(244a) Entropic Trap-Based Tunable Short-Pass Filter to Recover Long DNA for Genomic Applications | AIChE

(244a) Entropic Trap-Based Tunable Short-Pass Filter to Recover Long DNA for Genomic Applications


Agrawal, P. - Presenter, University of Minnesota
Dorfman, K., University of Minnesota-Twin Cities
Bognár, Z., University of Minnesota
Long DNA molecules are of extreme importance for genome technologies such as long-read sequencing, whole-genome mapping and cell engineering. In many situations, the long DNA sample is contaminated by a significant amount of small DNA that results from random shearing or biochemical processing. These small DNA fragments contribute noise to the analysis; for example, genome mapping in nanochannels requires DNA greater than 150 kbp and small DNA can create spurious signals when they overlap with the larger molecules. Gel electrophoresis is the standard method to purify long DNA molecules, but the method is time consuming, due to the slow mobility of long DNA in a gel, and requires a high initial DNA concentration for purification. Here, we demonstrate that entropic trap-based filters, fabricated by reactive ion etching in a fused silica substrate, can selectively trap long DNA at a nanoslit-microchannel interface while passing the smaller DNA. The trapping ability of this short-pass filter can be tuned by optimizing the strength of the electric field at the interface and the relative height of nanoslit to the radius of gyration of the DNA. Our approach also involves designing an automated, continuous separation system that decouples the injection and filtration steps by using air pressure and electric potential, respectively. This tunable short-pass filter system provides an efficient alternative for gel electrophoresis for sample preparation of rare long DNA molecules, which can be integrated to lab-on-chip devices for next-generation genome technologies.