Abstract
Oligonucleotide-directed triple helix formation is one of the most powerful methods for the sequence-specific recognition of double-helical DNA. Pyrimidine oligonucleotides bind purine tracts in the major groove of DNA parallel to the purine Watson-Crick strand through the formation of specific Hoogsteen-type hydrogen bonds. Specificity is derived from thymine (T) recognition of adenine·thymine (A·T) base pairs (T·A·T triplet) and N3-protonated cytosine (C+) recognition of guanine-cytosine (G·C) base pairs (C + G·C triplets). The sequence-specific recognition of double-helical DNA by a third strand to form a triple helix is limited to mostly purine tracts. Although G in the third strand has been found to specifically bind to T·A, the lower stability of the G·T·A triplet and its dependence on the sequence of the neigh boring triplets reveals that this will have limitations. In an attempt to extend the recognition code to all four Watson-Crick base pairs, the nonnatural deoxyribonucleoside 1-(2-deoxy/ β-D-ribofuranosyl)-4-(3-benzamido)phenylimidazole [D_3] was synthesized and incorporated into pyrimidine DNA oligonucleotides (Figure 1a). It was found that D_3 selectively recognizes both T·A and C·G Watson-Crick base pairs within the pyrimidine·purine·pyrimidine triple-helix motif. This was also found to have a nearest neighbor dependence.
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