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The rapid advance of phosphorothioate oligonucleotides in clinical development has accelerated the need for accurate quantitation of these compounds for quality control and bioanalytical applications (
1
). Whereas slab-gel polyacrylamide gel electrophoresis has been in routine use for the analysis of oligonucleotides, it has been replaced by capillary gel electrophoresis (CGE) as the technique of choice for length-based separation of synthetic oligonucleotides (
2
–
10
). This can be attributed to many factors including, superior resolution as a result of 10–100-fold higher electric fields, on line detection, and automation.