SELECTIVITY OF ANION-EXCHANGE CHROMATOGRAPHY AND CAPILLARY GEL-ELECTROPHORESIS FOR THE ANALYSIS OF PHOSPHOROTHIOATE OLIGONUCLEOTIDES

The complementary nature of anion exchange chromatography and capillar y gel electrophoresis for oligonucleotide analysis is demonstrated by evaluating a comprehensive series of authentic deletion sequences and partial phosphodiester analogs of five phosphorothioate oligonucleotid es of different base composition and sequence. While anion exchange HP LC is sensitive to differences in backbone length of phosphorothioate oligonucleotides, oligomers with length difference of one base unit ar e not resolved. Capillary gel electrophoresis, on the other hand, has excellent single-base resolution while being relatively insensitive to phosphate in the phosphorothioate backbone. The data definitively est ablish the necessity of employing both separation techniques for adequ ate characterization of lower order process-related impurities potenti ally found in synthetic phosphorothioate oligonucleotides. (C) 1997 El sevier Science B.V.