May 30, 2006
Microfluidics Device Integrates Sanger DNA Sequencing Process
While researchers have developed several powerful methods for sequencing DNA, only the Sanger method can accurately sequence long stretches of DNA. And while the Sanger method is the sole technology that has been used successfully to sequence entire plant and animal genomes, including the human genome, the method's intensive use of expensive reagents and equipment, and its time demand on laboratory personnel, limit its usefulness as a tool for routine sequencing of human clinical samples, such as those from malignant tissue.
Those limitations could become moot, however, as a result of a new microfluidics device developed by Richard Mathies, Ph.D., and colleagues at the University of California, Berkeley. This new device incorporates all of the steps in the Sanger process onto a single lab-on-a-chip capable of sequencing over 500 continuous bases with 99 percent accuracy.
Writing in the Proceedings of the National Academy of Science, Mathies and his collaborators describe how they constructed their bilaterally symmetric bioprocessor using a combination of glass and the biocompatible polymer polydimethylsiloxane (PDMS) to create twin independent DNA sequencing systems. Using these two materials enabled the investigators to fabricate a system with process complexity and performance previously unattainable in a microfluidics device.
The device itself comprises a 250-nanoliter reaction chamber capable of thermal cycling, purification gels utilizing DNA affinity capture, reagent dispensing chambers, a microvalve pumping system, and gel-filled capillary electrophoresis channels. The combination of these features in one microfluidics device greatly reduces the amount of reagents needed for Sanger sequencing. Most importantly, the new device fully integrates and automates the Sanger process.
Despite the advance that this device represents, the investigators believe that they can improve their design to further reduce reagent use. The researchers believe that ultimately, the next generation microfluidic Sanger sequencing chip will use 400-fold less reagent and sequence 800-fold more DNA than current technology allows.
The investigators also note that the various components of their Sanger sequencing will enable a variety of biomedical applications, including genotyping and single nucleotide polymorphism (SNP) screening, that will be useful for tumor biopsy screening. Currently, Microchip Biotechnologies, Inc., in Dublin, CA, is working to develop commercial devices using this technology.
This work is detailed in a paper titled, "Microfabricated bioprocessor for integrated nanoliter-scale Sanger DNA sequencing." An abstract of this paper is available through PubMed.