Oligonucleotide-mediated inhibition of genomic RNA dimerization of HIV-1 strains MAL and LAI: A comparative analysis

An essential step in the replication cycle of retroviruses is the dimerizat ion of two copies of the genomic RNA. In vitro and in vivo studies have dem onstrated that dimerization is mediated at least partially by RNA-RNA inter actions. In HIV-1, the cis-element most important for dimerization is the d imerization initiation site (DIS), a stem-loop structure with an autocomple mentary loop located between the primer binding site and the splice donor s ite in the 5' leader region of genomic RNA. We have studied the inhibition of dimerization of RNA corresponding to the first 615 nt of HIV-1 strains M AL and LAI in vitro using RNA and DNA oligonucleotides. The oligonucleotide s were identical to or complementary to the DIS of the MAL and LAI strains, which are representative of the two most common DIS moths found in natural isolates. The loop sequence of the DIS of the MAL isolate is AGGUGCACA, an d that of the LAI sequence is AAGCGCGCA (the autocomplementary sequences ar e GUGCAC and GCGCGC, respectively). Several of the oligonucleotides were ve ry efficient inhibitors of dimerization, However, homologous oligonucleotid es displayed vastly different inhibition efficiencies between the two strai ns despite relatively modest sequence differences, Some of the oligonucleot ides bound the viral RNA via a loop-loop interaction alone, whereas others recruited stem nucleotides to form an extended duplex even in the absence o f loop complementarity. Furthermore, oligonucleotide inhibition was ineffec tive at low temperature, suggesting that a conformational change in the DIS is necessary for disruption of the dimeric structure of the DIS or binding of oligonucleotide or both.