Electrokinetically Based Approach for Single-Nucleotide Polymorphism Discrimination Using a Microfluidic Device

Biomarker Analysis on a Power-free Microfluidic Chip Driven by Degassed Poly(dimethylsiloxane)

Point-of-care testing (POCT) of biomarkers, such as proteins and nucleic acids, is a hot topic in modern medical engineering toward the early diagnosis of various diseases including cancer. Although microfluidic chips show great promise as a new platform for POCT, external pumps and valves for driving those chips have hindered the realization of POCT on the chips. To eliminate the need for pumps and valves, a power-free microfluidic pumping method utilizing degassed poly(dimethylsiloxane) (PDMS) was invented in 2004. In this article, the working principle of the degas-driven power-free microfluidic chip is first described, and then applications of those chips to biomarker analysis are reviewed. The biomarker analysis on the chip was typically achieved with a small sample volume of ∼1 μL and a short analysis time of ∼20 min. For protein analysis, the sandwich immunoassay format was adopted. The limit of detection (LOD) was improved by three orders of magnitude by using laminar flow-assisted dendritic amplification (LFDA), which was a newly devised amplification method specialized for microfluidic chips. For analysis of nucleic acids such as DNA and microRNA, the sandwich hybridization format was adopted, and the LFDA was also effective to reduce the LOD. With the LFDA, typical LOD values for proteins and nucleic acids were both around 1 pM.

Recent advances in microfluidic methods in cancer liquid biopsy

Early cancer detection, its monitoring, and therapeutical prediction are highly valuable, though extremely challenging targets in oncology. Significant progress has been made recently, resulting in a group of devices and techniques that are now capable of successfully detecting, interpreting, and monitoring cancer biomarkers in body fluids. Precise information about malignancies can be obtained from liquid biopsies by isolating and analyzing circulating tumor cells (CTCs) or nucleic acids, tumor-derived vesicles or proteins, and metabolites. The current work provides a general overview of the latest on-chip technological developments for cancer liquid biopsy. Current challenges for their translation and their application in various clinical settings are discussed. Microfluidic solutions for each set of biomarkers are compared, and a global overview of the major trends and ongoing research challenges is given. A detailed analysis of the microfluidic isolation of CTCs with recent efforts that aimed at increasing purity and capture efficiency is provided as well. Although CTCs have been the focus of a vast microfluidic research effort as the key element for obtaining relevant information, important clinical insights can also be achieved from alternative biomarkers, such as classical protein biomarkers, exosomes, or circulating-free nucleic acids. Finally, while most work has been devoted to the analysis of blood-based biomarkers, we highlight the less explored potential of urine as an ideal source of molecular cancer biomarkers for point-of-care lab-on-chip devices.

Detection of cancer antigens (CA-125) using gold nano particles on interdigitated electrode-based microfluidic biosensor

Integrating microfluidics with biosensors is of great research interest with the increasing trend of lab-on-the chip and point-of-care devices. Though there have been numerous studies performed relating microfluidics to the biosensing mechanisms, the study of the sensitivity variation due to microfluidic flow is very much limited. In this paper, the sensitivity of interdigitated electrodes was evaluated at the static drop condition and the microfluidic flow condition. In addition, this study demonstrates the use of gold nanoparticles to enhance the sensor signal response and provides experimental results of the capacitance difference during cancer antigen-125 (CA-125) antigen-antibody conjugation at multiple concentrations of CA-125 antigens. The experimental results also provide evidence of disease-specific detection of CA-125 antigen at multiple concentrations with the increase in capacitive signal response proportional to the concentration of the CA-125 antigens. The capacitive signal response of antigen-antibody conjugation on interdigitate electrodes has been enhanced by approximately 2.8 times (from 260.80 to 736.33 pF at 20 kHz frequency) in static drop condition and approximately 2.5 times (from 205.85 to 518.48 pF at 20 kHz frequency) in microfluidic flow condition with gold nanoparticle-coating. The capacitive signal response is observed to decrease at microfluidic flow condition at both plain interdigitated electrodes (from 260.80 to 205.85 pF at 20 kHz frequency) and gold nano particle coated interdigitated electrodes (from 736.33 to 518.48 pF at 20 kHz frequency), due to the strong shear effect compared to static drop condition. However, the microfluidic channel in the biosensor has the potential to increase the signal to noise ratio due to plasma separation from the whole blood and lead to the increase concentration of the biomarkers in the blood volume for sensing.

