Multiple sample PCR amplification and electrophoretic analysis on a microchip

Spatiotemporal Characteristics of Intercellular Calcium Wave Communication in Micropatterned Assemblies of Single Cells

Micropatterned substrates offer a unique possibility to define and control spatial organization of biological cells at the microscale, which greatly facilitates investigations of the cell-to-cell communication in vitro. Here, we developed a simple micropatterning strategy to resolve various spatiotemporal characteristics of intercellular calcium wave (ICW) communication among isolated BV-2 microglial cells. By using a single-ring assembly, we found that the direction of the initial transmitter secretion was strongly correlated with the site of the cell at which the mechanical stimulus triggering the ICWs was imposed. By using multiring assemblies, we observed that the response ratio of the same outmost cells 160 μm away from the center increased from 0% in the single-ring assembly to 9.6% in the four-ring assembly. This revealed that cells located in the interring acted as regenerative amplifiers for the ICWs generated by the central cell. By using a special oval-type micropattern, we found that calcium mobilization in lamellipodia of a fusiform BV-2 microglia cell occurred 2.9 times faster than that in the middle part of the cell, demonstrating a higher region-specific sensitivity of lamellipodia to the transmitter. Taken together, our micropatterning strategy opened up new experimental prospects to study ICWs and revealed novel spatiotemporal characteristics of ICW communication including stimulation site-dependent secretion, regenerative propagation, and region-specific cell sensitivity.

The Incredibly Shrinking Laboratory Reactions, Separations and Detections

Microfluidic systems are developing in application and importance in many aspects of chemistry. This short review aims to provide a simple introduction to some of the concepts and instrumentation involved in this field. In particular, a number of systems for reactions, detections and analysis that have arisen from the research of our group are illustrated.

Charging YOYO-1 on capillary wall for online DNA intercalation and integrating this approach with multiplex PCR and bare narrow capillary-hydrodynamic chromatography for online DNA analysis

Multiplex polymerase chain reaction (PCR) has been widely utilized for high-throughput pathogen identification. Often, a dye is used to intercalate the amplified DNA fragments, and identifications of the pathogens are carried out by DNA melting curve analysis or gel electrophoresis. Integrating DNA amplification and identification is a logic path toward maximizing the benefit of multiplex PCR. Although PCR and gel electrophoresis have been integrated, replenishing the gels after each run is tedious and time-consuming. In this technical note, we develop an approach to address this issue. We perform multiplex PCR inside a capillary, transfer the amplified fragments to a bare narrow capillary, and measure their lengths online using bare narrow capillary–hydrodynamic chromatography (BaNC-HDC), a new technique recently developed in our laboratory for free-solution DNA separation. To intercalate the DNA with YOYO-1 (a fluorescent dye) for BaNC-HDC, we flush the capillary column with a YOYO-1 solution; positively charged YOYO-1 is adsorbed (or charged) onto the negatively charged capillary wall. As DNA molecules are driven down the column for separation, they react with the YOYO-1 stored on the capillary wall and are online-intercalated with the dye. With a single YOYO-1 charging, the column can be used for more than 40 runs, although the fluorescence signal intensities of the DNA peaks decrease gradually. Although the dye-DNA intercalation occurs during the separation, it does not affect the retention times, separation efficiencies, or resolutions.

Microfluidic Paper-Based Analytical Devices (μPADs) and Micro Total Analysis Systems (μTAS): Development, Applications and Future Trends

Microfluidic paper-based analytical devices and micro total analysis systems are relatively new group of analytical tools, capable of analyzing complex biochemical samples containing macromolecules, proteins, nucleic acids, toxins, cells or pathogens. Within one analytical run, fluidic manipulations like transportation, sorting, mixing or separation are available. Recently, microfluidic devices are a subject of extensive research, mostly for fast and non-expensive biochemical analysis but also for screening of medical samples and forensic diagnostics. They are used for neurotransmitter detection, cancer diagnosis and treatment, cell and tissue culture growth and amplification, drug discovery and determination, detection and identification of microorganisms. This review summarizes development history, basic fabrication methods, applications and also future development trends for production of such devices.

