Self-Assembled Nanoscale Matrices for DNA Electrophoresis

PIs: Kevin Dorfman, Eray Aydil

DNA electrophoresis is one of the most important techniques in molecular biology and genetics. Separating long DNA (greater than 10 kilobase pairs) is important for genome mapping and DNA fingerprinting, as well as for screening long segments prior to sequencing. The standard method for separating long DNA is pulsed field gel electrophoresis (PFGE). In this method, the DNA are separated by the time required to reorient when the direction of the field switches. However, reorientation is a slow process, and PFGE requires several days to achieve an acceptable separation resolution.

Nanofabricated artificial gels can separate long DNA in minutes, with better reproducibility and lower reagent consumption when compared to PFGE. Although prototype artificial gel systems present numerous advantages relative to PFGE, they remain the province of dedicated micro- and nanofluidic laboratories. The main hindrance to adopting these systems for day-to-day research tasks is fabrication, in particular at the nanoscale. Nanopillar arrays are either produced one-by-one in a multi-step nanofabrication process through e-beam lithography or through dry reactive ion etching, difficult and time-consuming methods.

In this project, we propose to use self-assembled, nanoscale artificial gels in a microfluidic channel to separate long DNA. Fabricating this system will be commensurate with the difficulty in preparing a polyacrylamide gel, a standard method in molecular biology. However, due to the ability to control the order and density of the self-assembled system through kinetic and thermodynamic factors, we will be able to tune the device for separating a particular size range of DNA, reduce dispersion during the separation, and increase the reproducibility. The availability of such a system will greatly accelerate biological research. Based on a nominal separation time of 1 min, the throughput of our device is over 1000 times higher than PFGE, while concomitantly greatly reducing the amount of DNA required per analysis. The devices will be disposable, a major advance over existing nanolithographic devices.