Conjugates of oligonucleotides with triplex-specific intercalating agents. Stabilization of triple-helical DNA in the promoter region of the gene for the alpha-subunit of interleukin 2 (IL-2R alpha).

The stabilization of triple-helical DNA under physiological conditions is an important goal for the control of gene expression using the antigen strategy, an approach whereby an oligonucleotide binds to the major groove of double-helical DNA to fom a triple helix. To this end, triplex-specific intercalators, namely benzopyridoindole (BPI) and benzopyridoquinoxaline (BPQ) derivatives, have been conjugated to the 5' end or to an internucleotide position of a 15-mer oligonucleotide. These conjugates were then tested, using thermal denaturation experiments, for their ability to form and stabilize a triple-helical structure involving a 42-mer duplex target. All of the conjugates were found to do so. The B[h]PQ derivatives stabilized particularly well when attached to the 5' end with a delta Tm of 15 degrees C and -delta delta G degrees 37 of 3.4 kcal mol-1 (pH 6.9, 140 mM KCI, 15 mM sodium cacodylate, 2 mM MgCl2, 0.8 mM spermine). Though most of the derivatives when attached to the internucleotide position were not able to stabilize triple-helical DNA as well as when attached to the 5' end, one B[f]PQ derivative with an internucleotide attachment did so, with a delta Tm of 13 degrees C and -delta delta G degrees 37 of 2.8 kcal mol-1. To a lesser degree, these conjugates were also able to stabilize duplex structures with single-stranded targets. Results were compared to the stabilization obtained with acridine conjugates as well as to a similar study performed with a different sequence.