Nuclear magnetic resonance structural studies of A.AT base triple alignments in intramolecular purine.purine.pyrimidine DNA triplexes in solution.

This study reports on an NMR characterization of an intramolecular purine.purine.pyrimidine (R.RY) triplex containing a central A.AT triple in addition to G.GC and T.AT triples. Our studies establish an A(anti).AT alignment with reversed Hoogsteen pairing stabilized by two N6H ... N hydrogen bonds between adenine residues in the third strand and the purine strand of the duplex. This result, combined with our earlier demonstration of G(anti).GC and T(anti).AT pairing alignments, has provided a definitive experimental approach for differentiating between the base triple pairing possibilities proposed previously by Beal and Dervan for R.RY triplexes.