Binding of oligopyrimidines to the RNA hairpin responsible for the ribosome gag-pol frameshift in HIV-1

The 12 bp stem of the RNA hairpin responsible for the gag-pol frameshifting of the ribosomes during translation of the polycistronic HIV-1 mRNA has a pyrimidine-rich 5' strand and, consequently, a purine-rich 3' strand. Elect rophoretic mobility shift assays have shown that DNA oligopyrimidines, 12 a nd 20 nucleotides long (but not oligopurines or G,T-containing oligomers), designed to form triplexes actually bind to the double-stranded RNA target. RNase V1 footprinting studies have confirmed the interaction between the h airpin stem and the. RNA and 2'-O-methyl oligoribonucleotide analogues of t he 12-mer oligodeoxypyrimidine as well as 5 propynyl,cytosine, containing t he 12-mer oligodeoxypyrimidine, bind more strongly to the RNA target than t he unmodified parent DNA oligomer, The complexes formed by the RNA hairpin and either the 12-mer oligodeoxypyrimidine or the 20-mer oligopyrimidine ar e stable at a neutral pH and in the absence of Mg2+ but blocked neither the reverse transcription nor cell-free translation of a RNA template in which the gag-pol frameshifting hairpin,vas inserted at the 5' end of the lucife rase open reading frame. (C) 1999 Federation of European Biochemical Societ ies.