Detection of triplex-forming RNA oligonucleotides by triplex blotting

Triplex formation with RNA oligonucleotides and double-stranded (ds) DNA may provide a means of controlling gene expression from specific promoters and/or creating more selective DNA cleaving agents. We report the development of a novel technique, called triplex blotting, designed to detect RNA species capable of triplex formation with radiolabeled dsDNA probes within a background of total cellular RNA. Triplex blotting offers a new approach for screening potential RNA sequences for triplex formation with dsDNA targets, for comparing relative binding affinities of various triplex-forming RNAs and for confirming the specificity of triplex formation of a DNA target probe within total cellular RNA. In addition, the technique allows for repeated probing of the same filter while varying critical hybridization conditions such as pH, temperature or ionic strength.