3D Printing-Enabled DNA Extraction for Long-Read Genomics

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.