Inorganic Nanoparticles as Donors in Resonance Energy Transfer for Solid-Phase Bioassays and Biosensors

Bioassays for the rapid detection and quantification of specific nucleic acids, proteins, and peptides are fundamental tools in many clinical settings. Traditional optical emission methods have focused on the use of molecular dyes as labels to track selective binding interactions and as probes that are sensitive to environmental changes. Such dyes can offer good detection limits based on brightness but typically have broad emission bands and suffer from time-dependent photobleaching. Inorganic nanoparticles such as quantum dots and upconversion nanoparticles are photostable over prolonged exposure to excitation radiation and tend to offer narrow emission bands, providing a greater opportunity for multiwavelength multiplexing. Importantly, in contrast to molecular dyes, nanoparticles offer substantial surface area and can serve as platforms to carry a large number of conjugated molecules. The surface chemistry of inorganic nanoparticles offers both challenges and opportunities for the control of solubility and functionality for selective molecular interactions by the assembly of coatings through coordination chemistry. This report reviews advances in the compositional design and methods of conjugation of inorganic quantum dots and upconversion nanoparticles and the assembly of combinations of nanoparticles to achieve energy exchange. Our interest is the exploration of configurations where the modified nanoparticles can be immobilized to solid substrates for the development of bioassays and biosensors that operate by resonance energy transfer (RET).

Hydrodynamic lift forces on solutes in a tilted nanopillar array: A computer simulation study

We study solute transport in a microfluidic channel, where the walls hold an array of tilted rigid nanopillars. By solving numerically the flow equations in the channel, we show that a combination of hydrodynamic effects with excluded volume interactions between the solute particles and the pillars leads to a hydrodynamic lift effect, which varies with the particle size, and depends in a strongly nonlinear fashion on the flow rate. We show that the lift force can be sufficiently strong to drive the solute accumulation or removal from the pillar region and can be switched to the opposite direction by variation of the shear rate or driving pressure. We also demonstrate that the nanopillar array can be used to selectively attract particles of certain size and enhance solute trapping at the surface.

Compartmentalized Microfluidic Platforms: The Unrivaled Breakthrough of In Vitro Tools for Neurobiological Research

Microfluidic technology has become a valuable tool to the scientific community, allowing researchers to study fine cellular mechanisms with higher variable control compared with conventional systems. It has evolved tremendously, and its applicability and flexibility made its usage grow exponentially and transversely to several research fields. This has been particularly noticeable in neuroscience research, where microfluidic platforms made it possible to address specific questions extending from axonal guidance, synapse formation, or axonal transport to the development of 3D models of the CNS to allow pharmacological testing and drug screening. Furthermore, the continuous upgrade of microfluidic platforms has allowed a deeper study of the communication occurring between different neuronal and glial cells or between neurons and other peripheral tissues, both in physiological and pathological conditions. Importantly, the evolution of microfluidic technology has always been accompanied by the development of new computational tools addressing data acquisition, analysis, and modeling.

A valve-free 2D concentration gradient generator

Our designed chip with a criss-cross 3D flow path realizes a valve-free 2D concentration gradient generator.

Laser-induced heating integrated with a microfluidic platform for real-time DNA replication and detection

This study developed a microfluidic platform for replicating and detecting DNA in real time by integrating a laser and a microfluidic device composed of polydimethylsiloxane. The design of the microchannels consisted of a laser-heating area and a detection area. An infrared laser was used as the heating source for DNA replication, and the laser power was adjusted to heat the solutions directly. In addition, strong biotin–avidin binding was used to capture and detect the replicated products. The biotin on one end was bound to avidin and anchored to the surface of the microchannels, whereas the biotin on the other end was bound to the quantum dots (Qdots). The results showed that the fluorescent intensity of the Qdots bound to the replicated products in the detection area increased with the number of thermal cycles created by the laser. When the number of thermal cycles was ≥10, the fluorescent intensity of the Qdots was directly detectable on the surface of the microchannels. The proposed method is more sensitive than detection methods entailing gel electrophoresis.

A polymer lab-on-a-chip for genetic analysis using the arrayed primer extension on microarray chips

In this work a polymer lab-on-a-chip (LOC), fabricated through MEMS technology, was employed to execute a genetic protocol for the Single Nucleotide Polymorphisms (SNPs) detection. The LOC was made in Poly (methyl methacrylate) (PMMA) and has two levels: the lower one for the insertion and mixing of the reagents, the upper one for the interfacing with the DNA microarray chip. The hereditary hearing loss was chosen as case of study, since the demand for testing such a particular disorder is high and genetics behind the condition is quite clear. The Arrayed Primer EXtension (APEX) genetic protocol was implemented on the LOC to analyze the SNPs. A low density (for detection of up to 10 mutations) and a high density microarray chips (for detection of 245 mutations in 12 genes), containing the primers for the extension, were employed to carry out the APEX reaction on the LOC. Both the microarray chips provide a signal to noise ratio and efficiency comparable with a detection obtained in a conventional protocol in standard conditions. Moreover, significant reduction of the employed PCR volume (from 30 μL to 10 μL) was obtained using the low density chip.

