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

Abstract

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