ANALYSIS OF MODIFIED OLIGONUCLEOTIDES BY CAPILLARY ELECTROPHORESIS INA POLYVINYLPYRROLIDONE MATRIX COUPLED WITH ELECTROSPRAY MASS-SPECTROMETRY

This paper describes the coupling of capillary electrophoresis (CE) wi th a polyvinylpyrrolidone (PVP) matrix and electrospray mass spectrome try for the analysis of a series of short modified oligonucleotides. T he separation of modified oligonucleotides, four, five and six bases i n length, was accomplished by CE in a coated fused-silica column fille d with an aqueous solution of PVP. The resolved components were then i dentified by electrospray mass spectrometry with negative-ion detectio n. Importantly, oligonucleotides with the same length and sequence but differing only by the presence or absence of a small modification (su ch as a methyl group) on a single base were easily resolved by CE. Thi s observation suggests that the matrix, PVP, is behaving as a pseudo-p hase in which oligomers with hydrophobic modifications are retained lo nger than their normal unmodified analogs.