Optical mapping of single-molecule human DNA in disposable, mass-produced all-polymer devices

Abstract

We demonstrate all-polymer injection molded devices for optical mapping of denaturationrenaturation (DR) patterns on long, single DNA-molecules from the human genome. The devices have channels with ultra-low aspect ratio, only 110 nm deep while 20 μm wide, and are superior to the silica devices used previously in the field. With these polymer devices, we demonstrate on-chip recording of DR images of DNA-molecules stretched to more than 95% of their contour length. The stretching is done by opposing flows Marie et al (2013 Proc. Natl Acad. Sci. USA 110 4893-8). The performance is validated by mapping 20 out of 24 Mbp-long DNA fragments to the human reference genome. We optimized fabrication of the devices to a yield exceeding 95%. This permits a substantial economies-of-scale driven cost-reduction, leading to device costs as low as 3 USD per device, about a factor 70 lower than the cost of silica devices. This lowers the barrier to a wide use of DR mapping of native, megabase-size DNA molecules, which has a huge potential as a complementary method to next-generation sequencing.

Comparison of Ultrasonic Welding and Thermal Bonding for the Integration of Thin Film Metal Electrodes in Injection Molded Polymeric Lab-on-Chip Systems for Electrochemistry

“…This is particularly true when the bonding of thermoplastic devices is required on a large scale. Several bonding techniques have been proposed for thermoplastics, the most common being solvent bonding [2], laser welding [3], adhesive bonding [4], and thermal bonding (TB) [5,6]. The bonding step is particularly critical in Lab-on-Chip (LoC) systems with integrated electrodes, the performance of which needs to be maintained while achieving a completely leakage-free system.…”

Applications of Optical DNA Mapping in Microbiology

“…Novel OM techniques use commercially available reagents in combination with epifluorescence microscopy, standard equipment, and reagents found in many microbiology laboratories. Furthermore, with emerging developments in plastic nanofluidic devices, it has been suggested that the cost per device could be kept as low as $3 (69). The small amount of sample needed for OM is another factor contributing to work-time reduction, as bacterial cultivation steps can potentially be shortened or even omitted.…”

Sequencing of human genomes extracted from single cancer cells isolated in a valveless microfluidic device

“…We introduce a novel valve-less microfluidic device for single cell genomics that is manufactured in a thermoplastic material by injection moulding, a process that is scalable at low cost. 23 Our chip design is based on a hydrodynamic cell trap 24 derived from a previously described device for cell culture. 25 Our device design enables the process to be carried out on an optical microscope or in "Cell-O-Matic" a specially built single cell processing instrument (Philips BioCell), in either case allowing us to monitor both cell trapping and genome extraction.…”