High-throughput genetic analysis using microfabricated 96-sample capillary array electrophoresis microplates

Highly sensitive restriction enzyme assay and analysis: a review

Biological assays at the single molecule level are crucial to fundamental studies of DNA-protein mechanisms. In order to cater for high throughput applications, one area of immense research potential is single-molecule bioassays where miniaturized devices are developed to perform rapid and effective biological reactions and analyses. With the success of various emerging technologies for engineering miniaturized structures down to the nanoscale level, supported by specialized equipment for detection, many investigations in the field of life science that were once thought impossible can now be actively explored. In this review, the significance of downscaling to the single-molecule level is firstly presented in selected examples, with the focus placed on restriction enzyme assays. To determine the effectiveness of single-molecule restriction enzyme reactions, simple and direct analytical methods based on DNA stretching have often been reliably employed. DNA stretching can be realized based on a number of working principles related to the physical forces exerted on the DNA samples. We then discuss two examples of a nanochannel system and a microchamber system where single-molecule restriction enzyme digestion and DNA stretching have been integrated, which possess prospective capabilities of developing into highly sensitive and high-throughput restriction enzyme assays. Finally, we take a brief look at the general trends in technological development in this field by comparing the advantages and disadvantages of performing assays at bulk, microscale and single-molecule levels.

Monitoring FET flow control and wall adsorption of charged fluorescent dye molecules in nanochannels integrated into a multiple internal reflection infrared waveguide

Using Si as the substrate, we have fabricated multiple internal reflection infrared waveguides embedded with a parallel array of nanofluidic channels. The channel width is maintained substantially below the mid-infrared wavelength to minimize infrared scattering from the channel structure and to ensure total internal reflection at the channel bottom. A Pyrex slide is anodically bonded to the top of the waveguide to seal the nanochannels, while simultaneously enabling optical access in the visible range from the top. The Si channel bottom and sidewalls are thermally oxidized to provide an electrically insulating barrier, and the Si substrate surrounding the insulating SiO(2) layer is selectively doped to function as a gate. For fluidic field effect transistor (FET) control, a DC potential is applied to the gate to manipulate the surface charge on SiO(2) channel bottom and sidewalls and therefore their zeta-potential. Depending on the polarity and magnitude, the gate potential can accelerate, decelerate, or reverse the flow. Here, we demonstrate that this nanofluidic infrared waveguide can be used to monitor the FET flow control of charged, fluorescent dye molecules during electroosmosis by multiple internal reflection Fourier transform infrared spectroscopy. Laser scanning confocal fluorescence microscopy is simultaneously used to provide a comparison and verification of the IR analysis. Using the infrared technique, we probe the vibrational modes of dye molecules, as well as those of the solvent. The observed infrared absorbance accounts for the amount of dye molecules advancing or retracting in the nanochannels, as well as adsorbing to and desorbing from the channel bottom and sidewalls.

Ionic conductance of nanopores in microscale analysis systems: where microfluidics meets nanofluidics

In this tutorial review we illustrate the origin and dependence on various system parameters of the ionic conductance that exists in discrete nanochannels as well as in nanoporous separation and preconcentration units contained as hybrid configurations, membranes, packed beds, or monoliths in microscale liquid phase analysis systems. A particular complexity arises as external electrical fields are superimposed on internal chemical and electrical potential gradients for tailoring molecular transport. It is demonstrated that the variety of geometries in which the microfluidic/nanofluidic interfaces are realized share common, fundamental features of coupled mass and charge transport, but that phenomena behind the key steps in a particular application can be significantly tuned, depending on the morphology of a material. Thus, the understanding of morphology-related transport in internal and external electrical potential gradients is critical to the performance of a device. This addresses a variety of geometries (slits, channels, filters, membranes, random or regular networks of pores, etc.) and applications, e. g., the gating, sensing, preconcentration, and separation in multifunctional miniaturized devices. Inherently coupled mass and charge transport through ion-permselective (charge-selective) microfluidic/nanofluidic interfaces is analyzed with a stepwise-added complexity and discussed with respect to the morphology of the charge-selective spatial domains. Within this scenario, the electrostatics and electrokinetics in microfluidic and nanofluidic channels, as well as the electrohydrodynamics evolving at microfluidic/nanofluidic interfaces, where microfluidics meets nanofluidics, define the platform of central phenomena.

Fabrication of a monolithic sampling probe system for automated and continuous sample introduction in microchip-based CE

A fabrication process for producing monolithic sampling probes on glass chips, with tip diameters of a few hundred micrometers was developed, using simple tools including a glass cutter and a bench drill. Microfluidic chips with probes fabricated by this approach were coupled to a linearly moving slotted-vial array sample presentation system for performing continuous sample introduction in the chip-based CE system. On-chip horizontal tubular reservoirs containing working electrolyte and waste were used to maintain a stable hydrostatic pressure in the chip channels during prolonged working periods. The performance of the system was demonstrated in the separation of FITC-labeled amino acids with LIF detection, by continuously introducing a train of different samples without interruption. Throughputs of 30-60/h were achieved with <1.0% carry-over and reproducibilities in peak height of 3.6, 3.3, and 3.5% RSD for arginine, FITC, and phenylalanine, respectively (n = 11). Continuous analysis of a mixture of FITC-labeled amino acids for 2 h, involving 60 analytical cycles, yielded an RSD of 7.5 and 6.8% for arginine and FITC (n = 60), respectively. An extremely low sample consumption of 30 nL for each analysis was obtained. Separation efficiencies in plate numbers were in the range of 0.8-2x10(5)/m. In addition to the application in sample introduction, the sample/reagent introduction system was also used to produce working electrolyte gradients during a CE separation to improve the separation efficiency. Comparing with isocratic electrophoresis separation, gradient CE demonstrated better separation efficiencies for a mixture of FITC-labeled amino acids.