Dynamic radial positioning of a hydrodynamically focused particle stream enabled by a three-dimensional microfluidic nozzle

The ability to confine flows and focus particle streams has become an integral component of the design of microfluidic systems for the analysis of a wide range of samples. Presented here is the implementation of a 3D microfluidic nozzle capable of both focusing particles as well as dynamically positioning those particles in selected flow lamina within the downstream analysis channel. Through the independent adjustment of the three sheath inlet flows, the nozzle controlled the size of a focused stream for 6, 10, and 15 μm polystyrene microparticles. Additional flow adjustment allowed the nozzle to dynamically position the focused particle stream to a specific area within the downstream channel. This unique ability provides additional capability and sample flexibility to the system. In order to gain insight into the fluidic behavior of the system, experimental conditions and results were duplicated within 4.75 μm using a COMSOL Multiphysics(®) model to elucidate the structure, direction, proportion, and fate of fluid lamina throughout the nozzle region. The COMSOL Multiphysics model showed that the position and distribution of particles upon entering the nozzle have negligible influence over its focusing ability, extending the experimental results into a wider range of particle sizes and system flow rates. These results are promising for the application of this design to allow for a relatively simple, fast, fully fluidically controlled nozzle for selective particle focusing and positioning for further particle analysis and sorting.

Temporal and spatial temperature measurement in insulator-based dielectrophoretic devices

Insulator-based dielectrophoresis is a relatively new analytical technique with a large potential for a number of applications, such as sorting, separation, purification, fractionation, and preconcentration. The application of insulator-based dielectrophoresis (iDEP) for biological samples, however, requires the precise control of the microenvironment with temporal and spatial resolution. Temperature variations during an iDEP experiment are a critical aspect in iDEP since Joule heating could lead to various detrimental effects hampering reproducibility. Additionally, Joule heating can potentially induce thermal flow and more importantly can degrade biomolecules and other biological species. Here, we investigate temperature variations in iDEP devices experimentally employing the thermosensitive dye Rhodamin B (RhB) and compare the measured results with numerical simulations. We performed the temperature measurement experiments at a relevant buffer conductivity range commonly used for iDEP applications under applied electric potentials. To this aim, we employed an in-channel measurement method and an alternative method employing a thin film located slightly below the iDEP channel. We found that the temperature does not deviate significantly from room temperature at 100 μS/cm up to 3000 V applied such as in protein iDEP experiments. At a conductivity of 300 μS/cm, such as previously used for mitochondria iDEP experiments at 3000 V, the temperature never exceeds 34 °C. This observation suggests that temperature effects for iDEP of proteins and mitochondria under these conditions are marginal. However, at larger conductivities (1 mS/cm) and only at 3000 V applied, temperature increases were significant, reaching a regime in which degradation is likely to occur. Moreover, the thin layer method resulted in lower temperature enhancement which was also confirmed with numerical simulations. We thus conclude that the thin film method is preferable providing closer agreement with numerical simulations and further since it does not depend on the iDEP channel material. Overall, our study provides a thorough comparison of two experimental techniques for direct temperature measurement, which can be adapted to a variety of iDEP applications in the future. The good agreement between simulation and experiment will also allow one to assess temperature variations for iDEP devices prior to experiments.

Rapid antimicrobial susceptibility testing with electrokinetics enhanced biosensors for diagnosis of acute bacterial infections

Rapid pathogen detection and antimicrobial susceptibility testing (AST) are required in diagnosis of acute bacterial infections to determine the appropriate antibiotic treatment. Molecular approaches for AST are often based on the detection of known antibiotic resistance genes. Phenotypic culture analysis requires several days from sample collection to result reporting. Toward rapid diagnosis of bacterial infection in non-traditional healthcare settings, we have developed a rapid AST approach that combines phenotypic culture of bacterial pathogens in physiological samples and electrochemical sensing of bacterial 16S rRNA. The assay determines the susceptibility of pathogens by detecting bacterial growth under various antibiotic conditions. AC electrokinetic fluid motion and Joule heating induced temperature elevation are optimized to enhance the sensor signal and minimize the matrix effect, which improve the overall sensitivity of the assay. The electrokinetics enhanced biosensor directly detects the bacterial pathogens in blood culture without prior purification. Rapid determination of the antibiotic resistance profile of Escherichia coli clinical isolates is demonstrated.

