Plastic microchip electrophoresis for genetic screening: The analysis of polymerase chain reactions products of fragile X (CGG)n alleles

Molecular diagnosis of neurogenetic disorders involving trinucleotide repeat expansions

There are more than 15 known neurogenetic disorders involving trinucleotide repeat expansion. Expanded repeats range from small expansions of 20-100 copies to larger expansions of up to several thousand units. These dynamic expansions result in variability in age of onset, degree of severity and clinical presentation. Individuals carrying alleles in the intermediate range, known as premutation alleles, are often asymptomatic, but can potentially transmit a further expanded allele to his/her offspring. For autosomal dominant adult-onset disorders, carriers are asymptomatic prior to disease onset. With current molecular tools, it is now possible to determine the presence and number of expanded repeats for accurate diagnosis, presymptomatic testing and carrier status screening. This review examines some of the current approaches for molecular diagnosis and discusses the issues unique to triplet repeat diseases.

DNA mutation detection and analysis using miniaturized microfluidic systems

Identification of genetic sequence variations occurring on a population-wide scale is key to unraveling the complex interactions that are the underlying cause of many medical disorders and diseases. A critical need exists, however, for advanced technology to enable DNA mutation analysis to be performed with significantly higher throughput and at significantly lower cost than is currently attainable. Microfluidic systems offer an attractive platform to address these needs by combining the ability to perform rapid analysis with a simplified device format that can be inexpensively mass-produced. This paper will review recent progress toward developing these next-generation systems and discuss challenges associated with adapting these technologies for routine laboratory use.

Recent Progress in Lab-on-a-Chip Technology and Its Potential Application to Clinical Diagnoses

We present the construction of the lab-on-a-chip (LOC) system, a state-of-the-art technology that uses polymer materials (i.e., poly[dimethylsiloxane]) for the miniaturization of conventional laboratory apparatuses, and show the potential use of these microfluidic devices in clinical applications. In particular, we introduce the independent unit components of the LOC system and demonstrate how each component can be functionally integrated into one monolithic system for the realization of a LOC system. In specific, we demonstrate microscale polymerase chain reaction with the use of a single heater, a microscale sample injection device with a disposable plastic syringe and a strategy for device assembly under environmentally mild conditions assisted by surface modification techniques. In this way, we endeavor to construct a totally integrated, disposable microfluidic system operated by a single mode, the pressure, which can be applied on-site with enhanced device portability and disposability and with simple and rapid operation for medical and clinical diagnoses, potentially extending its application to urodynamic studies in molecular level.

Disposable roll-to-roll hot embossed electrophoresis chip for detection of antibiotic resistance gene mecA in bacteria

We present a high-throughput roll-to-roll (R2R) manufacturing process for foil-based polymethyl methacrylate (PMMA) chips of excellent optical quality. These disposable, R2R hot embossed microfluidic chips are used for the identification of the antibiotic resistance gene mecA in Staphylococcus epidermidis. R2R hot embossing is an emerging manufacturing technology for polymer microfluidic devices. It is based on continuous feeding of a thermoplastic foil through a pressurized area between a heated embossing cylinder and a blank counter cylinder. Although mass fabrication of foil-based microfluidic chips and their use for biological applications were foreseen already some years ago, no such studies have been published previously.

Band-broadening suppressed effect in long turned geometry channel and high-sensitive analysis of DNA sample by using floating electrokinetic supercharging on a microchip