Optical filtering technologies for integrated fluorescence sensors

Numerous approaches have been taken to miniaturizing fluorescence sensing, which is a key capability for micro-total-analysis systems. This critical, comprehensive review focuses on the optical hardware required to attenuate excitation light while transmitting fluorescence. It summarizes, evaluates, and compares the various technologies, including filtering approaches such as interference filters and absorption filters and filterless approaches such as multicolor sensors and light-guiding elements. It presents the physical principles behind the different architectures, the state-of-the-art micro-fluorometers and how they were microfabricated, and their performance metrics. Promising technologies that have not yet been integrated are also described. This information will permit the identification of methods that meet particular design requirements, from both performance and integration perspectives, and the recognition of the remaining technological challenges. Finally, a set of performance metrics are proposed for evaluating and reporting spectral discrimination characteristics of integrated devices in order to promote side-by-side comparisons among diverse technologies and, ultimately, to facilitate optimized designs of micro-fluorometers for specific applications.

A cam-based laser-induced fluorescence scanner for capillary array electrophoresis

Capillary array electrophoresis (CAE) is an important high throughput analytical technique. Laser-induced fluorescence (LIF) has been the dominant detection method for CAE owing to its low limit of detection (LOD) and wide linear dynamic range (LDR). Linear LIF scanners were first used in CAE because linear motions of an objective match well with a common planar array of capillaries. A problem with linear scanners is that the motor is required accelerating/decelerating so that all capillaries can be properly scanned, which makes motion control complicated and reduces the duty cycle. Rotary scanners were developed to overcome this problem. While rotary scanners have been successfully applied in CAE, the capillaries have to be arranged in a circular format, which can be inconvenient in some cases. In this report, we describe a cam-based LIF scanner as an alternative technique for CAE detection. In this system, a rotary motor is mechanically linked with a capillary holder via a cam. During operation, the motor carries the cam in a rotary motion that drives an array of capillaries on the holder to move back and forth across the objective for fluorescence detection. Using this design, the capillaries can be parallel-arranged in a plane while the motor acceleration/deceleration is avoided. To demonstrate the feasibility of this approach, we constructed a prototype instrument with a constant-velocity scanning distance of approximately 10 mm, a scanning frequency of 3 Hz and a duty cycle of approximately 70%. The scanner exhibited a LOD of 69 pM of fluorescein and a LDR of 3.5 orders of magnitude. Multiplexed capillary SDS-PAGE was performed on this scanner for protein separations.

Microfluidic serial dilution circuit

In vitro evolution of RNA molecules requires a method for executing many consecutive serial dilutions. To solve this problem, a microfluidic circuit has been fabricated in a three-layer glass-PDMS-glass device. The 400-nL serial dilution circuit contains five integrated membrane valves: three two-way valves arranged in a loop to drive cyclic mixing of the diluent and carryover, and two bus valves to control fluidic access to the circuit through input and output channels. By varying the valve placement in the circuit, carryover fractions from 0.04 to 0.2 were obtained. Each dilution process, which is composed of a diluent flush cycle followed by a mixing cycle, is carried out with no pipeting, and a sample volume of 400 nL is sufficient for conducting an arbitrary number of serial dilutions. Mixing is precisely controlled by changing the cyclic pumping rate, with a minimum mixing time of 22 s. This microfluidic circuit is generally applicable for integrating automated serial dilution and sample preparation in almost any microfluidic architecture.

Parallel separation of multiple samples with negative pressure sample injection on a 3-D microfluidic array chip

A simple and powerful microfluidic array chip-based electrophoresis system, which is composed of a 3-D microfluidic array chip, a microvacuum pump-based negative pressure sampling device, a high-voltage supply and an LIF detector, was developed. The 3-D microfluidic array chip was fabricated with three glass plates, in which a common sample waste bus (SW(bus)) was etched in the bottom layer plate to avoid intersecting with the separation channel array. The negative pressure sampling device consists of a microvacuum air pump, a buffer vessel, a 3-way electromagnet valve, and a vacuum gauge. In the sample loading step, all the six samples and buffer solutions were drawn from their reservoirs across the injection intersections through the SW(bus) toward the common sample waste reservoir (SW(T)) by negative pressure. Only 0.5 s was required to obtain six pinched sample plugs at the channel crossings. By switching the three-way electromagnetic valve to release the vacuum in the reservoir SW(T), six sample plugs were simultaneously injected into the separation channels by EOF and electrophoretic separation was activated. Parallel separations of different analytes are presented on the 3-D array chip by using the newly developed sampling device.

Rapid and High-Throughput Forensic Short Tandem Repeat Typing Using a 96-Lane Microfabricated Capillary Array Electrophoresis Microdevice*

A 96-channel microfabricated capillary array electrophoresis (muCAE) device was evaluated for forensic short tandem repeat (STR) typing using PowerPlex 16 and AmpFlSTR Profiler Plus multiplex PCR systems. The high-throughput muCAE system produced high-speed <30-min parallel sample separations with single-base resolution. Forty-eight previously analyzed single-source samples were accurately typed, as confirmed on an ABI Prism 310 and/or the Hitachi FMBIO II. Minor alleles in 3:1 mixture samples containing female and male DNA were reliably typed as well. The instrument produced full profiles from sample DNA down to 0.17 ng, a threshold similar to that found for the ABI 310. Seventeen nonprobative samples from various evidentiary biological stains were also correctly typed. The successful application of the muCAE device to actual forensic STR typing samples is a significant step toward the development of a completely integrated STR analysis microdevice.

