FORMATION OF DNA TRIPLE HELICES INCORPORATING BLOCKS OF G-CENTER-DOT-GC AND T-CENTER-DOT-AT TRIPLETS USING SHORT ACRIDINE-LINKED OLIGONUCLEOTIDES

We have used DNase I footprinting to assess triple helix formation at target sites containing the sequences A(6)G(6).C6T6 and G(6)A(6).T6C6. These sequences can be recognized by the acridine-linked oligopyrimidines Acr-T5C5 and Acr-C5T5 respectively at low pH, using well-characterised T.AT and C+.GC triplets. At pH 7.5 A(6)G(6).C6T6 is specifically bound by Acr-G(5)T(5), utilising G.GC and T.AT triplets in which the third strand runs antiparallel to the purine strand of the duplex. This interaction requires the presence of magnesium ions. No interaction was detected with Acr-T(5)G(5), an oligonucleotide designed to form parallel G.GC and T.AT triplets. In contrast neither Acr-T(5)G(5) nor Acr-G(5)T(5) produced DNase I footprints with the target sequence G(6)A(6).T6C6. These results suggest that, in an antiparallel R.RY triple helix, the T.AT triplet is weaker than the G.GC triplet. We find no evidence for the formation of structures containing parallel G.GC triplets.