Quantitative analysis of molecular absorption into PDMS microfluidic channels

Microfluidic devices fabricated using poly(dimethylsiloxane) (PDMS) polymer are routinely used for in vitro cell culture for a wide range of cellular assays. These assays typically involve the incubation of cultured cells with a drug molecule or a fluorescent marker while monitoring a cellular response. The accuracy of these assays depends on achieving a consistent and reproducible concentration of solute molecules in solution. However, hydrophobic therapeutic and fluorescent molecules tend to diffuse into the PDMS walls of the microfluidic devices, which reduce their concentration in solution and consequently affect the accuracy and reliability of these assays. In this paper, we quantitatively investigate the relationship between the partition coefficient (log P) of a series of markers routinely used in in vitro cellular assays including [3H]-dexamethasone, [3H]-diazepam, [14C]-mannitol, [3H]-phenytoin, and rhodamine 6G and their absorption into PDMS microfluidic channels. Our results show that the absorption of a given solute into PDMS depends on the hydrophilic/hydrophobic balance defined by its log P value. Specifically, results demonstrate that molecules with log P less than 2.47 exhibit minimal absorption (<10%) into PDMS channels whereas molecules with log P larger than 2.62 exhibit extensive absorption (>90%) into PDMS channels. Further investigations showed that TiO(2) and glass coatings of PDMS channels reduced the absorption of hydrophobic molecules (log P > 2.62) by 2- and 4.5-folds, respectively.

On-line cell lysis of bacteria and its spores using a microfluidic biochip

Optimal detection of pathogens by molecular methods in water samples depends on the ability to extract DNA rapidly and efficiently. In this study, an innovative method was developed using a microfluidic biochip, produced by microelectrochemical system technology, and capable of performing online cell lysis and DNA extraction during a continuous flow process. On-chip cell lysis based on chemical/physical methods was performed by employing a sufficient blend of water with the lysing buffer. The efficiency of lysis with microfluidic biochip was compared with thermal lysis in Eppendorf tubes and with two commercial DNA extraction kits: Power Water DNA isolation kit and ForensicGEM Saliva isolation kit in parallel tests. Two lysing buffers containing 1% Triton X-100 or 5% Chelex were assessed for their lysis effectiveness on a microfluidic biochip. SYBR Green real-time PCR analysis revealed that cell lysis on a microfluidic biochip using 5% Chelex buffer provided better or comparable recovery of DNA than commercial isolation kits. The system yielded better results for Gram-positive bacteria than for Gram-negative bacteria and spores of Gram-positive bacteria, within the limits of detection at 103 CFU/ml. During the continuous flow process in the system, rapid cells lysis with PCR-amplifiable genomic DNA were achieved within 20 minutes.

Microfluidic reactors for diagnostics applications

Diagnostic assays are an important part of health care, both in the clinic and in research laboratories. In addition to improving treatments and clinical outcomes, rapid and reliable diagnostics help track disease epidemiology, curb infectious outbreaks, and further the understanding of chronic illness. Disease markers such as antigens, RNA, and DNA are present at low concentrations in biological samples, such that the majority of diagnostic assays rely on an amplification reaction before detection is possible. Ideally, these amplification reactions would be sensitive, specific, inexpensive, rapid, integrated, and automated. Microfluidic technology currently in development offers many advantages over conventional benchtop reactions that help achieve these goals. The small reaction volumes and energy consumption make reactions cheaper and more efficient in a microfluidic reactor. Additionally, the channel architecture could be designed to perform multiple tests or experimental steps on one integrated, automated platform. This review explores the current research on microfluidic reactors designed to aid diagnostic applications, covering a broad spectrum of amplification techniques and designs.

Electrical detection of dsDNA and polymerase chain reaction amplification

Food-borne pathogens and food safety-related outbreaks have come to the forefront over recent years. Estimates on the annual cost of sicknesses, hospitalizations, and deaths run into the billions of dollars. There is a large body of research on detection of food-borne pathogens; however, the widely accepted current systems are limited by costly reagents, lengthy time to completion, and expensive equipment. Our aim is to develop a label-free method for determining a change in DNA concentration after a PCR assay. We first used impedance spectroscopy to characterize the change in concentration of purified DNA in deionized water within a microfluidic biochip. To adequately measure the change in DNA concentration in PCR solution, it was necessary to go through a purification and precipitation step to minimize the effects of primers, PCR reagents, and excess salts. It was then shown that the purification and precipitation of the fully amplified PCR reaction showed results similar to the control tests performed with DNA in deionized water. We believe that this work has brought label free electrical biosensors for PCR amplification one step closer to reality.

