Multiscale microfluidic platform with vacuum-driven chambers for automated high-volume ssDNA generation

We present a multiscale microfluidic platform for automated high-volume single-stranded DNA (ssDNA) generation through plasmonic bead-based PCR. Central to the system are vacuum-driven chambers capable of handling fluid volumes in the tens of microliters-at least an order of magnitude larger than conventional microfluidic chambers. These chambers are seamlessly integrated with microfluidic components such as micromixers and pneumatically actuated microvalves, enabling precise fluidic transport in processing high volumes. This architecture overcomes limitations of pressure-driven flow in exchanging fluids in deep geometries. Direct vacuum access to these chambers improves fluid handling efficiency while reducing hardware complexity. We demonstrate the platform's capabilities through automated ssDNA preparation where plasmonic thermocycling is achieved via volumetric heating using gold nanorods dispersed in the reaction mixture. Magnetic beads functionalized with reverse primers facilitate selective amplification and effective strand separation. Despite the large reaction volume (20 μL), 20 PCR cycles are completed within 12 minutes. Fluorescence-based assays confirm 66% recovery of ssDNA from the beads, with 92% retention of complementary strands, indicating minimal contamination by double-stranded DNA (dsDNA). This multiscale integration of vacuum-driven chambers with microfluidic control offers a scalable and automated platform for preparative applications where high-volume processing is essential.