Recently, while developing an assay for a siRNA complex using the LNA approach, we observed interferences from the probe to the antisense strand when it was analyzed by mass spectrometry. We modified the melting temperature to release the streptavidin/biotinylated hybridized to avoid releasing most of the biotinylated probe/antisense complex, but the limited release still had enough of the probe in the final extracts to cause interferences in the LLOQ samples. Modifying LC conditions helped to resolve the interference, but those changes were not entirely successful due to peak shape issues with the internal standard. After reviewing the probe design, we implemented an alternate PNA probe with the intention that any residual PNA probe would be easier to resolve chromatographically.
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