STABLE TRIPLE-HELICAL DNA COMPLEXES FORMED BY BENZOPYRIDOINDOLE-OLIGONUCLEOTIDE AND BENZOPYRIDOQUINOXALINE-OLIGONUCLEOTIDE CONJUGATES

Benzopyridoindole and benzopyridoquinoxaline derivatives were conjugat ed to a 14-mer oligonucleotide at either of two different positions: t he 5' end or an internucleotide position in the center of the 14-mer. These oligonucleotide-intercalator conjugates were then tested for the ir ability to form stable DNA triple helices with a DNA target duplex under physiological conditions. All of the derivatives synthesized wer e found to do so. Two derivatives in particular, a benzo[h]pyridoquino xaline (B[h]PQ) attached to the 5' end and a benzo[e]pyridoindole (B[e ]PI) attached to the internal position on the phosphate diester backbo ne, dramatically stabilized the triple helix under physiological condi tions. In the absence of spermine, the melting temperature bf the trip ler-to-duplex transition increased from 11 degrees C for a non-modifie d tripler to 38 and 37 degrees C, respectively, for the B [h]PQ and B[ e]PI conjugates. Acridine-oligonucleolide conjugates were much less st able, melting at 25 degrees C (5' attachment) and at 23 degrees C (int ernucleotide linkage). In the presence of spermine, the melting temper ature increased from 28 degrees C for a nonmodified tripler to 51 and 54 degrees C for the B[h]PQ and B[e]PI conjugates, respectively, equiv alent to a stabilization of similar to 4 kcal mol(-1) at 37 degrees C. Furthermore, the conjugation of these intercalators to the third stra nd was not detrimental to the selectivity of recognition of the target duplex sequence. Molecular modeling reinforced and provided possible models for some of the intercalator-triple helix interactions investig ated. These results demonstrate the possibility for forming stable DNA triple helices at physiological pH and temperature.