Analysis of modified oligonucleotides by capillary electrophoresis in a polyvinylpyrrolidone matrix coupled with electrospray mass spectrometry

Abstract This paper describes the coupling of capillary electrophoresis (CE) with a olyvinylpyrrolidone (PVP) matrix and electrospray mass spectrometry for the analysis of a series of short modified oligonucleotides. The separation of modified oligonucleotides, four, five and six bases in length, was accomplished by CE in a coated fused-silica column filled with an aqueous solution of PVP. The resolved components were then identified by electrospray mass spectrometry with negative-ion detection. Importantly, oligonucleotides with the same length and sequence but differing only by the presence or absence of a small modification (such as a methyl group) on a single base were easily resolved by CE. This observation suggests that the matrix, PVP, is behaving as a pseudo-phase in which oligomers with hydrophobic modifications are retained longer than their normal unmodified analogs.