Abstract. Phosporothioate oligonucleotides represent an important class of therapeutic oligonucleotides,
in which none-bridging oxygen atoms of the phosphate groups are replaced by sulfur. These
oligonucleotides are designed to treat disease by modulating gene expression of an affected individual.
As the development and application of these therapeutical oligonucleotides require analytical support,
the development, validation, and application of an assay for the quantitative analysis of a
phosporothioate oligonucleotide in rat plasma is described. The method employs ion-pair reversedphase
chromatography on a monolithic capillary column with acetonitrile gradients in cyclohexyldimethylammonium
acetate for separation and high-resolution tandem mass spectrometry for detection of
nucleic acids. Chromatographic parameters (i.e. column temperature, mobile phase composition) as well
as mass spectrometric parameters (i.e. spray voltage, gas flow, and capillary position, scan mode) have
been optimized for sensitive oligonucleotide quantification. Furthermore, a solid-phase extraction
method was developed which enabled processing of 10 μl of plasma. The five-point calibration curve
showed linearity over the range of concentrations from 100 to 1,000 nM of the oligonucleotide. The limit
of detection was 50 nM. The intra- and inter-day precision and accuracies were always better than
10.2 %. Using this assay, we performed a pharmacokinetic study of the phosporothioate oligonucleotide
in rat treated with a single intravenous dose of 0.39 μmol/kg. The assay sensitivity was sufficient to study
the early phase elimination of the oligonucleotide. Small amounts of the oligonucleotide were detectable