Development and multiplexed control of latching pneumatic valves using microfluidic logical structures

Novel latching microfluidic valve structures are developed, characterized, and controlled independently using an on-chip pneumatic demultiplexer. These structures are based on pneumatic monolithic membrane valves and depend upon their normally-closed nature. Latching valves consisting of both three- and four-valve circuits are demonstrated. Vacuum or pressure pulses as short as 120 ms are adequate to hold these latching valves open or closed for several minutes. In addition, an on-chip demultiplexer is demonstrated that requires only n pneumatic inputs to control 2(n-1) independent latching valves. These structures can reduce the size, power consumption, and cost of microfluidic analysis devices by decreasing the number of off-chip controllers. Since these valve assemblies can form the standard logic gates familiar in electronic circuit design, they should be useful in developing complex pneumatic circuits.

Microfabricated bioprocessor for integrated nanoliter-scale Sanger DNA sequencing

An efficient, nanoliter-scale microfabricated bioprocessor integrating all three Sanger sequencing steps, thermal cycling, sample purification, and capillary electrophoresis, has been developed and evaluated. Hybrid glass-polydimethylsiloxane (PDMS) wafer-scale construction is used to combine 250-nl reactors, affinity-capture purification chambers, high-performance capillary electrophoresis channels, and pneumatic valves and pumps onto a single microfabricated device. Lab-on-a-chip-level integration enables complete Sanger sequencing from only 1 fmol of DNA template. Up to 556 continuous bases were sequenced with 99% accuracy, demonstrating read lengths required for de novo sequencing of human and other complex genomes. The performance of this miniaturized DNA sequencer provides a benchmark for predicting the ultimate cost and efficiency limits of Sanger sequencing.

Lab-on-a-chip: microfluidics in drug discovery

Miniaturization can expand the capability of existing bioassays, separation technologies and chemical synthesis techniques. Although a reduction in size to the micrometre scale will usually not change the nature of molecular reactions, laws of scale for surface per volume, molecular diffusion and heat transport enable dramatic increases in throughput. Besides the many microwell-plate- or bead-based methods, microfluidic chips have been widely used to provide small volumes and fluid connections and could eventually outperform conventionally used robotic fluid handling. Moreover, completely novel applications without a macroscopic equivalent have recently been developed. This article reviews current and future applications of microfluidics and highlights the potential of 'lab-on-a-chip' technology for drug discovery.

Parallel analysis of biomolecules on a microfabricated capillary array chip

This paper focused on a self-developed microfluidic array system with microfabricated capillary array electrophoresis (mu-CAE) chip for parallel chip electrophoresis of biomolecules. The microfluidic array layout consists of two common reservoirs coupled to four separation channels connected to sample injection channel on the soda-lime glass substrate. The excitation scheme for distributing a 20 mW laser beam to separation channels in an array is achieved. Under the control of program, the sample injection and separation in multichannel can be achieved through six high-voltage modules' output. A CCD camera was used to monitor electrophoretic separations simultaneously in four channels with LIF detection, and the electropherograms can be plotted directly without reconstruction by additional software. Parallel multichannel electrophoresis of series biomolecules including amino acids, proteins, and nucleic acids was performed on this system and the results showed fine reproducibility.

An integrated microfluidic processor for single nucleotide polymorphism-based DNA computing

An integrated microfluidic processor is developed that performs molecular computations using single nucleotide polymorphisms (SNPs) as binary bits. A complete population of fluorescein-labeled DNA "answers" is synthesized containing three distinct polymorphic bases; the identity of each base (A or T) is used to encode the value of a binary bit (TRUE or FALSE). Computation and readout occur by hybridization to complementary capture DNA oligonucleotides bound to magnetic beads in the microfluidic device. Beads are loaded into sixteen capture chambers in the processor and suspended in place by an external magnetic field. Integrated microfluidic valves and pumps circulate the input DNA population through the bead suspensions. In this example, a program consisting of a series of capture/rinse/release steps is executed and the DNA molecules remaining at the end of the computation provide the solution to a three-variable, four-clause Boolean satisfiability problem. The improved capture kinetics, transfer efficiency, and single-base specificity enabled by microfluidics make our processor well-suited for performing larger-scale DNA computations.

Applications of capillary electrophoresis on microchip

CE on microchip is an emerging separation technique that has attracted wide attention and gained considerable popularity. Because of miniaturization of the separation format, CE on chip typically offers shorter analysis time and lower reagent consumption with potential development of portable analytical instrumentation. This review with 143 references is focused on proteins and peptides analysis, DNA separation including fragment sizing, genotyping, mutation detection and sequencing, and also the analysis of low-molecular-weight compounds, namely explosive residues and warfare agents, pharmaceuticals and drugs of abuse, and various small molecules in body fluids.

