Oligonucleotide manufacturing has evolved from early solid-phase synthesis to large-scale production of chemically modified and conjugated therapeutics. As molecular complexity increases, so do CMC challenges in process development, analytical characterization, impurity control, and scale-up. An effective CMC strategy must satisfy development timelines and clinical supply needs while considering commercial scale, quality and regulatory expectations, and cost of goods. Optimizing CMC requires a phase-appropriate approach—building the right process and analytical understanding at the right stage, while anticipating commercial requirements and identifying critical scale-up, quality, and supply risks early.

At Wave Life Sciences, stereopure oligonucleotides are designed to enhance pharmacology and efficacy across various modalities. Because chirality is controlled at each phosphorothioate (PS) and phosphoryl guanidine (PN) linkage, analytical method development has the unique challenge of confirming the stereochemistry at each of these linkages. Here we show how enzymatic digestion and dimer modeling/trityl-on shortmer modeling can confirm oligonucleotide identity and study the stereochemical selectivity of each linkage, respectively.

Analytical methods often support GLP and GMP activities while the product, process, and methods are still evolving, raising the question: how much analytical evidence is enough, and when? This presentation will explore practical considerations for phase-appropriate method qualification and validation, from demonstrating fitness for purpose in early development through GMP validation and late-stage readiness. A case study will illustrate how analytical evidence and validation expectations may evolve as a program matures.

Lipid nanoparticles (LNPs) were formulated with RNA cargos spanning a broad size range, using varying N:P ratios and lipid compositions. We demonstrate the effect of RNA size and formulation parameters on encapsulation efficiency, particle size distribution, RNA payload heterogeneity and lipid nanoparticle structure. Advanced analytics provide new insights into the relationship between cargo properties, LNP loading, full versus empty particle populations, and internal lipid organization.

Process development, optimization, and characterization are critical experiments during oligonucleotide development. Accurate and precise analytical methods are required to evaluate these experiments. The methods require a high level of fidelity, particularly in terms of measuring small changes in impurity levels for process optimisation and to establish proven acceptable ranges for key process parameters. The talk will cover the requirements for these methods to support effective manufacturing development.

Solid‑phase oligonucleotide synthesis (SPOS) remains central to commercial production, yet its environmental burden demands process improvements. This talk outlines practical sustainability solutions, from optimizing the current SPOS process to the application of new technologies such as enzymatic synthesis. Together, these approaches define a realistic path toward greener, more efficient oligo manufacturing.

The stereocontrolled synthesis of oligonucleotides remains a major challenge in nucleic acid chemistry and therapeutics. This presentation will highlight our recent advances in developing catalytic asymmetric strategies for the stereoselective synthesis of phosphorus-stereogenic oligonucleotides. Particular emphasis will be placed on catalytic control of phosphorus stereochemistry, the efficient synthesis of stereodefined phosphorothioate (PS) and phosphorodiamidate morpholino (PMO) oligonucleotides, and innovative methods for sugar and nucleobase modifications. These advances offer new opportunities for the precise construction of chemically modified oligonucleotides and the development of next-generation nucleic acid therapeutics.

QurAlis recently completed a Phase I/II clinical trial of its lead splice modulating ASO and is now preparing for late-phase clinical development. The talk will focus on strategies for successfully scaling up the manufacturing process while maintaining drug substance quality and impurity profile. Particular emphasis will be placed on effective collaboration with the CMO from early clinical stages through NDA submission with a focus on stage appropriate regulatory expectations.

Purification is a major driver of cost and timelines in oligonucleotide manufacturing. This talk presents a framework for selecting appropriate purification methods based on oligonucleotide structure and program needs. It also highlights statistical process control (SPC) as a tool for achieving reproducible purification performance in clinical manufacturing, where batch history is limited.