Evaluation of the Selective Binding Ability of Oligodeoxynucleotides to Poly(9-vinyladenine) Using Capillary Affinity Gel Electrophoresis

Abstract

During the past decade, technical advances in the synthesis of nucleic acid analogues have stimulated further research in the development of gene-targeted drugs.l Nucleic acid analogues, in which the entire phosphate-sugar backbone of DNA has been replaced with a polyvinyl or a polyamide chain2-4, have recently been synthesized as potential therapeutic agents and found to form extremely stable heteroduplexes with complementary singleand double-stranded DNA. Although the evaluation of the binding ability of nucleic acid analogue to DNA is helpful for designing sequenceselective gene-targeted drugs using nucleic acid analogues, very little is known about it, because of a lack of research tools for evaluating the selective binding ability, except for melting-temperature (Tm) measurements. We recently developed capillary affinity gel electrophoresis (CAGE)S_8 by combining the high resolving power of capillary gel electrophoresis and the high specificity of a bioaffinity ligand. CAGE is a powerful new tool for the specific-recognition of DNA through selective binding of DNA to the bioaffinity ligand and the characterization of DNA-drug binding properties. In this study, the CAGE technique was examined and found to be applicable to evaluating the selective binding ability of oligodeoxynucleotides to a nucleic acid analogue. In the CAGE system, one of the nucleic acid analogues, poly(9-vinyladenine) [PVAd], is used as an affinity ligand, which interacts with the target oligodeoxynucleotide, which is injected into capillary as a sample to form a heteroduplex via a complementary hydrogen bonding. The migration times for some oligodeoxynucleotides were measured by changing the total concentration of PVAd. For a reliable measurement of the binding ability we used cytidine 5'-monophosphate (CMP) as an internal standard, and calculated the relative migration