Recognition of GC base pairs by triplex forming oligonucleotides containing nucleosides derived from 2-aminopyridine

We have attempted to alleviate the pH dependency of tripler 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 beta-anomer of AP, the complex between (AP)(6)T-6 and the target site G(6)A(6).T6C6 is stable, generating a clear DNase I footprint at oligonucleotide concentrations as low as 0.25 mu M at pH 5.0, in contrast to 50 mu M C6T6 which has no effect on the cleavage pattern, This complex is still stable at pH 6.5 producing a footprint with 1 mu M oligonucleotide. Oligonucleotides containing the alpha-anomer of AP are much less effective than the beta-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.