Kinetic studies on the formation of acridine-linked DNA triple helices.

We have used DNase I footprinting to measure the rate of intermolecular triple helix formation at the target sites A6G6.C6T6 and G6A6.T6C6 with the acridine-linked oligonucleotides Acr-T5C5 and Acr-C5T5, 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-T5C5 binding to A6G6.C6T6 and 2000 M-1.s-1 for the interaction of Acr-C5T5 with G6A6.T6C6.