Abstract
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 N 6H … 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.
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