A featured microchip owning three big reservoirs and long turned geometry channel was designed to improve the detection limit of DNA fragments by using floating electrokinetic supercharging (FEKS) method. The novel design matches the FEKS preconcentration needs of a large sample volume introduction with electrokinetic injection (EKI), as well as long duration of isotachophoresis (ITP) process to enrich low concentration sample. In the curved channel [ approximately 45.6 mm long between port 1 (P1) and the intersection point of two channels], EKI and ITP were performed while the side port 3 (P3) was electrically floated. The turn-induced band broadening with or without ITP process was investigated by a computer simulation (using CFD-ACE+ software) when the analytes traveling through the U-shaped geometry. It was found that the channel curvature determined the extent of band broadening, however, which could be effectively eliminated by the way of ITP. After the ITP-stacked zones passed the intersection point from P1, they were rapidly destacked for separation and detection from ITP to zone electrophoresis by using leading ions from P3. The FEKS carried on the novel chip successfully contributed to higher sensitivities of DNA fragments in comparison with our previous results realized on either a single channel or a cross microchip. The analysis of low concentration 50 bp DNA step ladders (0.23 mugml after 1500-fold diluted) was achieved with normal UV detection at 260 nm. The obtained limit of detections (LODs) were on average 100 times better than using conventional pinched injection, down to several ngml for individual DNA fragment.

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.

Ultra-fast simultaneous analysis of genetically modified organisms in maize by microchip electrophoresis with LIF detector

This study examined the potential of microchip electrophoresis (ME) with a LIF detector using a programmed field strength gradient (PFSG) in a conventional glass double-T microchip for the ultra-fast detection and simultaneous analysis of genetically modified (GM) maize. The separation efficiency and sensitivity at various sieving gels (poly(ethylene oxide) (PEO, M(r) 8,000,000) and 2-hydroxyethylcellulose (HEC) (M(r) 250,000)) and fluorescent dye concentrations were investigated. The PCR products of both the GM and non-GM maize were analyzed within 30 s under the PFSG (470.6 V/cm for 20 s, 117.6 V/cm for 12 s, and 470.6 V/cm for 30 s) with a 2.5% HEC sieving matrix in the running buffer, 1 x Tris-borate EDTA (TBE) (pH 8.30) and 0.5 ppm ethidium bromide. The five transgenic maize varieties (Event176, MON810, Bt11, GA21, and T25) examined in this study were also clearly differentiated by ME-PFSG within 30 s in a single run without any loss of resolution. The ME-PFSG technique is a powerful tool for the ultra-fast detection and simultaneous analysis of GMOs in a variety of foods including maize.

High resolution DNA separations using microchip electrophoresis

Planar microfluidic devices have emerged as effective tools for the electrophoretic separation of a variety of different DNA inputs. The advancement of this miniaturized platform was inspired initially by demands placed on electrophoretic performance metrics by the human genome project and has provided a viable alternative to slab gel and even capillary formats due to its ability to offer high resolution separations of nucleic acid materials in a fraction of the time associated with its predecessors, consumption of substantially less sample and reagents while maintaining the ability to perform many separations in parallel for realizing ultra-high throughputs. Another compelling advantage of this separation platform is that it offers the potential for integrating front-end sample preprocessing steps onto the separation device eliminating the need for manual sample handling. This review aims to compile a recent survey of various electrophoretic separations using either glass or polymer-based microchips in the areas of genotyping and DNA sequencing as well as those involving the growing field of DNA-based forensics.

CE chips fabricated by injection molding and polyethylene/thermoplastic elastomer film packaging methods

This study presents a new packaging method using a polyethylene/thermoplastic elastomer (PE/TPE) film to seal an injection-molded CE chip made of either poly(methyl methacrylate) (PMMA) or polycarbonate (PC) materials. The packaging is performed at atmospheric pressure and at room temperature, which is a fast, easy, and reliable bonding method to form a sealed CE chip for chemical analysis and biomedical applications. The fabrication of PMMA and PC microfluidic channels is accomplished by using an injection-molding process, which could be mass-produced for commercial applications. In addition to microfluidic CE channels, 3-D reservoirs for storing biosamples, and CE buffers are also formed during this injection-molding process. With this approach, a commercial CE chip can be of low cost and disposable. Finally, the functionality of the mass-produced CE chip is demonstrated through its successful separation of phiX174 DNA/HaeIII markers. Experimental data show that the S/N for the CE chips using the PE/TPE film has a value of 5.34, when utilizing DNA markers with a concentration of 2 ng/microL and a CE buffer of 2% hydroxypropyl-methylcellulose (HPMC) in Tris-borate-EDTA (TBE) with 1% YO-PRO-1 fluorescent dye. Thus, the detection limit of the developed chips is improved. Lastly, the developed CE chips are used for the separation and detection of PCR products. A mixture of an amplified antibiotic gene for Streptococcus pneumoniae and phiX174 DNA/HaeIII markers was successfully separated and detected by using the proposed CE chips. Experimental data show that these DNA samples were separated within 2 min. The study proposed a promising method for the development of mass-produced CE chips.

