Study of deoxyribonucleic acid-ligand interactions by partial filling affinity capillary electrophoresis

In this work, a new partial filling affinity capillary electrophoresis (PF-ACE) method has been developed and applied to investigation of non-covalent molecular interactions between double stranded DNA oligonucleotide (Dickerson dodecamer) and classical DNA intercalator ligand-ethidiumbromide (EtBr) or oligophenylene derivatives-based potential new type of DNA ligands. Binding constants of DNA-ligand 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 (0-75 mm with 12.5 mm step) in hydroxypropylcellulose coated fused silica capillary of 50/375 mu m I.D./O.D. and 400/300 mm total/effective length. PF-ACE experiments were performed in two background electrolytes, Tris-borate, pH 8.0, ionic strength 14.3 mM (BGE1), and sodium phosphate, pH 7.5, ionic strength 133 mM (BGE2). Binding constants of DNA-EtBr complex (ca 15300 L/mol in the BGE1 and 4200 L/mol in the BGE2) were found to be significantly higher than those of DNA complexes with oligophenylene derivatives (ca 2200-3600 L/mol in the BGE1 and 1600-2300 L/mol in the BGE2). (C) 2014 Elsevier B.V. All rights reserved.