Triple helix formation at A8XA8.T8YT8.

We have examined the formation of DNA triple helices between the oligonucleotides T8XT8 (X = A,C,G,T) and DNA fragments containing the target sequences A8XA8.T8YT8 (X = T,C,G; Y = A,G,C), by DNase I footprinting. We find that A8GA8.T8CT8 yields a footprint with T8CT8 and shows a weaker interaction with T17 and T8GT8. A8CA8.T8GT8 yields a footprint with T17, and shows weaker interaction with T8CT8. A8TA8.T8AT8 yields a footprint with T8GT8 and shows weaker interaction with T17. Each of the successful complexes is characterised by enhanced DNase I cleavage at the 3' end of the purine strand of the target, as well as protection at the 5' end. We have been unable to from triplexes with third strands of the type A8XA8.