Capillary electrophoresis for studying drug-DNA interactions

The development of new drugs to treat disease by binding directly to DNA offers much promise but is reliant on methods to determine the relative affinity of the putative drug for different DNA sequences. Such methods should ideally be rapid and inexpensive as well as reliable. Use of capillary electrophoresis in simple silica columns offers such a method. The development of systems in which the solvent carries a soluble polymer allows the reliable separation of DNA oligomers, of 12-20 bp in length, which can then be titrated with the ligand in competition experiments. The results obtained are comparable with those obtained by footprinting and give direct graphical output, easily analysed for relative binding affinity.