Microfluidic genetic analysis with an integrated a-Si:H detector

We have developed an integrated hydrogenated amorphous silicon (a-Si:H) fluorescence detector for microfluidic genetic analysis. It consists of a half-ball lens, a ZnS/YF3 multilayer optical interference filter with a pinhole, and an annular a-Si:H PIN photodiode allowing the laser excitation to pass up through the central aperture in the photodiode and the filter. Microfluidic separations of multiplex PCR products generated from methicillin-resistant/sensitive Staphylococcus aureus (MRSA/MSSA) DNA on microfluidic capillary electrophoresis (CE) devices are successfully detected with the integrated detector. Similarly, multiplex PCR amplicons from the kanamycin resistant and K12 serotype-specific genes of E. coli cells are detected. The direct detection of multiplex PCR amplicons indicates that the fluorescence detector can be successfully coupled with current microfluidic PCR-CE platforms. This work establishes that the integrated a-Si:H detector provides relevant limits of detection for point-of-care genetic and pathogen analysis with microfluidic devices.

Disposable microfluidic devices: fabrication, function, and application

This review article describes recent developments in microfluidics, with special emphasis on disposable plastic devices. Included is an overview of the common methods used in the fabrication of polymer microfluidic systems, including replica and injection molding, embossing, and laser ablation. Also described are the different methods by which on-chip operations--such as the pumping and valving of fluid flow, the mixing of different reagents, and the separation and detection of different chemical species--have been implemented in a microfluidic format. Finally, a few select biotechnological applications of microfluidics are presented to illustrate both the utility of this technology and its potential for development in the future.

High-throughput single-strand conformation polymorphism analysis on a microfabricated capillary array electrophoresis device

A high-density 384-lane microfabricated capillary array electrophoresis device is evaluated for high-throughput single-strand conformation polymorphism (SSCP) analysis. A delayed back bias direct electrokinetic injection scheme is used to provide better than 10-bp resolution with an 8.0-cm effective separation length. Separation of a HaeIII digest of PhiX174 yielded theoretical plate numbers of 4.0 x 10(6). Using 5% PDMA containing 10% glycerol and 15% urea, 21 single-nucleotide polymorphisms (SNPs) from HFE, MYL2, MYL3, and MYH7 genes associated with hereditary hemochromatosis (HHC) and hereditary hypertrophic cardiomyopathy (HCM) are discriminated at two running temperatures (25 degrees C and 40 degrees C), providing 100% sensitivity. The data in this study demonstrate that the 384-lane microCAE device provides the resolution and detection sensitivity required for SSCP analysis, showing its potential for ultrahigh-throughput mutation detection.

Chip-based gel electrophoresis method for the quantification of half-antibody species in IgG4 and their by- and degradation products

The inter-heavy-chain disulfide bonds of the IgG4 subclass can be described as being at equilibrium with the intra-chain disulfide bonds. This means that a fraction of IgG4 has noncovalently linked heavy chains (half-antibody). The percentage of half-antibodies produced depends upon the expression system used. Nondenaturing assays fail to separate the half-antibodies from the native form because two half-molecules are held together by noncovalent forces. The pharmaceutical industry needs a reliable denaturing assay for checking batch-to-batch consistency. Until now sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) has been the standard method used to detect the presence of half-antibodies. However, this technique is laborious and cannot be automated. Furthermore, cumbersome densitometric measurements are necessary for quantification. To overcome these disadvantages a chip-based gel electrophoresis method was investigated. In the nonreduced format the separation profile is compared with that from SDS-PAGE. The limit of quantification as a percentage of the amount applied, repeatability, reproducibility, and linearity are compared with those of SDS-PAGE. The amounts of half-antibody and of by- and degradation products were determined for several batches by using area percentage and by external calibration with IgG4 as a reference standard. Both methods allow avoidance of error introduction for the quantification as is the case by application of myosin as reference concentration. Both sets of results are compared with each other and with the results from SDS-PAGE. In the reduced format it is noted that the reduction of the inter-heavy-chain disulfide bridges proceeds faster than the reduction of the heavy-light-chain bonds. Therefore optimized conditions are necessary to obtain a complete reduction.

Replica multichannel polymer chips with a network of sacrificial channels sealed by adhesive printing method

Replica microchips for capillary array electrophoresis containing 10 separation channels (50 microm width, 50 microm depth and 100 microm pitch) and a network of sacrificial channels (100 microm width and 50 microm depth) were successfully fabricated on a poly(methyl methacrylate) (PMMA) substrate by injection molding. The strategy involved development of moving mask deep X-ray lithography to fabricate an array of channels with inclined channel sidewalls. A slight inclination of channel sidewalls, which can not be fabricated by conventional deep X-ray lithography, is highly required to ensure the release of replicated polymer chips from a mold. Moreover, the sealing of molded PMMA multichannel chips with a PMMA cover film was achieved by a novel bonding technique involving adhesive printing and a network of sacrificial channels. An adhesive printing process enables us to precisely control the thickness of an adhesive layer, and a network of sacrificial channels makes it possible to remove air bubbles and an excess adhesive, which are crucial to achieving perfect sealing of replica PMMA chips with well-defined channel and injection structures. A CCD camera equipped with an image intensifier was used to simultaneously monitor electrophoretic separations in ten micro-channels with laser-induced fluorescence detection. High-speed and high-throughput separations of a 100 bp DNA ladder and phi X174 Hae III DNA restriction fragments have been demonstrated using a 10-channel PMMA chip. The current work establishes the feasibility of mass production of PMMA multichannel chips at a cost-effective basis.

