Relative stability of triplexes containing different numbers of T.AT and C+.GC triplets

We have used DNase I footprinting to compare the stability of parallel triple helices containing different numbers of T·AT and C+·GC triplets. We have targeted a fragment containing the 17mer sequence 5′-AGGAA-GAGAAAAAAGAA with the 9mer oligonucleotides 5′-TCCTTCTCT, 5′-TTCTCTTTT and 5′-TTTTTTCTT, which form triplexes at the 5′-end, centre and 3′-end of the target site respectively. Quantitative DNase I foot-printing has shown that at pH 5.0 the dissociation constants of these oligonucleotides are 0.13, 4.7 and>30 µM respectively, revealing that increasing the proportion of C+·GC triplets increases triplex stability. The results suggest that the positive charge on the protonated cytosine contributes to triplex stability, either by a favourable interaction with the stacked pi system or by screening the charge on the phosphate groups. In the presence of a naphthylquinoline triplex binding ligand all three oligonucleotides bind with similar affinities. At pH 6.0 these triplexes only form in the presence of the triplex binding ligand, while at pH 7.5 footprints are only seen with the oligonucleotide which generates the fewest number of C+·GC triplets (TTTTTTCTT) in the presence of the ligand