Automated Data Processing For Mass Confirmation And Impurities Analysis Of Oligonucleotides

By Catalin E. Doneanu, Patrick Boyce, Henry Shion, Joseph Fredette, Scott J. Berger, Heidi Gastall, Ying Qing Yu

During the past decade there has been increased interest in oligonucleotide therapeutics as an alternative to small molecule and protein therapeutics. Manufacturing and quality control of oligonucleotide therapeutics requires highly selective and sensitive LC-MS methods. Despite significant progress in solid phase oligomerization chemistry, synthetic oligonucleotides still contain multiple classes of low-level (0.1–2%) impurities. IP-RP is one of the traditional LC-MS methods used for characterizing oligonucleotide products.

This application note demonstrates an automated, compliance-ready liquid chromatography-mass spectrometry (LC-MS) worflow for intact mass confirmation and purity analysis of synthetic oligonucleotides including small interfering RNA (siRNA) and large single guide (sg) RNA oligonucleotides and their impurities. The data presented here shows the challenging aspects of analyzing very long oligonucleotides, from the chromatographic separation to purity assessment. The new INTACT Mass Application, within the compliance-ready waters_connect™ informatics platform, allows scientists to analyze both short and long oligonucleotides with automated data processing features that streamline nucleic acid analysis.