Genotyping with microfluidic devices

In the past few years, electrophoresis microchips have been increasingly utilized to interrogate genetic variations in the human and other genomes. Microfluidic devices can be readily applied to speed up existing genotyping protocols, in particular the ones that require electric field-mediated separations in conjunction with restriction fragment analysis, DNA sequencing, hybridization-based techniques, allele-specific amplification, heteroduplex analysis, just to list the most important ones. As a result of recent developments, microfabricated electrophoresis devices offer several advantages over conventional slab-gel electrophoresis, such as small sample volume requirement, low reagent consumption, the option of system integration and easy multiplexing. The analysis speed of microchip electrophoresis is significantly higher than that of any other electric field-mediated separation techniques. State-of-the-art microfluidic bioanalytical devices already claim their place in most molecular biology laboratories. This review summarizes the recent developments in microchip electrophoresis methods of nucleic acids, particularly for rapid genotyping, that will most likely play a significant role in the future of clinical diagnostics.

Gold nanoparticles for microfluidics-based biosensing of PCR products by hybridization-induced fluorescence quenching

Colloidal gold nanoparticles were used to develop a simple microfluidics-based bioassay that is able to recognize and detect specific DNA sequences via conformational change-induced fluorescence quenching. In this method, a self-assembled monolayer of gold nanoparticles was fabricated on the channel wall of a microfluidic chip, and DNA probes were bonded to the monolayer via thiol groups at one end and a fluorophore dye was attached to the other end of the probe. The created construct is spontaneously assembled into a constrained arch-like conformation on the particle surface and, under which, the fluorescence of fluorophores is quenched by gold nanoparticles. Hybridization of target DNAs results in a conformational change of the construct and then restores the fluorescence, which serves as a sensing method for the target genes. The nanocomposite constructed on the glass surface was characterized by UV absorbance measurement and the quenching efficiency for different fluorophores was evaluated by Stern-Volmer studies. The applicability of proposed assay was first demonstrated by the use of a pair of synthesized complementary and noncomplementary DNA sequences. The method was further applied for the detection of the PCR product of dengue virus with the use of enterovirus as the negative control, and results indicate that the assay is specific for the target gene. Moreover, using this approach, dehybridization, hybridization, and detection of the target genes can be performed in situ on the same microfluidic channel. Thus, this method could be regarded as one-pot reaction and it holds great promises for clinical diagnostics.

Polymeric microfluidic system for DNA analysis

The application of micro total analysis system (microTAS) has grown exponentially in the past decade. DNA analysis is one of the primary applications of microTAS technology. This review mainly focuses on the recent development of the polymeric microfluidic devices for DNA analysis. After a brief introduction of material characteristics of polymers, the various microfabrication methods are presented. The most recent developments and trends in the area of DNA analysis are then explored. We focus on the rapidly developing fields of cell sorting, cell lysis, DNA extraction and purification, polymerase chain reaction (PCR), DNA separation and detection. Lastly, commercially available polymer-based microdevices are included.

Chip-based microfluidic devices coupled with electrospray ionization-mass spectrometry

We present the current status of the development of microfluidic devices fabricated on different substrates for coupling with electrospray ionization-mass spectrometry (ESI-MS). Until now, much success has been gained in fabricating the ESI chips, which show better performances due to miniaturization when compared with traditional methods. Integration of multiple steps for sample preparation and ESI sample introduction, however, remains a great challenge. This review covers the main technical development of electrospray device that were published from 1997 to 2004. This article does not attempt to be exclusive. Instead, it focuses on the publications that illustrated the breath of the development and applications of microchip devices for MS-based analysis.

