COOPERATIVE OLIGONUCLEOTIDE-DIRECTED TRIPLE-HELIX FORMATION AT ADJACENT DNA SITES

The changes in binding free energies due to cooperativity for oligodeo xyribonucleotides bound to adjacent sites by triple helix formation ha ve been determined by quantitative affinity cleavage titrations. A 20- fold enhancement in equilibrium association constant is realized for a n 11 mer pyrimidine oligonucleotide binding in the presence of a neigh boring bound site at 24-degrees-C and pH 7.0 (25 mM Tris-OAc, 10 mM Na Cl, 1 mM spermine). This corresponds to an increase in binding free en ergy of 1.8 +/- 0.2 kcal mol-1. This cooperativity is not observed whe n the two binding sites are separated by one base pair.