Capillary gel electrophoresis (CGE) is recognized as an effective meth
od for the analysis of normal phosphodiester deoxyoligonucleotides (DN
A). However, it was found that when the same electrophoretic principle
s were applied to the analysis of phosphorothioate DNA, peak broadenin
g due to the phosphorothioate moiety made CGE's utility questionable.
Therefore, optimization of several parameters is necessary for CGE to
be effective in leading to the precise and accurate analysis of phosph
orothioate DNA. Phosphorothioates are oligonucleotide analogs acknowle
dged as potential antisense therapeutics in the treatment of viral dis
eases and certain cancers. In order to improve a CGE approach to the a
nalysis of this class of therapeutics, several parameters were investi
gated and improved upon. Three factors which proved critical in provid
ing high resolution and good gel to gel reproducibility were: gel conc
entration, buffer additives, and pH.