Polymer systems designed specifically for DNA sequencing by microchip electrophoresis: A comparison with commercially available materials

TLDR

Electrophoresis-based DNA sequencing remains the sole proven method for de novo genome sequencing, but the scarcity of polymer matrices and wall coatings tailored for microchip platforms hampers the development of high‑performance, cost‑effective microchip sequencers. Microchip‑specific sequencing matrices produced read lengths 150–300 bases longer than commercial CAE matrices and revealed poor coating performance of commercial matrices on borosilicate chips, underscoring the need for new materials to enable high‑performance microfabricated DNA sequencers.

Abstract

Electrophoresis-based DNA sequencing is the only proven technology for the de novo sequencing of large and complex genomes. Miniaturization of capillary array electrophoresis (CAE) instruments can increase sequencing throughput and decrease cost while maintaining the high quality and long read lengths that has made CAE so successful for de novo sequencing. The limited availability of high-performance polymer matrices and wall coatings designed specifically for microchip-sequencing platforms continues to be a major barrier to the successful development of a commercial microchip-sequencing instrument. It has been generally assumed that the matrices and wall coatings that have been developed for use in commercial CAE instruments will be able to be implemented directly into microchip devices with little to no change in sequencing performance. Here, we show that sequencing matrices developed specifically for microchip electrophoresis systems can deliver read lengths that are 150-300 bases longer on chip than some of the most widely used polymer-sequencing matrices available commercially. Additionally, we show that the coating ability of commercial matrices is much less effective in the borosilicate chips used in this study. These results lead to the conclusion that new materials must be developed to make high-performance microfabricated DNA-sequencing instruments a reality.