Effect of urea concentration on the base-specific separation of oligodeoxynucleotides in capillary affinity gel...

Base-specific separations of oligodeoxynucleotides were achieved with high resolution by electrophoresis, using a urea-gel capillary, in which poly(9-vinyladenine) (PVAd) was utilized as an affinity ligand. The migration behaviour and the plate number of oligodeoxynucleotides were investigated as a function of urea concentration between 2 and 10 M in capillary gel electrophoresis (CGE) as well as capillary affinity gel electrophoresis (CAGE). The migration time in CGE separation increases as urea concentration increases. An increase in the viscosity of the gel buffer medium as well as a change in the conformation of oligodeoxynucleotides is found to be a predominant factor for an increase in the migration time. The migration time and the plate number of oligothymidylic acids, which interact with PVAd in CAGE, is manipulated by differing urea concentration, which leads to the change in the dissociation process of a specific hydrogen bonding between oligothymidylic acids and PVAd. The migration time of oligodeoxyadenylic acids, which do not interact with PVAd in CAGE, increases with an increase in urea concentration as in CGE separation. The plate number of oligodeoxyadenylic acid was not affected by the urea concentration.