Development of a lab-on-a-chip device for diagnosis of plant pathogens

A lab-on-a-chip system for rapid nucleic acid-based analysis was developed that can be applied for diagnosis of selected Phytophthora species as a first example for use in plant pathology. All necessary polymerase chain reaction process (PCR) and hybridization steps can be performed consecutively within a single chip consisting of two components, an inflexible and a flexible one, with integrated microchannels and microchambers. Data from the microarray is collected from a simple electrical measurement that is based on elementary silver deposition by enzymatical catalyzation. Temperatures in the PCR and in the hybridization zone are managed by two independent Peltier elements. The chip will be integrated in a compact portable system with a pump and power supply for use on site. The specificity of the lab-on-a-chip system could be demonstrated for the tested five Phytophthora species. The two Pythium species gave signals below the threshold. The results of the electrical detection of the microarray correspond to the values obtained with the control method (optical grey scale analysis).

Simply and reliably integrating micro heaters/sensors in a monolithic PCR-CE microfluidic genetic analysis system

A novel fabrication process was presented to construct a monolithic integrated PCR-CE microfluidic DNA analysis system as a step toward building a total genetic analysis microsystem. Microfabricated Titanium/Platinum (Ti/Pt) heaters and resistance temperature detectors (RTDs) were integrated on the backside of a bonded glass chip to provide good thermal transfer and precise temperature detection for the drilled PCR-wells. This heater/RTD integration procedure was simple and reliable, and the resulting metal layer can be easily renewed when the Ti/Pt layer was damaged in later use or novel heater/RTD design was desired. A straightforward "RTD-calibration" method was employed to optimize the chip-based thermal cycling conditions. This method was convenient and rapid, comparing with a conventional RTD-calibration/temperature adjustment method. The highest ramping rates of 14 degrees C/s for heating and 5 degrees C/s for cooling in a 3-microL reaction volume allow 30 complete PCR cycles in about 33 min. After effectively passivating the PCR-well surface, successful lambda-phage DNA amplifications were achieved using a two- or three-temperature cycling protocol. The functionality and performance of the integrated microsystem were demonstrated by successful amplification and subsequent on-line separation/sizing of lambda-phage DNA. A rapid assay for Hepatitis B virus, one of the major human pathogens, was performed in less than 45 min, demonstrating that the developed PCR-CE microsystem was capable of performing automatic and high-speed genetic analysis.

CE-based detection of methicillin-resistant Staphylococcus aureus

Rapid and sensitive detection of methicillin-resistant Staphylococcus aureus is crucial for effective treatment and control of clinical infections caused by this bacterium. The goal of this study is to develop a CE-based detection method for multiplexed identification of a femA sequence specific for S. aureus and a unique mecA sequence encoding methicillin resistance. Blood samples spiked with known concentrations of bacteria were used for testing. Crude cell lysates were prepared by treating the spiked blood samples with DNazol Direct reagent and used as the template for isothermal amplification of mecA and femA genes. The amplified gene products then underwent a cycling probe reaction (CPR)-based assay to generate a short fluorophore-labeled oligonucleotide for detection in a CZE-LIF system. The assay enables a gene-specific fluorophore-labeled DNA-RNA-DNA chimeric probe to hybridize with complementary target in the presence of RNase H enzyme. The RNase H enzyme specifically cleaves probe RNA residues of the duplex, releasing a fluorophore fragment for detection and the target for recycling and hybridization with another chimeric probe. Intact and cleaved probe fragments were separated and detected using a CZE-LIF system. The limit of detection for isothermal amplification and CPR-CZE-LIF was approximately 10(4) colony-forming units of bacteria/mL of blood. This method accurately detects methicillin-resistant S. aureus within 3 h.

