Triple helix formation on plasmid DNA determined by a size-exclusion chromatographic method

Triple-helix-forming oligodeoxynucleotides are receiving considerable attention due to their potential applications for the inhibition of specific genes in vivo. However, their development is impaired by the lack of triple helix formation under physiological conditions. It is thus crucial to be able to quantitatively assay triple helix formation of various oligodeoxynucleotides on different target sequences. Usual methods to detect triple helix formation are restricted under the experimental conditions that can be studied. In addition, quantitative techniques are limited. We present a novel method for rapid detection and quantification of triple helix formation between an oligodeoxynucleotide and a plasmid carrying a target sequence. The oligodeoxynucleotide was radiolabeled and, after incubation with the target plasmid, the unbound oligodeoxynucleotide was separated from the mixture of plasmids and plasmid-bound oligodeoxynucleotides by rapid gel filtration spun columns. The formation of a triple helix between a target plasmid and several oligodeoxynucleotides was demonstrated and compared. Temperature, sequence and ionic dependencies, and kinetics of association were analyzed. This new technique can be used under a variety of conditions and should allow the rapid determination of optimal conditions required for triple helix formation, as well as the easy selection of an oligodeoxynucleotide that specifically binds with the highest affinity to a target double-stranded sequence.