Next revolution in the molecular theranostics of infectious diseases: microfabricated systems for personalized medicine

The molecular diagnosis of infectious diseases is currently going through a revolution sustained by the regulatory approval of amplification tests that have been shown to be equivalent or superior to existing gold standard methods. The recent approval of a microarray system for the pharmacogenomic profiling of cytochrome P450-mediated drug metabolism is paving the way to novel, rapid, sensitive, robust and economical microfabricated systems for point-of-care diagnostics, which are utilized closer and closer to the patient's bedside. These systems will enable the multiparametric genetic evaluation of several medical conditions, including infectious diseases. This forecoming revolution will position molecular theranostics in a broader integrated view of personalized medicine, which exploits genetic information from microbes and human hosts to optimize patient management and disease treatment.

Electrokinetic stringency control in self-assembled monolayer-based biosensors for multiplex urinary tract infection diagnosis

Rapid detection of bacterial pathogens is critical toward judicious management of infectious diseases. Herein, we demonstrate an in situ electrokinetic stringency control approach for a self-assembled monolayer-based electrochemical biosensor toward urinary tract infection diagnosis. The in situ electrokinetic stringency control technique generates Joule heating induced temperature rise and electrothermal fluid motion directly on the sensor to improve its performance for detecting bacterial 16S rRNA, a phylogenetic biomarker. The dependence of the hybridization efficiency reveals that in situ electrokinetic stringency control is capable of discriminating single-base mismatches. With electrokinetic stringency control, the background noise due to the matrix effects of clinical urine samples can be reduced by 60%. The applicability of the system is demonstrated by multiplex detection of three uropathogenic clinical isolates with similar 16S rRNA sequences. The results demonstrate that electrokinetic stringency control can significantly improve the signal-to-noise ratio of the biosensor for multiplex urinary tract infection diagnosis.

FROM THE CLINICAL EDITOR

Urinary tract infections remain a significant cause of mortality and morbidity as secondary conditions often related to chronic diseases or to immunosuppression. Rapid and sensitive identification of the causative organisms is critical in the appropriate management of this condition. These investigators demonstrate an in situ electrokinetic stringency control approach for a self-assembled monolayer-based electrochemical biosensor toward urinary tract infection diagnosis, establishing that such an approach significantly improves the biosensor's signal-to-noise ratio.

Rapid and label-free single-nucleotide discrimination via an integrative nanoparticle-nanopore approach

Single-nucleotide polymorphism (SNP) is an important biomarker for disease diagnosis, treatment monitoring, and development of personalized medicine. Recent works focused primarily on ultrasensitive detection, while the need for rapid and label-free single-nucleotide discrimination techniques, which are crucial criteria for translation into clinical applications, remains relatively unexplored. In this work, we developed a novel SNP detection assay that integrates two complementary nanotechnology systems, namely, a highly selective nanoparticle-DNA detection system and a single-particle sensitive nanopore readout platform, for rapid detection of single-site mutations. Discrete nanoparticle-DNA structures formed in the presence of perfectly matched (PM) or single-mismatched (SM) targets exhibited distinct size differences, which were resolved on a size-tunable nanopore platform to generate corresponding "yes/no" readout signals. Leveraging the in situ reaction monitoring capability of the nanopore platform, we demonstrated that real-time single-nucleotide discrimination of a model G487A mutation, responsible for glucose-6-phosphate dehydrogenase deficiency, can be achieved within 30 min with no false positives. Semiquantification of DNA samples down to picomolar concentration was carried out using a simple parameter of particle count without the need for sample labeling or signal amplification. The unique combination of nanoparticle-based detection and nanopore readout presented in this work brings forth a rapid, specific, yet simple biosensing strategy that can potentially be developed for point-of-care application.

Integrated allele-specific polymerase chain reaction-capillary electrophoresis microdevice for single nucleotide polymorphism genotyping

An integrated allele-specific (AS) polymerase chain reaction (PCR) and capillary electrophoresis (CE) microdevice has been developed for multiplex single nucleotide polymorphism (SNP) genotyping on a portable instrumentation, which was applied for on-site identification of HANWOO (Korean indigenous beef cattle). Twelve sets of primers were designed for targeting beef cattle's eleven SNP loci for HANWOO verification and one primer set for a positive PCR control, and the success rate for identification of HANWOO was demonstrated statistically. The AS PCR and CE separation for multiplex SNP typing was carried out on a glass-based microchip consisting of four layers: a microchannel plate for microfluidic control, a Pt-electrode plate for a resistance temperature detector (RTD), a poly(dimethylsiloxane) (PDMS) membrane and a manifold glass for microvalve function. The operation of the sample loading, AS PCR, microvalve, and CE on a chip was automated with a portable genetic analyzer, and the laser-induced fluorescence detection was performed on a miniaturized fluorescence detector. The blind samples were correctly identified as a HANWOO by showing one or two amplicon peaks in the electropherogram, while the imported beef cattle revealed more than five peaks. Our genetic analysis platform provides rapid, accurate, and on-site multiplex SNP typing.

