Study of DNA oligonucleotides interactions with ethidium bromide by partial-filling affinity capillary electrophoresis

A partial filling affinity capillary electrophoresis was developed and applied to investigation of non-covalent molecular interactions between double stranded DNA oligonucleotide (Dickerson dodecamer) and classical DNA intercalator ligand –ethidium bromide (EtBr). Binding constants of DNA EtBr complexes were determined from the dependence of migration time changes of DNA oligomer (applied as analyte) on the length of ligand zones introduced beforehand as plugs of various lengths in hydroxypropylcellulose coated fused silica capillary. Binding constants of DNA-EtBr complex were found to be in the range 4.2 x 103 – 1.5 104 L/mol