Bulge defects in intramolecular pyrimidine.purine.pyrimidine DNA triplexes in solution

We report below on NMR studies of single base bulges in intramolecular pyrimidine (Y.RY) DNA triplexes in aqueous solution at acidic pH. The structural studies were undertaken with the goal of elucidating the dependence of the bulge site conformation on the nature of the base (adenine or thymine) and the location of the defect site (Watson-Crick pyrimidine and purine strands and Hoogsteen pyrimidine strand). The NMR parameters establish that an extra adenine loops out of the Y.RY triplex when it is positioned either on the Watson-Crick pyrimidine strand I (designated AI bulge triplex) or the Hoogsteen pyrimidine strand III (designated AIII bulge triplex) with the associated destabilization greater for the AIII bulge triplex relative to the AI bulge triplex. This observation that single adenine bulges loop out of Y.RY DNA triplexes contrasts with previous NMR structural studies, which established that single adenine bulges stack into DNA duplexes in solution. We also establish that an extra thymine on the Watson-Crick purine strand II (designated TII bulge triplex) loops out of a Y.RY DNA triplex. The single base bulges do not disrupt the pairing alignments of the flanking triples in all three bulge Y.RY triplexes. It therefore appears that structural constraints energetically disfavor stacking of extra bases into any of the three strands of Y.RY DNA triplexes in solution. Our NMR studies also establish that while intramolecular Y.RY DNA triplexes at low pH can accommodate single base bulges on each of the three strands, the triplex is disrupted following insertion of an A-G bulge in Hoogsteen strand III.