Biosensing with quantum dots: a microfluidic approach

Semiconductor quantum dots (QDs) have served as the basis for signal development in a variety of biosensing technologies and in applications using bioprobes. The use of QDs as physical platforms to develop biosensors and bioprobes has attracted considerable interest. This is largely due to the unique optical properties of QDs that make them excellent choices as donors in fluorescence resonance energy transfer (FRET) and well suited for optical multiplexing. The large majority of QD-based bioprobe and biosensing technologies that have been described operate in bulk solution environments, where selective binding events at the surface of QDs are often associated with relatively long periods to reach a steady-state signal. An alternative approach to the design of biosensor architectures may be provided by a microfluidic system (MFS). A MFS is able to integrate chemical and biological processes into a single platform and allows for manipulation of flow conditions to achieve, by sample transport and mixing, reaction rates that are not entirely diffusion controlled. Integrating assays in a MFS provides numerous additional advantages, which include the use of very small amounts of reagents and samples, possible sample processing before detection, ultra-high sensitivity, high throughput, short analysis time, and in situ monitoring. Herein, a comprehensive review is provided that addresses the key concepts and applications of QD-based microfluidic biosensors with an added emphasis on how this combination of technologies provides for innovations in bioassay designs. Examples from the literature are used to highlight the many advantages of biosensing in a MFS and illustrate the versatility that such a platform offers in the design strategy.

Three-dimensional continuous particle focusing in a microfluidic channel via standing surface acoustic waves (SSAW)

Three-dimensional (3D) continuous microparticle focusing has been achieved in a single-layer polydimethylsiloxane (PDMS) microfluidic channel using a standing surface acoustic wave (SSAW). The SSAW was generated by the interference of two identical surface acoustic waves (SAWs) created by two parallel interdigital transducers (IDTs) on a piezoelectric substrate with a microchannel precisely bonded between them. To understand the working principle of the SSAW-based 3D focusing and investigate the position of the focal point, we computed longitudinal waves, generated by the SAWs and radiated into the fluid media from opposite sides of the microchannel, and the resultant pressure and velocity fields due to the interference and reflection of the longitudinal waves. Simulation results predict the existence of a focusing point which is in good agreement with our experimental observations. Compared with other 3D focusing techniques, this method is non-invasive, robust, energy-efficient, easy to implement, and applicable to nearly all types of microparticles.

Interfacial chemistry and the design of solid-phase nucleic acid hybridization assays using immobilized quantum dots as donors in fluorescence resonance energy transfer

The use of quantum dots (QDs) as donors in fluorescence resonance energy transfer (FRET) offer several advantages for the development of multiplexed solid-phase QD-FRET nucleic acid hybridization assays. Designs for multiplexing have been demonstrated, but important challenges remain in the optimization of these systems. In this work, we identify several strategies based on the design of interfacial chemistry for improving sensitivity, obtaining lower limits of detection (LOD) and enabling the regeneration and reuse of solid-phase QD-FRET hybridization assays. FRET-sensitized emission from acceptor dyes associated with hybridization events at immobilized QD donors provides the analytical signal in these assays. The minimization of active sensing area reduces background from QD donor PL and allows the resolution of smaller amounts of acceptor emission, thus lowering the LOD. The association of multiple acceptor dyes with each hybridization event can enhance FRET efficiency, thereby improving sensitivity. Many previous studies have used interfacial protein layers to generate selectivity; however, transient destabilization of these layers is shown to prevent efficient regeneration. To this end, we report a protein-free interfacial chemistry and demonstrate the specific detection of as little as 2 pmol of target, as well as an improved capacity for regeneration.

Studies on Parylene C-caulked PDMS (pcPDMS) for low permeability required microfluidics applications

This note introduced a complete fabrication strategy of Parylene C-caulked PDMS (pcPDMS) for low permeability required microfluidics applications. The bonding issue enrolled in the pcPDMS fabrication was solved based on careful surface analyses of the Parylene C caulked status in the PDMS matrix.

