Use of capillary electrophoresis in the study of ligand-DNA interactions

Abstract

Free solution capillary electrophoresis (FSCE) has been used to separate two non-self-complementary 12mer oligonucleotide duplexes: d(AAATTATATTAT).d(ATAA-TATAATTT) and d(GGGCCGCGCCGC).d(GCGGCGCGGCCC). Titration of mixtures of the two oligonucleotides with model intercalators (ethidium bromide andactinomycin D) and minor groove binders (netropsin, Hoechst 33258 and distamycin) has shown the suitability of FSCE as a method to study the sequence selectivity of DNA binding agents. Binding data have shown cooperativity of binding for netropsin and Hoechst 33258 and have provided ligand:DNA binding ratios for all five compounds. Cooperativity of netropsin binding to a 12mer with two potential sites has been demonstrated for the first time. Ligands binding in the minor groove caused changes in migration time and peak shape which were significantly different from those caused by intercalators.

Interaction between netropsin and double-stranded DNA in capillary zone electrophoresis and affinity capillary electrophoresis

“…They observed a remarkable signal of the complex, which was separated from free DNA [18]. Our results differed from theirs, probably because we used a different sequence and length of DNA.…”

“…concerning the research of DNA-drug interactions Capillary electrophoresis (CE) has become a and even quantitative determination of the binding robust separation technique in the past few years constants using CE [17][18][19][20]. Small duplex oligoowing to its several advantages such as short analysis nucleotides can be used as appropriate molecules for time, low sample size requirement, high efficiency the investigation of binding properties.…”

Ranking Ligand Affinity for the DNA Minor Groove by Experiment and Simulation

“…24 In line with our previous study, we have therefore used the thermodynamic cycle represented in Figure 3 and expressed the parameters that can be calculated using the MM-PBSA methodology to obtain binding free energies of ligands with various ODNs by solving eqs 1-3.…”

Recent advances in the study of biomolecular interactions by capillary electrophoresis

“…However, the mismatched oligomer d(CGXCGXCG) [X = A or T] showed a mobility retardation on Act D binding [114]. Hamdan et al [115] studied the interactions of two 12-mer oligonucleotide duplexes d(AAATTATATTAT) 2 and d(GGGCCGCGCCGC) 2 with some intercalators (EB, Act D) and minor groove binders (netropsin, Hoechst33258, and distamycin). In studies on the sequence selectivity of drug binding to DNA, it was observed that the minor groove binders prefer AT over GC sequences.…”