Abstract
We have used DNase I footprinting to measure the rate of intermolecular triple helix formation at the target sites A 6G 6 · C 6T 6 and G 6A 6 · T 6C 6 with the acridine-linked oligonucleotides Acr-T 5C 5, and Acr-C 5T 5 respectively. Under pseudo first-order reaction conditions we find that the reactions are slow, with half-lives of several minutes. The rates are dependent on the concentration of the third strand oligonucleotide and yield bimolecular association rate constants of 300 M −1 · s −1 for Acr-T 5C 5 binding to A 6G 6 · C 6T 6 and 2000 M −1 · s −1 for the interaction of Acr-C 5T 5 with G 6A 6 · T 6C 6.
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