DNA detection on a power-free microchip with laminar flow-assisted dendritic amplification

In this paper, we describe DNA detection experiments using our two original technologies, power-free microchip and laminar flow-assisted dendritic amplification (LFDA), which were previously applied to immunoassays. A microchip was fabricated by combining a poly(dimethylsiloxane) (PDMS) part having microchannel patterns and a glass plate modified with probe DNA. We carried out two kinds of experiments: the detection of 21-base biotinylated target DNA and the detection of single-nucleotide polymorphism (SNP) in 56-base unlabeled target DNA by sandwich hybridization with biotinylated probe DNA. For both of the experiments, the necessary solutions were injected into microchannels not by an external power source, but by air dissolution into the PDMS part. After a hybridization reaction, the LFDA was started by injecting FITC-labeled streptavidin and biotinylated anti-streptavidin antibody onto the reaction site. With a detection time of 20 min, the limit of detection (LOD) for the biotinylated target was 2.2 pM, and the LOD for the SNP was 10-30 pM, depending on the SNP type.

Microfluidic devices for bioapplications

Harnessing the ability to precisely and reproducibly actuate fluids and manipulate bioparticles such as DNA, cells, and molecules at the microscale, microfluidics is a powerful tool that is currently revolutionizing chemical and biological analysis by replicating laboratory bench-top technology on a miniature chip-scale device, thus allowing assays to be carried out at a fraction of the time and cost while affording portability and field-use capability. Emerging from a decade of research and development in microfluidic technology are a wide range of promising laboratory and consumer biotechnological applications from microscale genetic and proteomic analysis kits, cell culture and manipulation platforms, biosensors, and pathogen detection systems to point-of-care diagnostic devices, high-throughput combinatorial drug screening platforms, schemes for targeted drug delivery and advanced therapeutics, and novel biomaterials synthesis for tissue engineering. The developments associated with these technological advances along with their respective applications to date are reviewed from a broad perspective and possible future directions that could arise from the current state of the art are discussed.

Multi-exon genotyping of SMN gene in spinal muscular atrophy by universal fluorescent PCR and capillary electrophoresis

In this study, we established the first method for simultaneous evaluation of nine exons in the survival motor neuron (SMN) genes for full-scale genotyping. This method was used not only to quantify the copy numbers of highly homogenous telomeric SMN (SMN1)/centromeric SMN genes in exons 7 and 8 but also to determine intragenic mutations in all nine exons for complete diagnosis of spinal muscular atrophy (SMA). Additionally, we utilized the "universal fluorescent PCR" for simultaneously fluorescent labeling of eleven gene fragments (nine exons in SMN and two internal standards). Such technique is very beneficial for multi-exon analysis due to only requirement of one universal fluorescent primer which could fluorescently amplify all gene fragments. Of all 262 detected individuals, three subjects possessing different ratios of SMN1/centromeric SMN in the two exons were determined as gene conversion, and we also detected three interesting intragenic mutations (c.1 -39A>G, c.22_23insA in exon 1, c.84C>T in exon 2a) which were associated with the SMA patients owning one copy of SMN1 including two mutations never reported previously. This high-resolved method provided better potential technique for genotyping and identifying SMA, carrier and normal controls in large population.

Toward a solid-phase nucleic acid hybridization assay within microfluidic channels using immobilized quantum dots as donors in fluorescence resonance energy transfer

The optical properties and surface area of quantum dots (QDs) have made them an attractive platform for the development of nucleic acid biosensors based on fluorescence resonance energy transfer (FRET). Solid-phase assays based on FRET using mixtures of immobilized QD-oligonucleotide conjugates (QD biosensors) have been developed. The typical challenges associated with solid-phase detection strategies include non-specific adsorption, slow kinetics of hybridization, and sample manipulation. The new work herein has considered the immobilization of QD biosensors onto the surfaces of microfluidic channels in order to address these challenges. Microfluidic flow can be used to dynamically control stringency by adjustment of the potential in an electrokinetic-based microfluidics environment. The shearing force, Joule heating, and the competition between electroosmotic and electrophoretic mobilities allow the optimization of hybridization conditions, convective delivery of target to the channel surface to speed hybridization, amelioration of adsorption, and regeneration of the sensing surface. Microfluidic flow can also be used to deliver (for immobilization) and remove QD biosensors. QDs that were conjugated with two different oligonucleotide sequences were used to demonstrate feasibility. One oligonucleotide sequence on the QD was available as a linker for immobilization via hybridization with complementary oligonucleotides located on a glass surface within a microfluidic channel. A second oligonucleotide sequence on the QD served as a probe to transduce hybridization with target nucleic acid in a sample solution. A Cy3 label on the target was excited by FRET using green-emitting CdSe/ZnS QD donors and provided an analytical signal to explore this detection strategy. The immobilized QDs could be removed under denaturing conditions by disrupting the duplex that was used as the surface linker and thus allowed a new layer of QD biosensors to be re-coated within the channel for re-use of the microfluidic chip.

