Solution structure of a pyrimidine purine pyrimidine triplex containing the sequence-specific intercalating non-natural base D-3

We have used NMR spectroscopy to study a pyrimidine . purine . pyrimidine DNA tripler containing a non-natural base, 1-(2-deoxy-beta-D-ribofuranosyl)4-(3-benzamido)phenylimidazole (D-3), in the third strand. The D-3 base has been previously shown to specifically recognize T . A and C . G base-pairs via intercalation on the 3' side (with respect to the purine strand) of the target base pair, instead of forming sequence-specific hydrogen bonds. H-1 resonance assignments have been made for the D-3 base and most of the non-loop portion of the tripler. The solution structure of the tripler was calculated using restrained molecular dynamics and complete relaxation matrix refinement. The duplex portion of the tripler has an over-all helical structure that is more similar to B-DNA than to A-DNA. The three aromatic rings of the D-3 base stack on the bases of all three strands and mimic a triplet. The conformation of the D-3 base and its sequence specificity are discussed. (C) 1996 Academic Press Limited