USE OF CAPILLARY ELECTROPHORESIS IN THE STUDY OF LIGAND-DNA INTERACTIONS

Free solution capillary electrophoresis (FSCE) has been used to separa te two non-self-complementary 12mer oligonucleotide duplexes: d(AAATTA TATTA).d(ATAATATAATTT) and d(GGGCCGCGCCGC).d(GCGGCGCGGCCC). Titration of mixtures of the two oligonucleotides with model intercalators (ethi dium bromide and actinomycin D) and minor groove binders (netropsin, H oechst 33258 and distamycin) has shown the suitability of FSCE as a me thod to study the sequence selectivity of DNA binding agents. Binding data have shown cooperativity of binding for netropsin and Hoechst 332 58 and have provided ligand:DNA binding ratios for all five compounds. Cooperativity of netropsin binding to a 12mer with two potential site s has been demonstrated for the first time. Ligands binding in the min or groove caused changes in migration time and peak shape which were s ignificantly different from those caused by intercalators.