Simplified transient isotachophoresis/capillary gel electrophoresis method for highly sensitive analysis of polymerase chain reaction samples on a microchip with laser-induced fluorescence detection

We present a sensitive, simple and robust on-chip transient isotachophoresis/capillary gel electrophoresis (tITP/CGE) method for the analysis of polymerase chain reaction (PCR) samples. Using chloride ions in the PCR buffer and N-2-hydroxyethylpiperazine-N'-2-ethanesulfonic acid (HEPES) in the background electrolyte, respectively, as the leading and terminating electrolytes, the tITP preconcentration was coupled with CGE separation with double-T shaped channel network. The tITP/CGE separation was carried out with a single running buffer. The separation process involved only two steps that were performed continuously with the sequential switching of four voltage outputs. The tITP/CGE method showed an analysis time and a separation efficiency comparable to those of standard CGE, while the signal intensity was enhanced by factors of over 20. The limit of detection of the chip-based tITP/CGE method was estimated to be 1.1 ng/mL of DNA in 1x PCR buffer using confocal fluorescence detection following 473 nm laser excitation.

Electrophoretic microfluidic devices for mutation detection in clinical diagnostics

BACKGROUND

In an era of growing interest in personalized medicine - where ubiquitous patient genotyping holds unprecedented clinical utility - rapid, sensitive and low-cost methodologies will be required for the detection of genetic variants correlative with disease. Electrophoretic microfluidic devices have emerged as a promising platform for such analyses, inherently offering faster analysis, excellent reagent economy, a small laboratory footprint and potentially seamless integration of multiple analytical steps.

OBJECTIVE

Although glass and polymeric microchips have recently been developed for a wide variety of medical applications, this review focuses on their application to the detection of clinically relevant genomic DNA mutations and polymorphisms.

METHOD

Mutation analysis techniques, including direct gene sizing, enzyme-based assays, heteroduplex analysis, single-strand conformational polymorphism analysis, and multiplex, allele-specific and methylation-specific PCR are included.

CONCLUSION

Further development of 'lab-on-a-chip' or 'micro total analysis system' technologies ultimately aims to streamline and miniaturize the entire genetic analysis process, enabling rapid, point-of-care analysis for molecular diagnostics.

Chemical cytometry on microfluidic chips

Chemical cytometry, referring to the analysis of the chemical contents in individual cells, has been in intensive study since Kennedy's first work that was published in Science. The early researches relied on fine-tip capillaries to capture the cells and do the analyses, which were lab- and time-intensive and required high skills of operation. The emergence of microfluidics has greatly spurred this research field and a great number of research papers have been published in the last decades. Highly integrated microfluidic chips have been developed to capture multiple single cells, lyse them, perform chemical reactions in enclosed microchambers, separate contents by CE and detect chemical species in individual cells. This review focuses on the development of relevant components and their integration for on-chip chemical cytometry.

Study of a novel sample injection method (floating electrokinetic supercharging) for high-performance microchip electrophoresis of DNA fragments

Aiming to achieve high-performance analysis of DNA fragments using microchip electrophoresis, we developed a novel sample injection method, which was given the name of floating electrokinetic supercharging (FEKS). In the method, electrokinetic injection (EKI) and ITP preconcentration of samples was performed in a separation channel, connecting two reservoir ports (P3 and P4) on a cross-geometry microchip. At these two stages, side channels, crossing the separation channel, and their ports (P1 and P2) were electrically floated. After the ITP-stacked zones passed the cross-part, they were eluted for detection by using leading ions from P1 and P2 that enabled electrophoresis mode changing rapidly from ITP to zone electrophoresis (ZE). Possible sample leakage at the cross-part toward P1 and P2 was studied in detail on the basis of computer simulation using a CFD-ACE+ software and real experiments, through which it was validated that the analyte recovery to the separation channel was almost complete. The FEKS method successfully contributed to higher resolution and shorter analysis time of DNA fragments on the cross-microchip owing to more rapid switching from ITP status to ZE separation in comparison with our previous EKS procedure realized on a single-channel microchip. Without any degradation of resolution, the achieved LODs were on average ten times better than using conventional pinched injection.