SNP genotyping of unpurified PCR products by sandwich-type affinity electrophoresis on a microchip with programmed autonomous solution filling

We demonstrate rapid single-nucleotide polymorphism (SNP) genotyping on a poly(dimethylsiloxane)-glass microchip. Sandwich-type affinity electrophoresis was employed to achieve sufficient specificity for reliable genotyping of unpurified PCR products. We tested three SNPs in different genes: CYP2D6 of artificial templates, and ALDH3A1 and CYP1A1 of human genomic samples. The target sequences were amplified by asymmetric PCR. For each SNP, we prepared a capture probe-poly(dimethylacrylamide) (CP-PDMA) conjugate and allele-specific, fluorescently-labeled detection probes (DPs). Prior to the electrophoresis, necessary solutions--the amplified sample, the CP-PDMA conjugate, the DPs, and a washer--were autonomously filled into their own regions of the microchannel in contact with each other. For precise control of this filling process, we have extended our published technique to a "programmed" version, in which additional passive stop valves synchronized the solution contacting events. Then we electrophoretically carried out a target DNA hybridization step, a DP hybridization step, and a washing step at the CP-PDMA conjugate region. This 3-step electrophoresis was completed in 2 min. The formation of the sandwich hybridization complex (CP-target-DP) was evaluated by fluorescence. Normalized fluorescence values of the different genotypes were clearly and reproducibly discriminated. The assay format presented here will be suitable for SNP genotyping at the point of care.

Oligonucleotide hybridization and free-solution electrokinetic separation in a nanofluidic device

There is significant interest in developing on-chip DNA hybridization assays to leverage the advantages of lab-on-a-chip systems, which include smaller sample and reagent volumes, faster processing speeds, and greater opportunities for large-scale integration. While much research has explored ways to integrate DNA microarrays on-chip, little work has been done to incorporate hybridization with existing microscale separation platforms. We present the first separation of single-stranded and double-stranded oligonucleotides in a nanofluidic device. We couple this separation with free-solution hybridization to develop a simple, electrokinetic technique that detects DNA hybridization without sample labeling. The technique is used both to detect target DNA sequences and to quantitatively measure hybridization kinetics. To demonstrate the method, we measured the second order reaction coefficient of complementary 20-mer oligonucleotides as a function of sodium ion concentration, which ranged from 0.0048 mol(-1).sec(-1) at 5 mM sodium to 0.42 mol(-1).sec(-1) at 50 mM. We also distinguished between a pair of complementary oligonucleotides and a pair with a single nucleotide mismatch, observing a two-fold difference in hybridization rate. Additionally, we observed a relative change in the mobility of single-stranded and double-stranded DNA with increasing sodium concentration, suggesting that our device may provide a useful platform for studying biomolecule transport in nanochannels.

Real-time DNA microarrays: reality check

DNA microarrays are plagued with inconsistent quantifications and false-positive results. Using established mechanisms of surface reactions, we argue that these problems are inherent to the current technology. In particular, the problem of multiplex non-equilibrium reactions cannot be resolved within the framework of the existing paradigm. We discuss the advantages and limitations of changing the paradigm to real-time data acquisition similar to real-time PCR methodology. Our analysis suggests that the fundamental problem of multiplex reactions is not resolved by the real-time approach itself. However, by introducing new detection chemistries and analysis approaches, it is possible to extract target-specific quantitative information from real-time microarray data. The possible scope of applications for real-time microarrays is discussed.

Bioconjugation techniques for microfluidic biosensors

We have evaluated five bioconjugation chemistries for immobilizing DNA onto silicon substrates for microfluidic biosensing applications. Conjugation by organosilanes is compared with linkage by carbonyldiimidazole (CDI) activation of silanol groups and utilization of dendrimers. Chemistries were compared in terms of immobilization and hybridization density, stability under microfluidic flow-induced shear stress, and stability after extended storage in aqueous solutions. Conjugation by dendrimer tether provided the greatest hybridization efficiency; however, conjugation by aminosilane treated with glutaraldehyde yielded the greatest immobilization and hybridization densities, as well as enhanced stability to both shear stress and extended storage in an aqueous environment. Direct linkage by CDI activation provided sufficient immobilization and hybridization density and represents a novel DNA bioconjugation strategy. Although these chemistries were evaluated for use in microfluidic biosensors, the results provide meaningful insight to a number of nanobiotechnology applications for which microfluidic devices require surface biofunctionalization, for example vascular prostheses and implanted devices.

