Co-op, Antisense Oligonucleotide Process Chemistry

This application is for a 6-month student role from January - June 2025. Resume review begins in October 2024. The co-op position provides an exciting opportunity to gain hands-on experience and exposure to the manufacturing process R&D activities. Working closely with the Antisense Oligonucleotide (ASO) chemistry and analytical development teams, the co-op will conduct the independent research project described below:  Phenylacetyl disulfide (PADS) is a highly effective sulfurization reagent for the synthesis of antisense oligonucleotides when aged with a base for a minimum of 12 hours. However, its utility is limited by a short shelf life of just 5 days, which presents challenges for large-scale manufacturing. Additionally, aged PADS is ineffective for 5’OH capping reactions. Conversely, PADS solutions stored in an inert solvent, designated as “Fresh PADS,” demonstrate prolonged stability and are effective for 5’OH capping. Nonetheless, the use of “Fresh PADS” introduces a significant limitation: the sulfurization reactions proceed at a slow rate and require the addition of a strong base to accelerate the reaction and reduce side reactions. The employment of a strong base also risks the loss of cyanoethyl groups, potentially compromising the stereoselectivity of subsequent coupling steps. The application of “Fresh PADS” in solid-phase synthesis remains underexplored, and its reaction conditions are not yet fully optimized. To address this, it is essential to determine the optimal reaction parameters and evaluate their effects on the stereochemistry of the phosphate backbone and the impurity profile of the crude product. The proposed study involves solid-phase synthesis experiments on a model antisense oligonucleotide, aiming to identify the ideal concentration of PADS and activating base, the appropriate solvent for the base, the stoichiometry of PADS and base, and the optimal reaction time. Each parameter will be optimized to achieve the best balance of sulfurization efficiency and impurity control. The optimized condition will be rigorously characterized and its impact on the stereochemistry of phosphorothioate centers relative to established processes will be assessed.  Position DescriptionConduct experiments designed to gain insight into oligonucleotide synthesis processes.  Learn to program, prepare, and operate oligonucleotide synthesis equipment.  Prepare full length ASOs using solid phase synthesis techniques. Fully characterize and evaluate product purity by HPLC-MS. Document all experiments performed, including analytical data collected and observations made. Provide regular progress updates to supervisor on a daily or weekly basis. Engage actively with supervisor to deepen understanding of principles, experimental design, and data interpretation. Complete research report prior to the conclusion of the co-op term.