Degenerate oligonucleotide primed-polymerase chain reaction and capillary electrophoretic analysis of human DNA on microchip-based devices

Capillary electrophoresis on microchip

Capillary electrophoresis and related techniques on microchips have made great strides in recent years. This review concentrates on progress in capillary zone electrophoresis, but also covers other capillary techniques such as isoelectric focusing, isotachophoresis, free flow electrophoresis, and micellar electrokinetic chromatography. The material and technologies used to prepare microchips, microchip designs, channel geometries, sample manipulation and derivatization, detection, and applications of capillary electrophoresis to microchips are discussed. The progress in separation of nucleic acids and proteins is particularly emphasized.

Fabrication of microfluidic systems in poly(dimethylsiloxane)

Microfluidic devices are finding increasing application as analytical systems, biomedical devices, tools for chemistry and biochemistry, and systems for fundamental research. Conventional methods of fabricating microfluidic devices have centered on etching in glass and silicon. Fabrication of microfluidic devices in poly(dimethylsiloxane) (PDMS) by soft lithography provides faster, less expensive routes than these conventional methods to devices that handle aqueous solutions. These soft-lithographic methods are based on rapid prototyping and replica molding and are more accessible to chemists and biologists working under benchtop conditions than are the microelectronics-derived methods because, in soft lithography, devices do not need to be fabricated in a cleanroom. This paper describes devices fabricated in PDMS for separations, patterning of biological and nonbiological material, and components for integrated systems.

Microfabricated isoelectric focusing device for direct electrospray ionization-mass spectrometry

A novel microfabricated device for isoelectric focusing (IEF) incorporating an optimized electrospray ionization (ESI) tip was constructed on polycarbonate plates using laser micromachining. The IEF microchip incorporated a separation channel (50 micro x 30 micro x 16 cm), three fluid connectors, and two buffer reservoirs. Electrical potentials used for IEF focusing and electrospray were applied through platinum electrodes placed in the buffer reservoirs, which were isolated from the separation channel by porous membranes. Direct ESI-mass spectrometry (MS) using electrosprays produced directly from a sharp emitter "tip" on the microchip was evaluated. The results indicated that this design can produce a stable electrospray and that performance was further improved and made more flexible with the assistance of a sheath gas and sheath liquid. Error analysis of the spectral data showed that the standard deviation in signal intensity for an analyte peak was less than approximately 5% over 3 h. The production of stable electrosprays directly from microchip IEF device represents a step towards easily fabricated microanalytical devices. Microchannel IEF separations of protein mixtures were demonstrated for uncoated polycarbonate microchips. Direct microchannel IEF-ESI-MS was demonstrated using the microfabricated chip with an ion-trap mass spectrometer for characterization of protein mixtures.

Rapid Diagnosis of Herpes Simplex Encephalitis Using Microchip Electrophoresis of PCR Products

Background: Herpes simplex virus (HSV) is the most common cause of acute sporadic encephalitis in the United States. PCR of DNA extracted from cerebrospinal fluid (CSF) allows for reliable diagnosis of herpes simplex encephalitis (HSE). A faster turnaround time for HSE testing would improve patient management and lead to better outcomes. The aims of this study, therefore, were to develop a microchip-based electrophoretic method for rapid detection of HSV PCR products, and to compare the performance characteristics of liquid hybridization/gel retardation as an established clinical PCR product detection method with the new microchip-based method.

Methods: The study examined archival DNA from 33 selected CSF specimens submitted for HSV PCR testing to the clinical laboratory. One aliquot of the HSV PCR product was analyzed by liquid hybridization/gel retardation analysis, and a second PCR aliquot was analyzed directly with a microchip capillary electrophoresis system using an instrument built in-house. PCR samples were introduced directly into the microchip without a desalting step by use of a novel fluidic interface. Channel surfaces on the glass microchip were silanized, followed by derivatization with polyvinylpyrrolidone.

