Nonnatural deoxyribonucleoside D3 incorporated in an intramolecular DNA triplex binds sequence-specifically by intercalation

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