Triplex complexes contain a single-stranded probe bound to a double-strandednucleic acid target, in which the probe includes a heteropolymeric nucleicacid or a heteropolymeric nucleic acid analog. All base triplets of thecomplex are members selected from the group consisting of A-T-A, T-A-T, U-A-T,T-A-U, A-U-A, U-A-U, G-C-G and C-G-C. A cation-facilitated assay includesdetecting the presence of such triplex complexes to determine the degree ofcomplementarity between the probe and target sequence. The assay preferablydetects a change in fluorescent intensity of a label as a function of bindingaffinity between the probe and target. The label can be covalently tethered tothe probe or to the target, or can be an intercalating fluorophore in thereaction medium.
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