists semidenaturing conditions and thelow-stability dimer cannot, which is consistentwith the model. At physiological temperatures, low-stabilitydimers are usually formed, as if dimerizationwithout nucleocapsid proteins corresponded to loop−loop interactionwithout switching from intra- tointerstrand hydrogen bonding. Our results show that the 3‘ DLS (asequence immediately 3‘ from the 5‘splice junction and originally thought to be the dimerization domain ofthe HIV-1 genome) and adjacentnucleotides are not necessary for efficient dimerization ofHIV-1Lai RNA at low and high ionic strength.Upstream of hairpin 248−270 exists another “DLS-like”sequence that we name 5‘ DLS: like the isolated3‘ DLS, the isolated 5‘ DLS forms an apparently nonphysiologicalstructure that can become substantiallydimeric at high ionic strength.
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