Cleavage of oligonucleotides in continuous flow

Scientists at Novo Nordisk in Denmark have applied flow chemistry to enhance the cleavage of oligonucleotides.

Utilising Vapourtec’s R-Series flow chemistry system to undertake their research, the Novo Nordisk team have made the data available in an application note that will be of interest to all chemists exploring oligonucleotides.

The improvements reported include a reduction in the time for cleavage and complete deprotection to less than 3 minutes, the elimination of risks associated with batch reactors having pressurised headspace, the production of repeatable results and crude cleaved oligonucleotides at higher concentrations, improvements in safety and a simplification of the route to scale-up.

Cleavage of oligonucleotides is the process of removing the oligonucleotide from a solid support. The traditional batch method involves heating an aqueous solution of ammonia or methylamine, or a mixture of both with the oligonucleotide-resin for over 15 hours. The oligonucleotide is both cleaved from the resin and the protecting groups are removed.

Cleavage and deprotection is a critical step in solid-phase oligonucleotide synthesis as impurities can be introduced. Minimising these impurities requires fine control of temperature and reaction time.

This lengthy batch process is necessary to ensure complete cleavage and removal of protective groups but often results in scalability issues and potential safety risks due to the high pressures generated within the headspace of the reactor. The high pressures are generated when the volatile reagents (ammonia or methylamine) are heated, reducing its concentration in the solution phase

Flow chemistry addresses these challenges by pumping the cleavage solution through a heated reactor containing the oligonucleotide-resin. A second heated tubular reactor is connected in series for deprotecting the oligonucleotide before collection. Both reactors are maintained under sufficient pressure to prevent the vaporisation of the volatile reagents.  There is no head space, all the reagent remains in the liquid phase.

This approach drastically reduces reaction times to less than 3 minutes, regardless of scale. Safety is improved by eliminating the need to handle pressurised batch reactors. Additionally, the flow method yields concentrated crude oligonucleotide solutions, simplifying downstream processing.

Vapourtec founder and MD Duncan Guthrie commented: “This advancement represents a significant step forward in oligonucleotide synthesis, offering a safer, faster and more efficient method for cleavage and deprotection of oligonucleotides.

“We would like to thank the Novo Nordisk team in Copenhagen and especially Alexander Davies for the ideation, lab-work and analysis presented in this application note.”

About Vapourtec

Vapourtec is the world’s leading manufacturer of laboratory scale flow chemistry instruments. Founded in 2003, the company has been at the forefront of the flow chemistry industry ever since.

Headquartered near Cambridge, UK, Vapourtec design and manufacture the R-Series and E-Series flow chemistry systems together with an exciting range of innovative fast-flow peptide synthesisers. Vapourtec instruments have empowered chemists throughout the world to further scientific discovery.

Trusted by scientists, chemists and fine chemical manufacturers around the world, the modular R-Series system has revolutionized the way many deliver the research, chemicals and products we all rely on. With an installation base of more than 750 instruments, resulting in being cited in over 1000 peer reviewed scientific publications, Vapourtec continues to support customers across the globe with world-class products and services.

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