Magnetic Microtweezers: A Tool for High-Throughput Bioseparation in Sub-Nanoliter Droplets

Abstract

Droplet microfluidics has revolutionized the field of single-cell analysis. Production of micro-droplets at high throughput allows for rapid isolation of single cells within micro-compartments, which are then subjected to different analytical processes. However, certain operations, such as physical separation from droplets, remain difficult to implement at high throughput and single-cell level but would be highly valuable to currently expanding multiomics techniques, where several biomolecular modalities are involved. This work presents a method based on microfabricated NiFe structures, the magnetic microtweezers, to trap and extract magnetic particles from a continuous stream of sub-nanoliter droplets, and enable physical separation from single cell-based droplets. Using a physical model, simulations, and experiments, a comprehensive description of the complex particle extraction process is provided. After optimization, the magnetic microtweezers provided unprecedented particle extraction performance, allowing extraction of high loads (10-20 ng) of magnetic particles from 500 pL droplets, with a capture rate close to 100% at 20 Hz. To evaluate the applicability to single-cell analysis, mRNA extraction is performed. It demonstrated around 72% specific recovery of mRNA from droplets containing purified nucleic acids, and 43% from single cells. Overall, this approach enables efficient physical separation that is compatible with existing high-throughput droplet-based single-cell workflows.