Microfabricated systems for nucleic acid analysis

High throughput and automation of nucleic acid analysis are required in order to exploit the information that has been accumulated from the Human Genome Project. Microfabricated analytical systems enable parallel sample processing, reduced analysis-times, low consumption of sample and reagents, portability, integration of various analytical procedures and automation. This review article discusses miniaturized analytical systems for nucleic acid amplification, separation by capillary electrophoresis, sequencing and hybridization. Microarrays are also covered as a new analytical tool for global analysis of gene expression. Thus. instead of studying the expression of a single gene or a few genes at a time we can now obtain the expression profiles of thousands of genes in a single experiment.

An automated electrokinetic continuous sample introduction system for microfluidic chip-based capillary electrophoresis

An automated and continuous sample introduction system for microfluidic chip-based capillary electrophoresis (CE) was developed in this work. An efficient world-to-chip interface for chip-based CE separation was produced by horizontally connecting a Z-shaped fused silica capillary sampling probe to the sample loading channel of a crossed-channel chip. The sample presentation system was composed of an array of bottom-slotted sample vials filled alternately with samples and working electrolyte, horizontally positioned on a programmable linearly moving platform. On moving the array from one vial to the next, and scanning the probe, which was fixed with a platinum electrode on its tip, through the slots of the vials, a series of samples, each followed by a flow of working electrolyte was continuously introduced electrokinetically from the off-chip vials into the sample loading channel of the chip. The performance of the system was demonstrated in the separation and determination of FITC-labeled arginine and phenylalanine with LIF detection, by continuously introducing a train of different samples. Employing 4.5 kV sampling voltage (1000 V cm(-1) field strength) for 30 s and 1.8 kV separation voltage (400 V cm(-1) field strength) for 70 s, throughputs of 36 h(-1) were achieved with <1.0% carryover and 4.6, 3.2 and 4.0% RSD for arginine, FITC and phenylalanine, respectively (n = 11). Net sample consumption was only 240 nL for each sample.

DNA sequencing and genotyping in miniaturized electrophoresis systems

Advances in microchannel electrophoretic separation systems for DNA analyses have had important impacts on biological and biomedical sciences, as exemplified by the successes of the Human Genome Project (HGP). As we enter a new era in genomic science, further technological innovations promise to provide other far-reaching benefits, many of which will require continual increases in sequencing and genotyping efficiency and throughput, as well as major decreases in the cost per analysis. Since the high-resolution size- and/or conformation-based electrophoretic separation of DNA is the most critical step in many genetic analyses, continual advances in the development of materials and methods for microchannel electrophoretic separations will be needed to meet the massive demand for high-quality, low-cost genomic data. In particular, the development (and commercialization) of miniaturized genotyping platforms is needed to support and enable the future breakthroughs of biomedical science. In this review, we briefly discuss the major sequencing and genotyping techniques in which high-throughput and high-resolution electrophoretic separations of DNA play a significant role. We review recent advances in the development of technology for capillary electrophoresis (CE), including capillary array electrophoresis (CAE) systems. Most of these CE/CAE innovations are equally applicable to implementation on microfabricated electrophoresis chips. Major effort is devoted to discussing various key elements needed for the development of integrated and practical microfluidic sequencing and genotyping platforms, including chip substrate selection, microchannel design and fabrication, microchannel surface modification, sample preparation, analyte detection, DNA sieving matrices, and device integration. Finally, we identify some of the remaining challenges, and some of the possible routes to further advances in high-throughput DNA sequencing and genotyping technologies.

Parallel separations of oligonucleotides with optically gated sample introduction on multichannel microchips

With the release of the human genome sequence, there has been increasing attention given to other genetic analyses, including the detection of genetic variations and fast sequencing of multiple samples for pharmacogenomics studies. Rapid injections of samples in multiplexed separation channels by optically gated sample introduction are shown here for DNA separation. Serial separations of four amino acids are shown in less than four seconds on a microchip with four multiplexed channels. Five short oligonucleotides have also been rapidly separated in 2% LPA with four channels using this technique. In addition, multiple unique samples have been simultaneously separated and five-base resolution has been demonstrated.

Microtechnologies and nanotechnologies for single-cell analysis

Many efforts are currently underway to try and mimic the properties of single cells with the aim of designing chips that are as efficient as cells. However, cells are nature's nanotechnology engineering at the scale of atoms and molecules, and it might be better to envision a microchip that utilizes a single cell as an experimentation platform. A novel, so-called laboratory-in-a-cell concept has been described, where advantage is taken of micro- and nanotechnological tools to enable precise control of the biochemical cellular environment; these tools also offer the possibility to analyse the composition of single cells. Methods for single-cell handling and analysis are being developed and will be required for this concept to progress further.

Microfabricated electrophoresis systems for DNA sequencing and genotyping applications: current technology and future directions

Many routine genomic-analysis assays rely on gel electrophoresis to perform size-selective fractionation of DNA fragments in the size range below 1 kb in length. Over the past decade, impressive progress has been made towards the development of microfabricated electrophoresis systems to conduct these assays in a microfluidic lab-on-a-chip format. Since these devices are inexpensive, require only nanolitre 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. The design and construction of microfabricated electrophoresis devices poses a variety of challenges, including the need to achieve high-resolution separations over distances of a few centimetres or less, and the need to easily interface with additional microfluidic components to produce self-contained integrated DNA-analysis systems. In this paper, we review recent efforts to develop devices to satisfy these requirements and live up to the promise of fulfilling the growing need for inexpensive portable genomic-analysis equipment.