Photobleaching absorbed Rhodamine B to improve temperature measurements in PDMS microchannels

Rhodamine B based fluorescence thermometry is commonly used in microfluidics to measure fluid temperatures in microchannels. Notable absorption of Rhodamine B into PDMS channel walls, however, causes difficulties in obtaining accurate temperature measurements due to a steady increase in the overall fluorescent signal. A simple and effective technique is reported that removes the fluorescent signal from absorbed Rhodamine B dye by means of photobleaching with a high intensity light source before taking images for thermometry analysis. The temperature field at the convergence of hot and cold streams in a Y-channel fabricated in PDMS/glass microfluidic chip is studied to demonstrate the execution of the photobleaching technique.

Fully integrated microfluidic separations systems for biochemical analysis

Over the past decade a tremendous amount of research has been performed using microfluidic analytical devices to detect over 200 different chemical species. Most of this work has involved substantial integration of fluid manipulation components such as separation channels, valves, and filters. This level of integration has enabled complex sample processing on miniscule sample volumes. Such devices have also demonstrated high throughput, sensitivity, and separation performance. Although the miniaturization of fluidics has been highly valuable, these devices typically rely on conventional ancillary equipment such as power supplies, detection systems, and pumps for operation. This auxiliary equipment prevents the full realization of a "lab-on-a-chip" device with complete portability, autonomous operation, and low cost. Integration and/or miniaturization of ancillary components would dramatically increase the capability and impact of microfluidic separations systems. This review describes recent efforts to incorporate auxiliary equipment either as miniaturized plug-in modules or directly fabricated into the microfluidic device.

Microfluidic platform for single nucleotide polymorphism genotyping of the thiopurine S-methyltransferase gene to evaluate risk for adverse drug events

Prospective clinical pharmacogenetic testing of the thiopurine S-methyltransferase gene remains to be realized despite the large body of evidence demonstrating clinical benefit for the patient and cost effectiveness for health care systems. We describe an entirely microchip-based method to genotype for common single nucleotide polymorphisms in the thiopurine S-methyltransferase gene that lead to serious adverse drug reactions for patients undergoing thiopurine therapy. Restriction fragment length polymorphism and allele-specific polymerase chain reaction have been adapted to a microfluidic chip-based polymerase chain reaction and capillary electrophoresis platform to genotype the common *2, *3A, and *3C functional alleles. In total, 80 patients being treated with thiopurines were genotyped, with 100% concordance between microchip and conventional methods. This is the first report of single nucleotide polymorphism detection using portable instrumentation and represents a significant step toward miniaturized for personalized treatment and automated point-of-care testing.

Discrimination of single mutations in cancer-related gene fragments with a surface acoustic wave sensor

Here, we report on using a surface acoustic wave sensor for the highly sensitive and accurate detection of individual point mutations in cancer-related gene DNA fragments from single injections. Our sensor measures both the mass and viscosity signals and, thus, allows discriminating between mass effects resulting from hybridization of short DNA strands and viscosity effects due to increasing amounts of DNA deposited on the sensor. Single nucleotide exchanges or deletions are distinguished reliably and with exceeding simplicity from the wild-type sequences, on the basis of differences in their dissociation or association rates starting at low nanomolar concentrations. Mutant oligonucleotides were identified immediately from viewing the recorded signal and without further processing of the data. Multiple repeated binding cycles were possible over days without affecting sensitivity. To achieve signal amplification, our new bioassay can also apply multiple hybridization steps based on sandwich hybridizations. Kinetic evaluations gave insight into the physicochemical properties of the fragments used that explain the differences in their binding processes.

Applications of microfluidics for neuronal studies

Microfabrication processes have changed the technology used in consumer goods, and have now advanced into applications in biology. Microfluidic platforms are microfabricated tools that are gaining popularity for studies of molecular and cellular biology. These platforms can allow precise control of the environment surrounding individual cells and they have been used to study physiologic and pharmacologic responses at the single-cell level. This article reviews microfluidic technology with emphasis on advances that could apply to the study of the nervous system, including architecture for isolation of axons, integrated electrophysiology, patterned physical and chemical substrate cues, and devices for the precisely controlled delivery of possible therapeutic agents such as trophic factors and drugs. The potential of these chips for the study of neurological diseases is also discussed.