Triple helices formed at oligopyrimidine·oligopurine sequences with base pair inversions: Effect of a triplex-specific ligand on stability and selectivity

Abstract

Oligonucleotide-directed triple helix formation is mostly restricted to oligopyrimidine·oligopuvine sequences of double helical DNA. An interruption of one or two pyrimidines in the oligopurine target strand leads to a strong triplex destabilisation. We have investigated the effect of nucleotide analogues introduced in the third strand at the site opposite the base pair inversion(s). We show that a 3-nitropyrrole derivative (M) discriminates G·C from C·G, A·T and T·A in the presence of a triplex-specific ligand (a benzo[e]pyridoindole derivative, BePI). N6-methoxy-2,6-diaminopurine (K) binds to an A·T base pair better than a T·A, G·C or C·G base pair. Some discrimination is still observed in the presence of BePI and triplex stability is markedly increased. These findings should help in designing BePI-oligonucleotide conjugates to extend the range of DNA sequences available for triplex formation.