Plastic substrates based separation channels in electromigration techniques

Three types of plastic materials (polyester, polyurethane and polymethylmethacrylate) were tested as materials for manufacturing separation columns (polyester and polyurethane capillaries were used) or separation channels (polymethylmethacrylate) in the chip format. A set of 11 fluorescein isothiocyanate amino acid derivatives was used as the test mixture. Using alpha-cyclodextrin additive to the background electrolyte in the case of the chip separation was also tested. The main problem with all plastic separation media was the selectivity of the separation. The best results, practically identical with bare fused silica capillary, were obtained with the polymethylmethacrylate chip, provided that alpha-cyclodextrin in a concentration 40 mmol/l was added to the background electrolyte. An important observation was that in SDS containing background electrolyte all the plastic materials used exhibited a distinct electroosmotic flow, which was ascribe to the sorption of the negatively charged constituents of the background electrolyte to the capillary wall. Regarding the order in which the individual components of the test mixture were brought to the detector only a single change was observed. Histidine migrated in the polystyrene and polymethylmethacrylate separation channels more slowly than in the bare silica or polyurethane based capillaries.

Rapid serial analysis of multiple oligonucleotide samples on a microchip using optically-gated injection

Optically-gated injection of fluorescently-labeled DNA has been accomplished for the first time. Rapid, serial analysis of oligonucleotide ladders has been shown on a microchip using this injection technique. Separations of five- and six-component samples have been completed in 60 s or less with a capability to carry out serial injections of these samples every 15 s. The technique has been shown to have better than five base resolution for small oligonucleotides and excellent reproducibility in migration times (< or = 0.75% RSD). Currently, the limit of detection for the system is 0.23 microM. Additionally, multiple unique samples of DNA have been consecutively analyzed in a single separation lane using optical gating. Six consecutive injections of three different samples have been achieved with no sample carryover and a total analysis time of approximately 10 min. These results show the potential of optical gating as an alternative injection technique for high-throughput DNA applications, such as genotyping and monitoring dynamic processes.

Microfluidic devices for DNA sequencing: sample preparation and electrophoretic analysis

Modern DNA sequencing 'factories' have revolutionized biology by completing the human genome sequence, but in the race to completion we are left with inefficient, cumbersome, and costly macroscale processes and supporting facilities. During the same period, microfabricated DNA sequencing, sample processing and analysis devices have advanced rapidly toward the goal of a 'sequencing lab-on-a-chip'. Integrated microfluidic processing dramatically reduces analysis time and reagent consumption, and eliminates costly and unreliable macroscale robotics and laboratory apparatus. A microfabricated device for high-throughput DNA sequencing that couples clone isolation, template amplification, Sanger extension, purification, and electrophoretic analysis in a single microfluidic circuit is now attainable.

Microchip electrophoresis-based separation of DNA

Miniaturized instruments have developed very quickly in the last decade. This review is focused on the microchip electrophoresis-based separation of DNA. Fundamentals, including the chip format, substrates and fabrication technologies, fluid control, as well as various detection methods, are summarized. Array electrophoresis microchip and the on-chip integration of electrophoresis with other systems are introduced as well. In addition, the application of microchip electrophoresis in DNA sizing, genetic analysis and DNA sequencing are also presented in this paper.

Biochips beyond DNA: technologies and applications

Technological advances in miniaturization have found a niche in biology and signal the beginning of a new revolution. Most of the attention and advances have been made with DNA chips yet a lot of progress is being made in the use of other biomolecules and cells. A variety of reviews have covered only different aspects and technologies but leading to the shared terminology of "biochips." This review provides a basic introduction and an in-depth survey of the different technologies and applications involving the use of non-DNA molecules such as proteins and cells. The review focuses on microarrays and microfluidics, but also describes some cellular systems (studies involving patterning and sensor chips) and nanotechnology. The principles of each technology including parameters involved in biochip design and operation are outlined. A discussion of the different biological and biomedical applications illustrates the significance of biochips in biotechnology.

Parallel analysis with optically gated sample introduction on a multichannel microchip

As an alternative to the T-type injection on microchips, optically gated sample introduction previously has been demonstrated to provide fast, serial, and reproducible injections on a single-channel microchip. Here, the ability to perform high throughput, multichannel analysis with optically gated sample introduction is described using a voice coil actuator. The microchip is fixed on a stage, which moves back and forth via the voice coil actuator, scanning two laser beams across the channels on the microchip. For parallel analysis on a multichannel microchip, both the gating beam and the probe beam are scanned at 10 Hz to perform multiple injections and parallel detection. Simultaneous, fast separations of 4-choloro-7-nitrobenzofurazan (NBD)-labeled amino acids are demonstrated in multiple channels on a microchip. Serial separations of different samples in multiple channels are also reported. Optically gated sample introduction on multiple, parallel channels shows the potential for high-speed, high-throughput separations that are easily automated by using a single electronic shutter.

Copolymer solutions as separation media for DNA capillary electrophoresis

A review on copolymers used as DNA separation media in capillary electrophoresis is presented. Copolymers can combine the desirable properties of different monomers, yielding many attractive features, such as high sieving ability, low viscosity, self-assembly behavior and dynamic coating ability. Copolymers with different molecular architecture, including block copolymers, random copolymers, and graft copolymers, have been developed and tested as DNA separation media with unique and tailored properties that cannot be achieved easily by using only homopolymers.

