Long-read genomics technologies such as nanopore sequencing and genome mapping in nanochannels extract genomic information in the kilobase to megabase pair range from single DNA molecules, thereby overcoming read-length limitations in next-generation DNA sequencing. Long-read technologies start with long DNA molecules as the input and thus benefit from universal sample preparation methods that are fast and shear-free and present a scope of automation and direct upstream integration. We describe a 3D printing-assisted poly(dimethylysiloxane)-based DNA sample preparation device, where diffusive chemical lysis followed by electrophoresis produces circa 100 ng of long DNA directly from cells with less than 5 min of labor. Assessment of the product DNA by confinement in nanochannels reveals that the DNA sizes are commensurate with the requirements for long-read single-molecule technologies. Microfluidics not only expedites sample preparation, but also offers the opportunity for integration with genomics technologies to eliminate DNA fragmentation and loss during transfer to the genomic device.
Bibliographical noteFunding Information:
We thank Michael Manno for help with FDM 3D printing. We also thank Samira Azarin for providing the MCF7 cell line and cell culture facilities. This work was supported by NIH (R21-HG009208).
Copyright © 2020 American Chemical Society.
Data for "3D Printing-Enabled DNA Extraction for Long-Read Genomics" published as ACS Omega 2020, 5, 20817-20824
Agrawal, P., Reifenberger, J. G. & Dorfman, K., Data Repository for the University of Minnesota, 2020