| Abstract
| - The four Watson−Crick base pairs of DNA can be distinguished in the minor groove by pairingside-by-side three five-membered aromatic carboxamides, imidazole (Im), pyrrole (Py), and hydroxypyrrole(Hp), four different ways. On the basis of the paradigm of unsymmetrical paired edges of aromatic ringsfor minor groove recognition, a second generation set of heterocycle pairs, imidazopyridine/pyrrole (Ip/Py)and hydroxybenzimidazole/pyrrole (Hz/Py), revealed that recognition elements not based on analogues ofdistamycin could be realized. A new set of end-cap heterocycle dimers, oxazole-hydroxybenzimidazole(No−Hz) and chlorothiophene-hydroxybenzimidazole (Ct−Hz), paired with Py−Py are shown to bindcontiguous base pairs of DNA in the minor groove, specifically 5‘-GT-3‘ and 5‘-TT-3‘, with high affinity andselectivity. Utilizing this technology, we have developed a new class of oligomers for sequence-specificDNA minor groove recognition no longer based on the N-methyl pyrrole carboxamides of distamycin.
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