DNA analysis on microfabricated electrophoretic devices with bubble cells

Microfluidic devices with bubble cells have been fabricated on poly(methyl methacrylate) (PMMA) plates and have been employed for the analysis of DNA using polyethylene oxide (PEO) solutions. First, the separation channel was fabricated using a wire-imprinting method. Then, wires with greater sizes or a razor blade glued in a polycarbonate plate was used to fabricate bubble cells, with sizes of 190-650 microm. The improvements in resolution and sensitivity have been achieved for large DNA (> 603 base pair, bp) using such devices, which depend on the geometry of the bubble cell. The main contributor for optimal resolution is mainly due to DNA migration at lower electric field strengths inside the bubble cell. On the other hand, slight losses of resolution for small DNA fragments have been found mainly due to diffusion, supported by the loss of resolution when separating two small solutes. With a bubble cell of 75 microm (width) x 500 microm (depth), the sensitivity improvement up to 17-fold has been achieved for the 271 bp fragment in the separation of PhiX-174/HaeIII DNA restriction fragments. We have also found that a microfluidic device with a bubble cell of 360 microm x 360 microm is appropriate for DNA analysis. Such a device has been used for separating DNA ranging from 8 to 2176 bp and polymerase chain reaction (PCR) products amplified after 30 cycles, with rapidity and improvements in the sensitivity as well as resolution.

High throughput genotyping technologies for pharmacogenomics

Genetic differences between individuals play a role in determining susceptibility to diseases as well as in drug response. The challenge today is first to discover the range of genetic variability in the human population and then to define the particular gene variants, or alleles, that contribute to clinically important outcomes. Consequently, high throughput, automated methods are being developed that allow rapid scoring of microsatellite alleles and single nucleotide polymorphisms (SNPs). Many detection technologies are being used to accomplish this goal, including electrophoresis, standard fluorescence, fluorescence polarization, fluorescence resonance energy transfer, and mass spectrometry. SNP alleles may be distinguished by any one of several methods, including single nucleotide primer extension, allele-specific hybridization, allele-specific primer extension, oligonucleotide ligation assay, and invasive signal amplification. Newer methods require less sample manipulation, increase sensitivity, allow more flexibility, and decrease reagent costs. Recent developments show promise for continuing these trends by combining amplification and detection steps and providing flexible, miniaturized platforms for genotyping.

Microfluidic chips for clinical and forensic analysis

This review gives an overview of developments in the field of microchip analysis for clinical diagnostic and forensic applications. The approach chosen to review the literature is different from that in most microchip reviews to date, in that the information is presented in terms of analytes tested rather than microchip method. Analyte categories for which examples are presented include (i) drugs (quality control, seizures) and explosives residues, (ii) drugs and endogenous small molecules and ions in biofluids, (iii) proteins and peptides, and (iv) analysis of nucleic acids and oligonucleotides. Few cases of microchip analysis of physiological samples or other "real-world" matrices were found. However, many of the examples presented have potential application for these samples, especially with ongoing parallel developments involving integration of sample pretreatment onto chips and the use of fluid propulsion mechanisms other than electrokinetic pumping.

Systems biology: a brief overview

To understand biology at the system level, we must examine the structure and dynamics of cellular and organismal function, rather than the characteristics of isolated parts of a cell or organism. Properties of systems, such as robustness, emerge as central issues, and understanding these properties may have an impact on the future of medicine. However, many breakthroughs in experimental devices, advanced software, and analytical methods are required before the achievements of systems biology can live up to their much-touted potential.

High throughput DNA sequencing with a microfabricated 96-lane capillary array electrophoresis bioprocessor

High throughput DNA sequencing has been performed by using a microfabricated 96-channel radial capillary array electrophoresis (microCAE) microchannel plate detected by a 4-color rotary confocal fluorescence scanner. The microchannel plate features a novel injector for uniform sieving matrix loading as well as high resolution, tapered turns that provide an effective separation length of 15.9 cm on a compact 150-mm diameter wafer. Expanded common buffer chambers for the cathode, anode, and waste reservoirs are used to simplify electrode addressing and to counteract buffering capacity depletion arising from the high electrophoretic current. DNA sequencing data from 95 successful lanes out of 96 lanes run in parallel were batch-processed with basefinder, producing an average read length of 430 bp (phred q > or = 20). Phred quality values were found to exceed 40 (0.01% probability of incorrectly calling a base) for over 80% of the read length. The microCAE system demonstrated here produces sequencing data at a rate of 1.7 kbp/min, a 5-fold increase over current commercial capillary array electrophoresis technology. Additionally, this system permits lower reagent volumes and lower sample concentrations, and it presents numerous possibilities for integrated sample preparation and handling. The unique capabilities of microCAE technology should make it the next generation, high performance DNA sequencing platform.

Fluorogenic assay for beta-glucuronidase using microchip-based capillary electrophoresis

Microchip capillary electrophoresis (CE) was used with a model enzyme assay to demonstrate its potential application to combinatorial drug screening. Hydrolysis with beta-glucuronidase of the conjugated glucuronide, fluorescein mono-beta-D-glucuronide (FMG), liberated the fluorescent product, fluorescein. FMG and fluorescein were detected by fluorescence, with excitation and emission at 480 and 520 nm, respectively. Microchip CE was used to separate FMG and fluorescein. Fluorescein production was monitored to assess beta-glucuronidase activity. Michaelis-Menten enzyme kinetics analysis yielded the Km value. The results were compared with those from experiments done by conventional CE. The Km value for beta-glucuronidase with FMG is being reported for the first time as 18 microM. The inhibition of beta-glucuronidase by the competitive inhibitor D-saccharic acid-1,4-lactone (SL) was also determined using microchip CE. Reactions were done with various concentrations of inhibitor and constant beta-glucuronidase and FMG concentrations. A dose-response plot was acquired and the IC50 value for SL was determined to be 3 microM.