Results: Of the 33 CSF specimens tested by liquid hybridization analysis of HSV PCR products, 10 tested positive for HSV DNA, 2 gave a weakly positive result, and 21 tested negative. Total analysis time for detection of HSV DNA by gel retardation assay was 18 h. Microchip electrophoresis provided identical results in <110 s/sample, achieving 100% sensitivity and specificity compared with the established method.

Conclusions: Microchip-based electrophoresis can rapidly and accurately separate HSV PCR products, giving results identical to those obtained by liquid hybridization but with substantially decreased turnaround time. Clinical implementation of the new method will help to improve patient management and outcomes.

Plastic Microchip Electrophoresis for Analysis of PCR Products of Hepatitis C Virus

Background: Electrophoresis on polymeric rather than glass microstructures is a promising separation method for analytical chemistry. Assays on such devices need to be explored to allow assessment of their utility for the clinical laboratory.

Methods: We compared capillary and plastic microchip electrophoresis for clinical post-PCR analysis of hepatitis C virus (HCV). For capillary electrophoresis (CE), we used a separation medium composed of 10 g/L hydroxypropyl methyl cellulose in Tris-borate-EDTA buffer and 10 μmol/L intercalating dye. For microchip electrophoresis, the HCV assay established on the fused silica tubing was transferred to the untreated polymethylmethacrylate microchip with minimum modifications.

Results: CE resolved the 145-bp amplicon of HCV in 15 min. The confidence interval of the migration time was <3.2%. The same HCV amplicon was resolved by microchip electrophoresis in <1.5 min with the confidence interval of the migration time <1.3%.

Conclusion: The polymer microchip, with advantages that include fast processing time, simple operation, and disposable use, holds great potential for clinical analysis.

Molecular Diagnostics on Microfabricated Electrophoretic Devices: From Slab Gel- to Capillary- to Microchip-based Assays for T- and B-Cell Lymphoproliferative Disorders

Background: Current methods for molecular-based diagnosis of disease rely heavily on modern molecular biology techniques for interrogating the genome for aberrant DNA sequences. These techniques typically include amplification of the target DNA sequences followed by separation of the amplified fragments by slab gel electrophoresis. As a result of the labor-intensive, time-consuming nature of slab gel electrophoresis, alternative electrophoretic formats have been developed in the form of capillary electrophoresis and, more recently, multichannel microchip electrophoresis.

Methods: Capillary electrophoresis was explored as an alternative to slab gel electrophoresis for the analysis of PCR-amplified products indicative of T- and B-cell malignancies as a means of defining the elements for silica microchip-based diagnosis. Capillary-based separations were replicated on electrophoretic microchips.

Results: The microchip-based electrophoretic separation effectively resolved PCR-amplified fragments from the variable region of the T-cell receptor-γ gene (150–250 bp range) and the immunoglobulin heavy chain gene (80–140 bp range), yielding diagnostically relevant information regarding the presence of clonal DNA populations. Although hydroxyethylcellulose provided adequate separation power, the need for a coated microchannel for effective resolution necessitated additional preparative steps. In addition, preliminary data are shown indicating that polyvinylpyrrolidone may provide an adequate matrix without the need for microchannel coating.

Conclusions: Separation of B- and T-cell gene rearrangement PCR products on microchips provides diagnostic information in dramatically reduced time (160 s vs 2.5 h) with no loss of diagnostic capacity when compared with current methodologies. As illustrated, this technology and methodology holds great potential for extrapolation to the abundance of similar molecular biology-based techniques.

