Microdevices for DNA analysis

(Contributor: Victor Ugaz, Assistant Professor, Texas A&M University

Microfabricated devices have the potential to offer portable low-cost alternatives to conventional benchtop-scale DNA analysis instrumentation, ultimately making a wide range of genomic-based assays feasible for routine use in the diagnosis and treatment of disease. Many applications of miniaturized technology also exist in the development of new and more powerful sensors to detect infectious disease agents (e.g. influenza, E. coli, SARS) and provide early warning capabilities for emerging biowarfare/bioterror threats (e.g. anthrax). Since these devices require only nanoliter sample volumes and do not rely on the availability of a pre-existing laboratory infrastructure, they are readily deployable in remote field locations for use in a variety of medical and biosensing applications. Impressive progress continues to be made toward improving separation performance in miniaturized DNA electrophoresis systems, largely as a result of efforts focused on scaling down conventional capillary electrophoresis (CE) technology's logical approach given the success of CE-based systems in high-throughput sequencing and genotyping applications.

By virtue of their small size, miniaturized systems offer the advantage of reduced reagent consumption, thereby lowering costs associated with performing biochemical reactions. However, the economic benefits of miniaturization extend even further to the hardware itself because photolithographic microfabrication techniques can be used to produce hundreds or thousands of devices at once, yielding per-device costs of $1 or less. These enormous savings are possible since per-wafer fabrication costs remain essentially constant regardless of whether the wafer contains a single device or 1,000 devices. A common analogy is that of your office photocopier, where the per-copy cost is independent of the number and arrangement of characters on the page. Consequently, as has been repeatedly demonstrated in the microelectronics industry, the cost benefits of microfabrication become most compelling when the device size is as small as possible. In terms of electrophoresis, this means that the ability to employ the shortest possible separation distance while still maintaining sufficient levels of resolution and sensitivity are issues of extreme importance.

Commercial DNA analysis systems based on microchip capillary electrophoresis technology are beginning to appear on the market. For example, the Agilent 2100 Bioanalyzer, the most widely used commercial chip-based DNA analysis device, is based on a Caliper LabChip platform incorporating arrays of glass electrophoresis microchannels loaded with a low viscosity gel-dye mixture. This system uses interchangeable electrophoresis chips that interface with a benchtop power supply and optical detection system. Newer systems, including Hitachi's SV1100 Microchip CE system and Network Biosystems' BioMEMS-768 sequencer, offer additional platforms for performing microdevice-based DNA analysis, although still operating as components of benchtop-scale systems.

Despite these remarkable advancements, the current generation of miniaturized devices have yet to offer improvements in cost or performance at a level compelling enough to seriously compete with existing macroscale CE systems. These limitations are primarily a consequence of (i) an inability to achieve high-resolution separations in devices occupying a footprint small enough to realize the enormous cost savings available through mass production via photolithographic fabrication, combined with (ii) difficulties in interfacing these devices with either microscale liquid handling components or macroscale laboratory workflow. These issues present a number of opportunities for advancements, particularly with respect to the development and characterization of improved sieving gel media. Systematic fundamental studies to gain a more complete understanding of the physics of gel electrophoresis and maximize separation performance in ultra-short distances are more important than ever.

Electrophoresis technology continues to maintain a ubiquitous presence in the modern molecular biology laboratory. However, unless significant progress can be made toward achieving orders of magnitude advances in cost and performance, electrophoresis may risk becoming less attractive for use as an analytical component in miniaturized systems. These challenges present tremendous opportunities for us in the electrophoresis community to make meaningful contributions toward the development of next-generation genomic analysis technology. The AES, which uniquely brings together researchers from academic, industrial, and health care settings, is ideally positioned to play a central role in promoting research aimed at addressing these needs.

Further reading: Recent progress toward the development of miniaturized electrophoresis technology for DNA sequencing and genotyping has been reviewed in the following articles.

Kan, C-W., Fredlake, C.P., Doherty, E.A.S., and Barron, A.E. “DNA sequencing and genotyping in miniaturized electrophoresis systems.” Electrophoresis 25 (2004): 3564-3588.

Ugaz, V.M., Elms, R.D., Lo, R.C., Shaikh, F.A., and Burns, M.A. “Microfabricated electrophoresis systems for DNA sequencing and genotyping applications: current technology and future directions.” Philosophical Transactions of the Royal Society (Series A: Mathematical, Physical and Engineering Sciences) 362 (2004): 1105-1129.