The ability of cationic phosphoramidate pyrimidine α‐oligonucleotides (ONs) to form triplexes with DNA duplexes was investigated by UV melting experiments, circular dichroism spectroscopy and gel mobility shift experiments. Replacement of the phosphodiester linkages in α‐ONs with positively charged phosphoramidate linkages results in more efficient triplex formation, the triplex stability increasing with the number of positive charges. At a neutral pH and in the absence of magnesium ions, it was found that a fully cationic phosphoramidate α‐TFO (triplex‐forming oligonucleotide) forms a highly stable triplex that melts at a higher temperature than the duplex target. No hysteresis between the annealing and melting curves was noticed; this indicates fast association. Moreover, the recognition of a DNA duplex with a cationic α‐TFO through Hoogsteen base pairing is highly sequence‐specific. To the best of our knowledge, this is the first report of stable triplexes in the pyrimidine motif formed by cationic α‐oligonucleotides and duplex targets.

At physiological pH and in the absence of magnesium ions, cationic phosphoramidate α‐oligonucleotides in the pyrimidine motif (see scheme) form highly stable and sequence‐specific triplexes with DNA duplexes.