title: Study of deoxyribonucleic acid-ligand interactions by partial filling affinity capillary electrophoresis.
abstract: 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 (0-75mm with 12.5mm step) in hydroxypropylcellulose coated fused silica capillary of 50/375μm I.D./O.D. and 400/300mm total/effective length. PF-ACE experiments were performed in two background electrolytes, Tris-borate, pH 8.0, ionic strength 14.3mM (BGE1), and sodium phosphate, pH 7.5, ionic strength 133mM (BGE2). Binding constants of DNA-EtBr complex (ca 15300L/mol in the BGE1 and 4200L/mol in the BGE2) were found to be significantly higher than those of DNA complexes with oligophenylene derivatives (ca 2200-3600L/mol in the BGE1 and 1600-2300L/mol in the BGE2).
authors.affiliation: Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo 2, 166 10 Prague 6, Czech Republic; Faculty of Science, Charles University in Prague, Albertov 6, 128 43 Prague 2, Czech Republic.
authors.forename: Martin
authors.initials: M
authors.lastname: Růžička
authors.affiliation: Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo 2, 166 10 Prague 6, Czech Republic.
authors.forename: Martina
authors.initials: M
authors.lastname: Čížková
authors.affiliation: Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo 2, 166 10 Prague 6, Czech Republic.
authors.forename: Michael
authors.initials: M
authors.lastname: Jirásek
authors.affiliation: Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo 2, 166 10 Prague 6, Czech Republic.
authors.forename: Filip
authors.initials: F
authors.lastname: Teplý
authors.affiliation: Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo 2, 166 10 Prague 6, Czech Republic.
authors.forename: Dušan
authors.initials: D
authors.lastname: Koval
authors.affiliation: Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo 2, 166 10 Prague 6, Czech Republic. Electronic address: kasicka@uochb.cas.cz.
authors.forename: Václav
authors.initials: V
authors.lastname: Kašička
mesh_terms: D052157:Aptamers, Nucleotide; D002623:Chemistry Techniques, Analytical / Q000379:methods*; D004247:DNA / Q000378:metabolism*; D019075:Electrophoresis, Capillary; D004996:Ethidium / Q000737:chemistry; D008024:Ligands
chemical_list: D052157:Aptamers, Nucleotide; D008024:Ligands; D004247:DNA; D004996:Ethidium
keywords: Affinity capillary electrophoresis; DNA; Ethidium bromide; Oligophenylene derivatives; Partial filling; Stability constant