Plastic Microfluidic Systems for High-Throughput Genomic Analysis and Drug Screening

Abstract

Genomic analysis and drug discovery depend increasingly on rapid, accurate analysis of large sets of sample and extensive compound collections at relatively low cost. By capitalizing on advances in microfabrication, genomics, combinatorial chemistry, and assay technologies, new analytical systems are expected to provide order-of-magnitude increases in analysis throughput along with comparable decreases in per-sample analysis costs. ACLARA’s single-use, plastic LabCard systems, which transport fluids between reservoirs and through interconnected microchannels using electrokinetic mechanisms, are intended to address these analytical needs. These devices take advantage of recent developments in microfluidic and microfabrication technologies to permit their application to DNA sequencing; genotyping and DNA fragment analysis, as well as pharmaceutical candidate screening, and preparing biological samples for analysis. In a parallel effort, ACLARA has developed a new class of reporter molecules that are particularly well suited to capillary electrophoretic analysis. These electrophoretic mobility tags, called eTag reporters, can be used to uniquely label multiplexed sets of oligonucleotide recognition probes or proteins, thereby permitting traditionally homogeneous biochemical reporter assays to be multiplexed for CE analysis. Biochemical multiplexing is key to achieving new thresholds in analytical throughput while maintaining economically viable formats in many application areas. ACLARA’s microfluidic, lab-on-a-chip concept promises to revolutionize chemical analysis, similar to the way miniaturization revolutionized computing, making tools continually smaller, more integrated, less expensive, and higher performing. Microfluidic devices are made up of interconnected networks of microchannels and tiny volume reservoirs in which all the processes required for single analyses may be miniaturized, integrated, and automated within a single substrate the size of a human hand or smaller. However, LabCard devices are more than tiny replicates of existing equipment. They are characterized by high speed, parallel analysis using designs devised to eliminate sample cross contamination while automating processes that are otherwise undesirably cumbersome at the macro laboratory scale. Electrophoresis is one of the most widely used analytical separation methodologies for life science research. Electrophoresis refers to the movement of a charged molecule under the influence of an electric field. Electrophoresis can be used to separate molecules that have different charge-to-mass ratios such as proteins; or, molecules that have similar charge-to-mass ratios but different masses such as DNA fragments. In recent years, the development of capillary electrophoresis (CE), which is performed in a fused silica capillary filled with a buffer or polymer solution, has increased the speed of analytical separations. Planar, microchannel devices offer further improvements over capillary electrophoresis. In general, both electrophoresis and electroosmosis occur when a high electric field is applied along a microchannel (Figure 1). In practice, these effects can be comparable in magnitude, in which case ions of one charge move rapidlyat velocities of millimeters per second-while those of opposite charge move backward or slowly forward, depending upon which of the two effects dominates. The amount of fixed charge on the inner surface of a channel can be controlled by pH, specific adsorption of charged species onto the surface, or surface chemical modification. Therefore, the contribution of electroosmosis (the pumping mechanism) can be tuned relative to electrophoresis (the separating mechanism). The capability to transport and separate exceptionally small liquid volumes with precise electrical control is a powerful tool, which is complemented by an additional benefit of using microchannels with micrometer cross-sections. While electrophoresis channels are of similar cross section in both capillaries and microchannel devices, the planar format of the microchannel devices enables structures more complex than a single, non-intersecting channel to be used. Two or more channels can intersect to