Real-time forensic DNA analysis at a crime scene using a portable microchip analyzer

An integrated lab-on-a-chip system has been developed and successfully utilized for real-time forensic short tandem repeat (STR) analysis. The microdevice comprises a 160-nL polymerase chain reaction reactor with an on-chip heater and a temperature sensor for thermal cycling, microvalves for fluidic manipulation, a co-injector for sizing standard injection, and a 7-cm-long separation channel for capillary electrophoretic analysis. A 9-plex autosomal STR typing system consisting of amelogenin and eight combined DNA index system (CODIS) core STR loci has been constructed and optimized for this real-time human identification study. Reproducible STR profiles of control DNA samples are obtained in 2h and 30min with <or=0.8bp allele typing accuracy. The minimal amount of DNA required for a complete DNA profile is 100 copies. To critically evaluate the capabilities of our portable microsystem as well as its compatibility with crime scene investigation processes, real-time STR analyses were carried out at a mock crime scene prepared by the Palm Beach County Sheriff's Office (PBSO). Blood stain sample collection, DNA extraction, and STR analyses on the portable microsystem were conducted in the field, and a successful "mock" CODIS hit was generated on the suspect's sample within 6h. This demonstration of on-site STR analysis establishes the feasibility of real-time DNA typing to identify the contributor of probative biological evidence at a crime scene and for real-time human identification.

Microfabricated valveless devices for thermal bioreactions based on diffusion-limited evaporation

Microfluidic devices that reduce evaporative loss during thermal bioreactions such as PCR without microvalves have been developed by relying on the principle of diffusion-limited evaporation. Both theoretical and experimental results demonstrate that the sample evaporative loss can be reduced by more than 20 times using long narrow diffusion channels on both sides of the reaction region. In order to further suppress the evaporation, the driving force for liquid evaporation is reduced by two additional techniques: decreasing the interfacial temperature using thermal isolation and reducing the vapor concentration gradient by replenishing water vapor in the diffusion channels. Both thermal isolation and vapor replenishment techniques can limit the sample evaporative loss to approximately 1% of the reaction content.

Total nucleic acid analysis integrated on microfluidic devices

The design and integration of microfluidic devices for on-chip amplification of nucleic acids from various biological samples has undergone extensive development. The actual benefit to the biological community is far from clear, with a growing, but limited, number of application successes in terms of a full on-chip integrated analysis. Several advances have been made, particularly with the integration of amplification and detection, where amplification is most often the polymerase chain reaction. Full integration including sample preparation remains a major obstacle for achieving a quantitative analysis. We review the recently described devices incorporating in vitro gene amplification and compare devices relative to each other and in terms of fully achieving a miniaturised total analysis system (micro-TAS).

Microfluidic chips for detecting the t(4;14) translocation and monitoring disease during treatment using reverse transcriptase-polymerase chain reaction analysis of IgH-MMSET hybrid transcripts

Diagnosis platforms incorporating low-cost microfluidic chips enable sensitive, rapid, and accurate genetic analysis that could facilitate customized therapies tailored to match the vulnerabilities of any types of cancer. Using ex vivo cancer cells, we have detected the unique molecular signature and a chromosomal translocation in multiple myeloma. Multiple myeloma is characterized by IgH rearrangements and translocations that enable unequivocal identification of malignant cells, detected here with integrated microfluidic chips incorporating genetic amplification via reverse transcriptase-polymerase chain reaction and capillary electrophoresis. On microfluidic chips, we demonstrated accurate and versatile detection of molecular signatures in individual cancer cells, with value for monitoring response to therapy, detecting residual cancer cells that mediate relapse, and evaluating prognosis. Thus, testing for two clinically important molecular biomarkers, the IgH VDJ signature and hybrid transcripts signaling the t(4;14) chro-mosomal translocation, with predictive value in diagnosis, treatment decisions, and monitoring has been efficiently implemented on a miniaturized microfluidic system.

Forensic DNA Analysis on Microfluidic Devices: A Review

The advent of microfluidic technology for genetic analysis has begun to impact forensic science. Recent advances in microfluidic separation of short-tandem-repeat (STR) fragments has provided unprecedented potential for improving speed and efficiency of DNA typing. In addition, the analytical processes associated with sample preparation--which include cell sorting, DNA extraction, DNA quantitation, and DNA amplification--can all be integrated with the STR separation in a seamless manner. The current state of these microfluidic methods as well as their advantages and potential shortcomings are detailed. Recent advances in microfluidic device technology, as they pertain to forensic DNA typing, are discussed with a focus on the forensic community.

