Development of an automated flow chemistry affinity-based purification process for DNA-encoded chemistry

An automated flow chemistry platform for DNA-encoded library (DEL) technologies requires the integration of a purification process for DNA-tagged substrates. It facilitates the development of further DEL reactions, building block rehearsal, and library synthesis. Therefore, a recently developed, manual affinity-based batch purification process for DNA-tagged substrates based on dispersive solid-phase extraction (DSPE) was transferred to automated flow chemistry using tailored 3D-printed microfluidic devices and open-source lab automation equipment. The immobilization and purification steps use Watson-Crick base pairing for a compound-encoding single-stranded DNA, which allows for the thorough removal of impurities and contaminations by washing steps and operationally simple recovery of the purified DNA-encoded compounds. This work optimized the annealing step for flow incubation and DNA purification was accomplished by flow DSPE washing/elution steps. The manually performed batch affinity-based purification process was compared with the microfluidic process by determining qualitative and quantitative DNA recovery parameters. It aimed at comparing batch and flow purification processes with regard to DNA recovery and purity to benefit from the high potential for automation, precise process control, and higher information density of the microfluidic purification process for DNA-tagged substrates. Manual operations were minimized by applying an automation strategy to demonstrate the potential for integrating the microfluidic affinity-based purification process for DNA-tagged substrates into an automated DNA-encoded flow chemistry platform.

Automated summary

An automated flow chemistry platform for DNA-encoded library (DEL) technologies was developed by transferring a recently developed manual purification process to automated flow chemistry using microfluidic devices and lab automation equipment. The immobilization and purification steps in the process utilize Watson-Crick base pairing for compound-encoding single-stranded DNA, enabling thorough removal of impurities and simple recovery of purified DNA-encoded compounds. The microfluidic process was compared to the manual process in terms of DNA recovery and purity, showing the potential for automation and precise process control of the microfluidic purification process.