A two-stranded template-based approach to G·(C-A) triad formation: designing novel structural elements into an existing DNA framework

We have designed a DNA sequence, d(G-G-G-T-T-C-A-G-G), which dimerizes to form a 2-fold symmetric G-quadruplex in which G(syn)·G(anti)·G(syn)·G(anti) tetrads are sandwiched between all trans G·(C-A) triads. The NMR-based solution structural analysis was greatly aided by monitoring hydrogen bond alignments across NH···N and NH···OC hydrogen bonds within the triad and tetrad, in a uniformly (13C,15N)-labeled sample of the d(G-G-G-T-T-C-A-G-G) sequence. The solution structure establishes that the guanine base-pairs with the cytosine through Watson-Crick G·C pair formation and with adenine through sheared G·A mismatch formation within the G·(C-A) triad. A model of triad DNA was constructed that contains the experimentally determined G·(C-A) triad alignment as the repeating stacked unit.