EVIDENCE FOR INTERSTRAND QUADRUPLEX FORMATION IN THE DIMERIZATION OF HUMAN IMMUNODEFICIENCY VIRUS-1 GENOMIC RNA

Retroviruses package two homologous single-stranded RNA genomes within a gag protein-RNA complex. In mature virion particles, the two RNA st rands are thought to associate primarily through direct RNA-RNA intera ctions, although the structural basis for this stable association is u nknown. We now report that a 127-nucleotide (nt) HIV-1NL4-3 RNA fragme nt (positions 732-858) encompassing the 5' end of the gag gene dimeriz es spontaneously under high ionic strength conditions in the absence o f any protein cofactor. The HIV-1 RNA dimer is dramatically and specif ically stabilized by the monovalent cation potassium. Thermal dissocia tion of the dimer occurs at 80-degrees-C in 100 mM K+ (5 mM Mg2+) but at significantly lower temperatures in the presence of either smaller or larger monovalent cations (100 mM Li+, 40-degrees-C; 100 mM Na+, 55 -degrees-C; 100 mM Cs+, 30-degrees-C). Deletion analyses of the 3' end of the 127-nt fragment reveal that an HIV-1 RNA fragment as short as 94 nt (732-825) can dimerize spontaneously, but a further 9-base delet ion of the purine-rich sequence, GGGGGAGAA from positions 817 through 825, eliminates dimerization. These experimental results support a mod el in which HIV-1 RNA dimerizes by forming an interstrand quadruple he lix stabilized by guanine (and/or purine)-base tetrads in analogy to t he well-known dimerization of telomeric DNA. We speculate that this st ructure may also mediate the association of genomic HIV-1 RNA in vivo, revealing how RNA itself can achieve the self-recognition required fo r subsequent genetic recombination.