Automated screening using microfluidic chip-based PCR and product detection to assess risk of BK virus-associated nephropathy in renal transplant recipients

The cost-effective detection of viral particles in bodily fluids could enable more effective responses to viral outbreaks, whether isolated clinical cases, or influenza epidemics. In renal transplant recipients, complications arising from high levels of BK virus can lead to graft dysfunction, graft loss, and/or reduced patient survival. We describe a microfluidic system for the sensitive analysis of BK virus (viral load) in unprocessed urine samples that are applied directly onto the chip, thus avoiding labor-intensive processing and sources of inter-assay variability. Integration of small volume genetic amplification (PCR) and electrophoretic analysis detects as few as 1-2 viral copies, distinguishes between high, medium and low levels of virus and reliably identifies viral loads requiring clinical intervention. As a first step to wider application in the clinic and in the field, the present work presents an entirely microchip-based system, validated against conventional clinical methods using clinical samples.

PCR in Integrated Microfluidic Systems

Miniaturized integrated DNA analysis systems offer the potential to provide unprecedented advances in cost and speed relative to current benchtop-scale instrumentation by allowing rapid bioanalysis assays to be performed in a portable self contained device format that can be inexpensively mass-produced. The polymerase chain reaction (PCR) has been a natural focus of many of these miniaturization efforts, owing to its capability to efficiently replicate target regions of interest from small quantities template DNA. Scale-down of PCR has proven to be particularly challenging, however, due to an unfavorable combination of relatively severe temperature extremes (resulting in the need to repeatedly heat minute aqueous sample volumes to temperatures in the vicinity of 95°C with minimal evaporation) and high surface area to volume conditions imposed by nanoliter reactor geometries (often leading to inhibition of the reaction by nonspecific adsorption of reagents at the reactor walls). Despite these daunting challenges, considerable progress has been made in the development of microfluidic devices capable of performing increasingly sophisticated PCR-based bioassays. This chapter reviews the progress that has been made to date and assesses the outlook for future advances.

Solution-phase DNA mutation scanning and SNP genotyping by nanoliter melting analysis

Solution-phase, DNA melting analysis for heterozygote scanning and single nucleotide polymorphism (SNP) genotyping was performed in 10 nl volumes on a custom microchip. Human genomic DNA was PCR amplified in the presence of the saturating fluorescent dye, LCGreen Plus, and placed within microfluidic channels that were created between two glass slides. The microchip was heated at 0.1 degrees C/s with a Peltier device and viewed with an inverted fluorescence microscope modified for photomulitiplier tube detection. The melting data was normalized and the negative first derivative plotted against temperature. Mutation scanning for heterozygotes was easily performed by comparing the shape of the melting curve to homozygous standards. Genotyping of homozygotes by melting temperature (T(m)) required absolute temperature comparisons. Mutation scanning of ATM exon 17 and CFTR exon 10 identified single base change heterozygotes in 84 and 201 base-pair (bp) products, respectively. All genotypes at HFE C282Y were distinguished by simple melting analysis of a 40-bp fragment. Sequential analysis of the same sample on the gold-standard, commercial high-resolution melting instrument HR-1, followed by melting in a 10 nl reaction chamber, produced similar results. DNA melting analysis requires only minutes after PCR and is a simple method for genotyping and scanning that can be reduced to nanoliter volumes. Microscale systems for performing DNA melting reduce the reagents/DNA template required with a promise for high throughput analysis in a closed chamber without risk of contamination.

Integration of nanoporous membranes for sample filtration/preconcentration in microchip electrophoresis

Microfluidic devices integrating membrane-based sample preparation with electrophoretic separation are demonstrated. These multilayer devices consist of 10 nm pore diameter membranes sandwiched between two layers of PDMS substrates with embedded microchannels. Because of the membrane isolation, material exchange between two fluidic layers can be precisely controlled by applied voltages. More importantly, since only small molecules can pass through the nanopores, the integrated membrane can serve as a filter or a concentrator prior to microchip electrophoresis under different design and operation modes. As a filter, they can be used for separation and selective injection of small analytes from sample matrix. This has been effectively applied in rapid determination of reduced glutathione in human plasma and red blood cells without any off-chip deproteinization procedure. Alternatively, in the concentrator mode, they can be used for online purification and preconcentration of macromolecules, which was illustrated by removing primers and preconcentrating the product DNA from a PCR product mixture.

What is the future of electrophoresis in large-scale genomic sequencing?

