New Bioanalysis Methods for Enhanced Recovery and Quantification

2nd Annual Oligos, Oligos, Oligos!

A special 3-part Live Webinar series focused on Oligonucleotide Analysis from Waters Corporation and Collaborators.

Seminar Series Summary

Oligonucleotide therapeutics are helping the world address previously untreatable diseases, and their clinical pipeline continues to see strong growth. In various forms, including small interfering RNA (siRNA), Antisense Oligonucleotides (ASOs), CRISPR single guide RNA (sgRNA), and others, these nucleic acid modalities often incorporate a range of modified nucleotides for enhanced stability, and are increasingly conjugated to tissue-specific ligands (GalNAc, lipids, peptides, mAb’s, etc.) to effect targeted cell delivery. To advance their development, these molecules and their impurities must be fully characterized, and their stability and pharmacokinetic properties must be accurately assessed.

In this webinar series, Waters’ scientists and collaborators from Novo Nordisk, Eli Lilly, and Synthon will provide state-of-the-art updates on the tools and techniques used to both confirm their identity and purity, and to quantify their pharmacokinetic properties in biological systems.  Join us as we delve into the science of oligos and explore the power of LC and LC-MS based approaches to analyze them.

EPISODE 1

On the Use of Stable Isotope Labeled Internal Standards (SILISs) in Oligonucleotide Bioanalysis

• Speaker: Ethan Sanford / Novo Nordisk

This talk highlights the development of a deuterated SILIS for lipid-conjugated siRNA and its application in LC-MS/MS bioanalysis. Key topics include MS and chromatographic characterization, SPE method optimization, and the use of plasma as a surrogate matrix for tissue quantitation. The presentation concludes with in vivo data demonstrating SILIS-enabled robust quantitation in plasma and tissues.

This talk provides practical guidance for scientists developing high-throughput, reproducible bioanalytical methods for oligonucleotide drug development.

Optimizing the Extraction of Lipid-Conjugated Oligonucleotides from Biomatrices, and using Ion-Pairing-Free (HILIC) Separations for Quantitative LC-MS Analyses

• Speaker: Joe Fredette / Waters Corporation

As the oligotherapeutic pipeline continues to expand, so does the need for robust, accurate LC-MS-based oligonucleotide bioanalysis.  Waters' OligoWorks SPE extraction method, combined with RapiZyme Proteinase K, provides a streamlined, LC-MS-compatible approach that enhances oligonucleotide recovery and repeatability.  However, given the diversity of oligonucleotide modifications and conjugation, small adjustments to the starting protocol are sometimes needed to maximize recovery.  In this presentation, we will highlight recent work from our applications science team that demonstrates how targeted adjustments to our starting protocol can significantly improve recovery of lipid-conjugated oligonucleotides.  We'll also highlight recent work that shows how the OligoWorks SPE protocol can be paired with HILIC-based separations for quantitative LC-MS analysis, providing end users with an ion-pairing-free alternative.      

Presenter: Ethan Sanford (Scientist II, Novo Nordisk)

Ethan Sanford is a bioanalytical scientist at Novo Nordisk whose primary focus area is innovating new methods for oligonucleotide and peptide LC-MS/MS quantitation. Prior to joining Novo Nordisk in August 2024, Ethan worked for 2 years at IQVIA, where he developed small molecule LC-MS methods for use in regulated bioanalysis, with a focus on chiral separations and laboratory automation. Ethan received his Ph.D. in biochemistry from Cornell University’s Weill Institute for Cell and Molecular Biology, where he used phosphoproteomics to uncover novel protein-protein interactions that safeguard genome stability.

Presenter: Joe Fredette (Principal Product Marketing Manager, Genetic Medicine Portfolio, Waters Corporation)

Joe Fredette is Principal Product Marketing Manager at Waters Corporation, where he leads the strategic direction and development of solutions for oligonucleotide bioanalysis. With a strong background in analytical sciences, Joe focuses on advancing LC-MS workflows that support the characterization and quantification of synthetic oligonucleotides in complex biological matrices. His work bridges the gap between cutting-edge instrumentation and the evolving needs of scientists working in the rapidly growing field of nucleic acid therapeutics. Joe is passionate about enabling robust, high-throughput bioanalytical methods that drive innovation in oligonucleotide drug development.