Long-read genomic applications, such as genome mapping in nanochannels, require long DNA that is free of small-DNA impurities. We have developed a chip-based system based on entropic trapping that can simultaneously concentrate and purify a long DNA sample under the alternating application of an applied pressure (for sample injection) and an electric field (for filtration and concentration). In contrast, short DNA tends to pass through the filter owing to its comparatively weak entropic penalty for entering the nanoslit. The single-stage prototype developed here, which operates in a continuous pulsatile manner, achieves selectivities of up to 3.5 for λ-phage DNA (48.5 kilobase pairs) compared to a 2 kilobase pair standard based on experimental data for the fraction filtered using pure samples of each species. The device is fabricated in fused silica using standard clean-room methods, making it compatible for integration with long-read genomics technologies.
Bibliographical noteFunding Information:
This work was supported by NIH (R01-HG006851). Funding for ZsB was provided from the University of Minnesota, made possible by a gift from Zsolt Rumy. Fabrication was performed in the Minnesota NanoCenter, which receives partial support from the NSF through the NNIN. We thank Yuval Ebenstein (Tel Aviv University) for useful discussions about DNA purification. COMSOL modeling was performed using the resources at Minnesota Supercomputing Institute. We also acknowledge COMSOL Inc. for their technical support.