Separation of double-stranded DNA fragments by capillary electrophoresis in interpenetrating networks of polyacrylamide and polyvinylpyrrolidone

Mixtures of two polymers with totally different chemical structures, polyacrylamide and polyvinylpyrrolidone (PVP) have been successfully used for double-stranded DNA separation. By polymerization of acrylamide in a matrix of PVP solution, the incompatibility of these two polymers was suppressed. Laser light scattering (LLS) studies showed that highly entangled interpenetrating networks were formed in the solution. Further systematic investigation showed that double-stranded DNA separation was very good in these interpenetrating networks. With a concentration combination of as low as 2% w/v PVP (weight-average molecular mass Mr = 1 x 10(6) g/mol) + 1% w/v polyacrylamide (Mr = 4 x 10(5) g/mol), the 22 fragments in pBR322/HaeIII DNA, including the doublet of 123/124 bp, have been successfully separated within 6.5 min. Under the same separation conditions, similar resolution could only be achieved by using polyacrylamide (Mr = 4 x 10(5) g/mol) with concentrations higher than 6% w/v and could not be achieved by using only PVP (Mr = 1 x 10(6) g/mol) with a concentration as high as 15% w/v. It is noted that the interpenetrating network formed by 2% PVP and 1% polyacrylamide has a very low viscosity and can dynamically coat the inner wall of a fused-silica capillary. The separation reached an efficiency of more than 10(7) theoretical plate numbers/m and a reproducibility of less than 1% relative standard deviation of migration time in a total of seven runs. The interpenetrating network could stabilize polymer chain entanglements. Consequently, the separation speed was increased while retaining resolution.

High-performance genetic analysis using microfabricated capillary array electrophoresis microplates

This review focuses on some recent advances in realizing microfabricated capillary array electrophoresis (microCAE). In particular, the development of a novel rotary scanning confocal fluorescence detector has facilitated the high-speed collection of sequencing and genotyping data from radially formatted microCAE devices. The concomitant development of a convenient energy-transfer cassette labeling chemistry allows sensitive multicolor labeling of any DNA genotyping or sequencing analyte. High-performance hereditary haemochromatosis and short tandem repeat genotyping assays are demonstrated on these devices along with rapid mitochondrial DNA sequence polymorphism analysis. Progress in supporting technology such as robotic fluid dispensing and batched data analysis is also presented. The ultimate goal is to develop a parallel analysis platform capable of integrated sample preparation and automated electrophoretic analysis with a throughput 10-100 times that of current technology.

Genotyping Energy-Transfer-Cassette-labeled Short-Tandem-Repeat Amplicons with Capillary Array Electrophoresis Microchannel Plates

Background: Genetic analysis of microsatellite DNA is a powerful tool used in linkage analysis, gene mapping, and clinical diagnosis. To address the expanding needs of studies of short tandem repeats (STRs), we demonstrated high-performance STR analysis on a high-throughput microchannel plate-based platform.

Methods: Energy-transfer-cassette-labeled STR amplicons were separated and typed on a microfabricated 96-channel radial capillary array electrophoresis (CAE) microchannel plate system. Four-color detection was accomplished with a laser-excited confocal fluorescence rotary scanner.

Results: Multiplex STR analysis with single base-pair resolution was demonstrated on denaturing polyacrylamide gel media. The high-throughput multiplex capabilities of this genetic analysis platform were demonstrated by the simultaneous separation of STR amplicons representing 122 samples in ninety-six 5.5-cm-long channels in &lt;8 min. Sizing values obtained for these amplicons on the CAE microchannel plate were comparable to those measured on a conventional commercial CAE instrument and exhibit &lt;1% sizing variance.

Conclusions: Energy-transfer-cassette labeling and microfabricated CAE microchannel plates allow high-performance multiplex STR analyses.

Microchip electrophoretic separation systems for biomedical and pharmaceutical analysis

The application of microchip capillary electrophoresis (CE) systems to biomedical and pharmaceutical analysis is described and reviewed. Fabrication, instrumentation, and operation of the systems are discussed. An overview of applications is presented, covering four main areas: DNA sequencing, genetic analysis, immunoassays, and protein and peptide analysis. These systems have the potential to dramatically change the way that biochemical analyses are performed.

Microfabricated capillary array electrophoresis DNA analysis systems

Microfabricated "laboratory-on-a-chip" systems are revolutionizing all aspects of genetic analysis. The development of capillary array electrophoresis (CAE) microchannel plate devices makes possible the performance of 96 or more high-speed separations in parallel on a single wafer-scale device. The fluorescently labeled DNA samples are detected within the microchannels with a novel four-color rotary confocal fluorescence scanner. The capabilities of this system for genotyping are demonstrated through multiplex separations of short tandem repeat and hereditary haemochromatosis allele-specific amplicons. Furthermore, with newly developed folded channel designs that maintain high resolution, these CAE microplate systems are used to perform 96 high-quality DNA sequencing separations in parallel to approximately 500 bases per capillary in less than 30 min. These densely packed microfabricated device technologies will facilitate the even more rapid collection of vast amounts of genetic data in the future.