DOUBLE HAIRPIN COMPLEXES ALLOW ACCOMMODATION OF ALL 4 BASE-PAIRS IN TRIPLE HELICES CONTAINING BOTH DNA AND RNA STRANDS

We investigated the binding of an antisense oligodeoxynucleotide to a stem-loop structure corresponding to the mini-exon sequence of the pro tozoan parasite Leishmania amazonensis. This oligomer was designed to anneal to the single-stranded region adjacent to the bottom of the hai rpin and to fold back on itself, giving rise to a ''double-hairpin'' c omplex that involved a local triplex. This imposed the recognition, by the third strand, of a ''purine'' strand containing 6 interspersed py rimidines out of 15 nucleic acid bases. The sequence of the complement ary oligonucleotide was derived from the so-called pyrimidine motif; t he third strand of the anti-mini-exon oligomer was parallel to the pur ine strand of the target. Electrophoretic mobility shift assays and fo otprinting studies demonstrated that such an antisense oligomer was ab le to bind to both the DNA and RNA versions of the Leishmania hairpin. These double hairpin complexes allowed the formation at pH 6.0 of a t riple-stranded structure, despite the presence of 4 A:TG and 2 G:C*T triplets out of 15.