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.