We have attempted to alleviate the pH dependency of triplex recognition of guanine by using intermolecular triplexes containing 2-amino-5-(2-deoxy-d-ribofuranosyl)pyridine (AP) as an analogue of 2′-deoxycytidine (dC). We find that for the β-anomer of AP, the complex between (AP)₆T₆ and the target site G₆A₆•T₆C₆ is stable, generating a clear DNase I footprint at oligonucleotide conc•entrations as low as 0.25 µM at pH 5.0, in contrast to 50 µM C₆T₆ which has no effect on the cleavage pattern. This complex is still stable at pH 6.5 producing a footprint with 1 µM oligonucleotide. Oligonucleotides containing the α-anomer of AP are much less effective than the β-anomer, though in some instances they are more stable than the unmodified oligonucleotides. The results of molecular dynamics studies on a range of AP-containing triplexes has rationalized the observed stability behaviour in terms of hydrogen-bonding behaviour.