Base composition analysis of phosphorothioate oligomers by capillary gel electrophoresis

Abstract The base composition analysis of synthetic oligodeoxyribonucleotides (ODN) by high-performance capillary gel electrophoresis (HPCGE) is reported here. This newly developed method is fats, sensitive and highly reproducible. It involves the separation of deoxyribonucleotides monophosphate (dNMPs) by capillary gel electrophoresis using a 47 cm × 100 μ m I.D. capillary and the samples were run at constant voltage (isoelectrostatic) and constant temperature (isothermal). We evaluated this technique by using commercially available dNMPs as well as dNMPs generated from enzymatic digestion of phosphorothioate ODNs. Our results indicated (a) picomoles of sample are sufficient, (b) the migration times of each of the four bases is less than 25 min, (c) the calculated empirical formila values of parent compound are matched up with the expected values, and (d) ther esults are highly reproducible. Thus we have developed an alternative method for the base composition analysis of synthetic ODN which we believe has the potential to become the method of choice in the future.