Impact of reservoir potentials on the analyte behavior in microchip electrophoresis: computer simulation and experimental validation for DNA fragments

Fundamental understanding of the impact of reservoir potentials on the analyte behavior on the microfluidic chips is an important issue in microchip electrophoresis (MCE) for suitable injection and separation of analytes, since the applied potentials may significantly affect the shape of sample plug, sample leakage from the injection channel to the separation channel, injected sample amount, and separation efficiency. This study addressed this issue for the case of a conventional cross-geometry microchip with four reservoirs using computer simulations, the results of which were verified by the analysis of DNA fragments. For the microchip with a definite structure and migration distance, the injected sample amount was shown to be the vital parameter for improving the limit of detection and resolution. During injection, the shape of the sample plug could be adjusted by varying the reservoir potentials. It was demonstrated that a "magnified injection" (applying high voltage on the three reservoirs to the sample reservoir) is useful to enhance the detection sensitivity depending on the analyte composition, although such injection was previously avoided because of introducing too large amounts of the analyte in comparison with two established modes, floating and pinched injection. Optimal magnified injection was proved to improve the sensitivity for about 4 times over that of pinched injection for the analysis of DNA step ladders using microchip gel electrophoresis (MCGE). Sample leakage of DNA fragments could be suppressed by applying a high positive voltage on injection channel during separation, but the voltage degraded the injected amount and resolution.

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.

Analysis of double-stranded DNA by microchip capillary electrophoresis using polymer solutions containing gold nanoparticles

The impact of gold nanoparticles (GNPs) on the microchip electrophoretic separation of double-stranded (ds) DNA using poly(ethylene oxide) (PEO) is described. Coating of the 75-microm separation channel on a poly(methyl methacrylate) (PMMA) plate in sequence with poly(vinyl pyrrolidone), PEO, and 13-nm GNPs is effective to improve reproducibility and resolution. In this study, we have also found that adding 13-nm GNPs to 1.5% PEO is extremely important to achieve high resolution and reproducibility for DNA separation. In terms of the stability of the GNPs, 100 mM glycine-citrate buffer at pH 9.2 is a good buffer system for preparing 1.5% PEO. The separation of DNA markers V and VI ranging in size from 8 to 2176 base pairs has been demonstrated using the three-layer-coated PMMA microdevice filled with 1.5% PEO containing the GNPs. Using these conditions, the analysis of the polymerase chain reaction products of UGT1A7 was complete in 7 min, with the relative standard deviation values of the peak heights and migration times less than 2.3% and 2.0%, respectively. In conjunction with stepwise changes of the concentrations of ethidium bromide (0.5 and 5 microg/ml), this method allows improved resolution and sensitivity for DNA markers V and VI.

Capillary electrophoresis and its application in the clinical laboratory

Over the past 10 years, capillary electrophoresis (CE) is an analytical tool that has shown great promise in replacing many conventional clinical laboratory methods, especially electrophoresis and high performance liquid chromatography (HPLC). The main attraction of CE was that it was fast, used small amounts of sample and reagents, and was extremely versatile, being able to separate large and small analytes, both neutral and charged. Because of this versatility, numerous methods for clinically relevant analytes have been developed. However, with the exception of the molecular diagnostic and forensic laboratories CE has not had a major impact. A possible reason is that CE is still perceived as requiring above-average technical expertise, precluding its use in a laboratory workforce that is less technically adept. With the introduction of multicapillary instruments that are more automated, less technique-dependent, in addition to the availability of commercial and cost effective test kit methods, CE may yet be accepted as a instrument routinely used in the clinical laboratories. Thus, this review will focus on the areas where CE shows the most potential to have the greatest impact on the clinical laboratory. These include analysis of proteins found in serum, urine, CSF and body fluids, immunosubstraction electrophoresis, hemoglobin variants, lipoproteins, carbohydrate-deficient transferrin (CDT), forensic and therapeutic drug screening, and molecular diagnostics.

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.