Although a finished human genome reference sequence is now available, the ability to sequence large, complex genomes remains critically important for researchers in the biological sciences, and in particular, continued human genomic sequence determination will ultimately help to realize the promise of medical care tailored to an individual's unique genetic identity. Many new technologies are being developed to decrease the costs and to dramatically increase the data acquisition rate of such sequencing projects. These new sequencing approaches include Sanger reaction-based technologies that have electrophoresis as the final separation step as well as those that use completely novel, nonelectrophoretic methods to generate sequence data. In this review, we discuss the various advances in sequencing technologies and evaluate the current limitations of novel methods that currently preclude their complete acceptance in large-scale sequencing projects. Our primary goal is to analyze and predict the continuing role of electrophoresis in large-scale DNA sequencing, both in the near and longer term.

On-chip pressure injection for integration of infrared-mediated DNA amplification with electrophoretic separation

Poly(dimethylsiloxane) (PDMS) membrane valves were utilized for diaphragm pumping on a PDMS-glass hybrid microdevice in order to couple infrared-mediated DNA amplification with electrophoretic separation of the products in a single device. Specific amplification products created during non-contact, infrared (IR) mediated polymerase chain reaction (PCR) were injected via chip-based diaphragm pumping into an electrophoretic separation channel. Channel dimensions were designed for injection plug shaping via preferential flow paths, which aided in minimizing the plug widths. Unbiased injection of sample could be achieved in as little as 190 ms, decreasing the time required with electrokinetic injection by two orders of magnitude. Additionally, sample stacking was promoted using laminar or biased-laminar loading to co-inject either water or low ionic strength DNA marker solution along with the PCR-amplified sample. Complete baseline resolution (Res = 2.11) of the 80- and 102-bp fragments of pUC-18 DNA marker solution was achieved, with partially resolved 257- and 267-bp fragments (Res = 0.56), in a separation channel having an effective length of only 3.0 cm. This resolution was deemed adequate for many PCR amplicon separations, with the added advantage of short separation time-typically complete in <120 s. Decreasing the amount of glass surrounding the PCR chamber reduced the DNA amplification time, yielding a further enhancement in analysis speed, with heating and cooling rates as high as 13.4 and -6.4 degrees C s(-1), respectively. With the time requirements greatly reduced for each step, it was possible to seamlessly couple IR-mediated amplification, sample injection, and separation/detection of a 278-bp fragment from the invA gene of <1000 starting copies of Salmonella typhimurium DNA in approximately 12 min on a single device, representing the fastest PCR-ME integration achieved to date.

Low Viscous Separation Media for Genomics and Proteomics Analysis on Microchip Electrophoresis System

Microchip electrophoresis has widely grown during the past few years, and it has showed a significant result as a strong separation tool for genomic as well as proteomic researches. To enhance and expand the role of microchip electrophoresis, several studies have been proposed especially for the low viscous separation media, which is an important factor for the success of microchip with its narrow separation channels. In this paper we show an overview for the done researches in the field of low viscous media developed for the use in microchip electrophoresis. For genomic separation studies polyhydroxy additives have been used enhance the separation of DNA at low polymer concentration of HPMC (Hydroxypropylmethyl cellulose) which could keep the viscosity low. Mixtures of poly(ethylene oxide) as well as Hydroxyporpyl cellulose have been successfully introduced for chip separation. Furthermore high molecular mass polyacrylamides at low concentrations have been studied for DNA separation. A mixture of polymer nanoparticle with conventional polymers could show a better resolution for DNA at low concentration of the polymer. For the proteomic field isoelectric focusing on chip has been well overviewed since it is the most viscous separation media which is well used for the protein separation. The different types of isoelectric focusing such as the ampholyte-free type, the thermal type as well as the ampholyte-depended type have been introduced in this paper. Isoelectric focusing on chip with its combination with sodium dodecyl sulfate (SDS) page or free solution could give a better separation. Several application for this low viscous separation medias for either genomic or proteomic could clearly show the importance of this field.