Microfabricated polymer devices for automated sample delivery of peptides for analysis by electrospray ionization tandem mass spectrometry

Delivery of proteins and peptides to electrospray ionization mass spectrometers (ESI-MS) has been demonstrated using glass and quartz microfabricated devices. This paper reports the construction and use of poly(dimethylsiloxane) (PDMS) microfabricated soft polymer devices with mass spectrometry for protein analysis. The PDMS devices were fabricated using replica molding against a patterned photoresist generated by photolithographic techniques. The PDMS devices were connected to the mass spectrometer via a derivatized transfer capillary and samples were transferred by electroosmotic pumping. The formulation of PDMS was optimized for compatibility with ESI, and the devices were tested for performance. The practical application of PDMS devices was demonstrated by the identification of rat serum albumin separated by 2-D gel electrophoresis. Extended contact of the sample with the surface of the PDMS device did not significantly affect the sample analysis, and the limit of detection for samples run on a PDMS device was comparable to the limit of detection achieved on glass devices. This study suggests that PDMS devices fabricated using replica molding are compatible with ESI-MS. This will potentially lead to the construction of inexpensive microfabricated devices with complex designs and advanced functionalities.

Multiple sample PCR amplification and electrophoretic analysis on a microchip

Polymerase chain reactions (PCRs) were carried out on as many as four DNA samples at a time on a microchip device. The PCR products were then analyzed, either individually or together on the same device, by microchip gel electrophoresis. A standard PCR protocol was used to amplify 199- and 500-base pair (bp) regions of bacteriophage lambda DNA and 346- and 410-bp regions of E. coli genomic and plasmid DNAs, respectively. Thermal lysis of the bacteria was integrated into the PCR cycle. A product sizing medium, poly(dimethylacrylamide), and an intercalating dye for fluorescence detection were used in the electrophoretic analysis of the products. PCR product sizes were determined by coelectrophoresis with marker DNA.

Rapid Prototyping of Microfluidic Systems in Poly(dimethylsiloxane)

This paper describes a procedure that makes it possible to design and fabricate (including sealing) microfluidic systems in an elastomeric material [Formula: see text] poly(dimethylsiloxane) (PDMS) [Formula: see text] in less than 24 h. A network of microfluidic channels (with width >20 μm) is designed in a CAD program. This design is converted into a transparency by a high-resolution printer; this transparency is used as a mask in photolithography to create a master in positive relief photoresist. PDMS cast against the master yields a polymeric replica containing a network of channels. The surface of this replica, and that of a flat slab of PDMS, are oxidized in an oxygen plasma. These oxidized surfaces seal tightly and irreversibly when brought into conformal contact. Oxidized PDMS also seals irreversibly to other materials used in microfluidic systems, such as glass, silicon, silicon oxide, and oxidized polystyrene; a number of substrates for devices are, therefore, practical options. Oxidation of the PDMS has the additional advantage that it yields channels whose walls are negatively charged when in contact with neutral and basic aqueous solutions; these channels support electroosmotic pumping and can be filled easily with liquids with high surface energies (especially water). The performance of microfluidic systems prepared using this rapid prototyping technique has been evaluated by fabricating a miniaturized capillary electrophoresis system. Amino acids, charge ladders of positively and negatively charged proteins, and DNA fragments were separated in aqueous solutions with this system with resolution comparable to that obtained using fused silica capillaries.

Preparation and hybridization analysis of DNA/RNA from E. coli on microfabricated bioelectronic chips

Escherichia coli were separated from a mixture containing human blood cells by means of dielectrophoresis and then subjected to electronic lysis followed by proteolytic digestion on a single microfabricated bioelectronic chip. An alternating current electric field was used to direct the bacteria to 25 microlocations above individually addressable platinum microelectrodes. The platinum electrodes were 80 microns in diameter and had center-to-center spacings of 200 microns. After the isolation, the bacteria were lysed by a series of high-voltage pulses. The lysate contained a spectrum of nucleic acids including RNA, plasmid DNA, and genomic DNA. The lysate was further examined by electronically enhanced hybridization on separate bioelectronic chips. Dielectrophoretic separation of cells followed by electronic lysis and digestion on an electronically active chip may have potential as a sample preparation process for chip-based hybridization assays in an integrated DNA/RNA analysis system.