PCR microfluidic devices for DNA amplification

The miniaturization of biological and chemical analytical devices by micro-electro-mechanical-systems (MEMS) technology has posed a vital influence on such fields as medical diagnostics, microbial detection and other bio-analysis. Among many miniaturized analytical devices, the polymerase chain reaction (PCR) microchip/microdevices are studied extensively, and thus great progress has been made on aspects of on-chip micromachining (fabrication, bonding and sealing), choice of substrate materials, surface chemistry and architecture of reaction vessel, handling of necessary sample fluid, controlling of three or two-step temperature thermocycling, detection of amplified nucleic acid products, integration with other analytical functional units such as sample preparation, capillary electrophoresis (CE), DNA microarray hybridization, etc. However, little has been done on the review of above-mentioned facets of the PCR microchips/microdevices including the two formats of flow-through and stationary chamber in spite of several earlier reviews [Zorbas, H. Miniature continuous-flow polymerase chain reaction: a breakthrough? Angew Chem Int Ed 1999; 38 (8):1055-1058; Krishnan, M., Namasivayam, V., Lin, R., Pal, R., Burns, M.A. Microfabricated reaction and separation systems. Curr Opin Biotechnol 2001; 12:92-98; Schneegabeta, I., Köhler, J.M. Flow-through polymerase chain reactions in chip themocyclers. Rev Mol Biotechnol 2001; 82:101-121; deMello, A.J. DNA amplification: does 'small' really mean 'efficient'? Lab Chip 2001; 1: 24N-29N; Mariella, Jr. R. MEMS for bio-assays. Biomed Microdevices 2002; 4 (2):77-87; deMello AJ. Microfluidics: DNA amplification moves on. Nature 2003; 422:28-29; Kricka, L.J., Wilding, P. Microchip PCR. Anal BioAnal Chem 2003; 377:820-825]. In this review, we survey the advances of the above aspects among the PCR microfluidic devices in detail. Finally, we also illuminate the potential and practical applications of PCR microfluidics to some fields such as microbial detection and disease diagnosis, based on the DNA/RNA templates used in PCR microfluidics. It is noted, especially, that this review is to help a novice in the field of on-chip PCR amplification to more easily find the original papers, because this review covers almost all of the papers related to on-chip PCR microfluidics.

Clinical analysis by microchip capillary electrophoresis

Clinical analysis often requires rapid, automated, and high-throughput analytical systems. Microchip capillary electrophoresis (CE) has the potential to achieve very rapid analysis (typically seconds), easy integration of multiple analytical steps, and parallel operation. Although it is currently still in an early stage of development, there are already many reports in the literature describing the applications of microchip CE in clinical analysis. At the same time, more fully automated and higher throughput commercial instruments for microchip CE are becoming available and are expected to further enhance the development of applications of microchip CE in routine clinical testing. To put into perspective its potential, we briefly compare microchip CE with conventional CE and review developments in this technique that may be useful in diagnosis of major diseases.

Clinical evaluation of micro-scale chip-based PCR system for rapid detection of hepatitis B virus

The polymerase chain reaction (PCR) is widely used to amplify a small amount of DNA in samples for genetic analysis. Rapid and accurate amplification is prerequisite for broad applications including molecular diagnostics of diseases, food safety, and biological warfare tests. We have developed a rapid real-time micro-scale chip-based PCR system, which consists of six individual thermal cycling modules capable of independent control of PCR protocols. The PCR volume is 1 microl and it takes less than 20 min to complete 40 thermal cycles. To test utility of a chip-based PCR system as a molecular diagnostic device, we have conducted the first large-scale clinical evaluation study. Three independent clinical evaluation studies (n = 563) for screening the hepatitis B virus (HBV) infection, the most popular social epidemic disease in Asia, showed an excellent sensitivity, e.g. 94%, and specificity, e.g. 93%, demonstrating micro-scale chip-based PCR can be applied in molecular diagnostics.

An integrated microfluidic device for influenza and other genetic analyses

An integrated microfluidic device capable of performing a variety of genetic assays has been developed as a step towards building systems for widespread dissemination. The device integrates fluidic and thermal components such as heaters, temperature sensors, and addressable valves to control two nanoliter reactors in series followed by an electrophoretic separation. This combination of components is suitable for a variety of genetic analyses. As an example, we have successfully identified sequence-specific hemagglutinin A subtype for the A/LA/1/87 strain of influenza virus. The device uses a compact design and mass production technologies, making it an attractive platform for a variety of widely disseminated applications.