Microarrays and microfluidic devices: miniaturized systems for biological analysis (original) (raw)
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Microfluidic DNA microarray analysis: A review
Analytica Chimica Acta, 2011
Microarray DNA hybridization techniques have been used widely from basic to applied molecular biology research. Generally, in a DNA microarray, different probe DNA molecules are immobilized on a solid support in groups and form an array of microspots. Then, hybridization to the microarray can be performed by applying sample DNA solutions in either the bulk or the microfluidic manner. Because the immobilized probe DNA binds and retains its complementary target DNA, detection is achieved through the read-out of the tagged markers on the sample target molecules. The recent microfluidic hybridization method shows the advantages of less sample usage and reduced incubation time. Here, sample solutions are confined in microfabricated channels and flow through the probe microarray area. The high surfaceto-volume ratio in microchannels of nanolitre volume greatly enhanced the sensitivity as obtained with the bulk solution method. To generate nanolitre flows, different techniques have been developed, and this including electrokinetic control, vacuum suction and syringe pumping. The latter two are pressuredriven methods which are more flexible without the need of considering the physicochemical properties of solutions. Recently, centrifugal force is employed to drive liquid movement in microchannels. This method utilizes the body force from the liquid itself and there are no additional solution interface contacts such as from electrodes or syringes and tubing. Centrifugal force driven flow also features the ease of parallel hybridizations. In this review, we will summarize the recent advances in microfluidic microarray hybridization and compare the applications of various flow methods.
Application of microtechnology in biotechnology. Microarray analytical systems- an overview
… of Optoelectronics and …, 2003
The evolution of modern biology, that recently entered the genome era, requires faster and cheaper analytical systems. Techniques as microlithography, micromachining, laser induced fluorescence detection, microfluidics contributed to the development of the DNA microarray technology, having as result complex analytical systems able to perform hybridization of nucleic acids in an array format on small bidimensional surfaces, and also to process huge quantities of information. The most significant achievements worldwide obtained are presented illustrating the state of the art in this domain. In order to automate the fluidic process involved in the DNA hybridization three micromachining techniques, slightly differing from each other have been approached by the authors team. Reservoirs with volumes ranging from 1nl to 2 µl in different materials have been obtained by means of reactive ion etching of polyimide, anisotropic etching of silicon respectively an optimised wet etching of borosilicate glass as well as a low temperature bonding of borosilicate glass on silicon nitride.
Analytical Chemistry, 2002
An isothermal signal amplification technique for specific DNA sequences, known as cycling probe technology (CPT), was performed within a microfluidic chip. The presence of DNA from methicillin-resistant Staphylococcus aureus was determined by signal amplification of a specific DNA sequence. The microfluidic device consisted of four channels intersecting to mix the sample and reagents within 55 s, as they were directed toward the reactor coil by electrokinetic pumping. The 160-nL CPT reactor occupied ∼220 mm 2 . Gel-free capillary electrophoresis separation of the biotin-and fluorescein-labeled probe from the probe fragments was performed on-chip following the on-chip reaction. An off-chip CPT reaction, with on-chip separation gave a detection limit of 2 fM (0.03 amol) target DNA and an amplification factor of 85 000. Calibration curves, linear at <5% probe fragmentation, obeyed a power law relationship with an argument of 0.5 [target] at higher target DNA concentrations for both on-chip and off-chip CPT reaction and analysis. An amplification factor of 42 000 at 250 fM target (25 000 target molecules) was observed on-chip, but the reaction was ∼4 times less sensitive than off-chip under the conditions used. Relative SD values for on-chip CPT were 0.8% for the peak migration times, 9% for the area of intact probe peak, and 8% for the fragment/probe peak area ratio Routine use of gene sequences for sample analysis requires the development of new methods for performing analytical assays, in terms of the reagents and reactions used, as well as the technology for performing those assays. 1 Microfluidic devices offer an attractive approach to miniaturizing the amounts of reagent required and automating or speeding up the analyses. 2-8 The focus to date has been on performing DNA separations within capillary gel electrophoresis (CGE) microchips for sequencing or sizing 9-12 and on integrating the polymerase chain reaction 13-21 (PCR). PCR is a common DNA sample preparation step, in which the target † University of Alberta. ‡ Both first and second authors have contributed equally. § Defence Research Establishment Suffield. |
Microfluidics and Sensors for DNA Analysis
— The manipulation of fluids in microchannels has been studied extensively due to its vast array of applications including genome sequencing, single cell detection, cost and time reduction with electronic microdevices. Microfluidics has the potential to influence subject areas from chemical synthesis and biological analysis to optics and information technology. The review paper introduces the advancement of microfluidics in DNA analysis. Wherever possible commercially available device information is also provided to emphasize the importance of that particular technology and its scope. It will briefly introduce you to different types of biosensor technology currently researched and one example that make the conceptual design into a reality.
Comparative modeling and analysis of microfluidic and conventional DNA microarrays
Analytical Biochemistry, 2006
A theoretical analysis was developed to predict molecular hybridization rates for microarrays where samples flow through microfluidic channels and for conventional microarrays where samples remain stationary during hybridization. The theory was validated by using a multiplexed microfluidic microarray where eight samples were hybridized simultaneously against eight probes using 60-mer DNA strands. Mass transfer coefficients ranged over three orders of magnitude where either kinetic reaction rates or molecular diffusion rates controlled overall hybridization rates. Probes were printed using microfluidic channels and also conventional spotting techniques. Consistent with the theoretical model, the microfluidic microarray demonstrated the ability to print DNA probes in less than 1 min and to detect 10-pM target concentrations with hybridization times in less than 5 min.
Fully Integrated Miniature Device for Automated Gene Expression DNA Microarray Processing
Analytical Chemistry, 2006
A DNA microarray with 12 000 features was integrated with a microfluidic cartridge to automate the fluidic handling steps required to carry out a gene expression study of the human leukemia cell line (K562). The fully integrated microfluidic device consists of microfluidic pumps/mixers, fluid channels, reagent chambers, and a DNA microarray silicon chip. Microarray hybridization and subsequent fluidic handling and reactions (including a number of washing and labeling steps) were performed in this fully automated and miniature device before fluorescent image scanning of the microarray chip. Electrochemical micropumps were integrated into the cartridge to provide pumping of liquid solutions. The device was completely self-contained: no external pressure sources, fluid storage, mechanical pumps, mixers, or valves were necessary for fluid manipulation, thus eliminating possible sample contamination and simplifying device operation. Fluidic experiments were performed to study the on-chip washing efficiency and uniformity. A single-color transcriptional analysis of K562 cells with a series of calibration controls (spiked-in controls) to characterize this new platform with regard to sensitivity, specificity, and dynamic range was performed. The device detected sample RNAs with a concentration as low as 0.375 pM. Experiment also showed that the performance of the integrated microfluidic device is comparable with the conventional hybridization chambers with manual operations, indicating that the on-chip fluidic handling (washing and reaction) is highly efficient and can be automated with no loss of performance. The device provides a cost-effective solution to eliminate laborintensive and time-consuming fluidic handling steps in genomic analysis.
PCR microfluidic devices for DNA amplification
Biotechnology Advances, 2006
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
Biomedical microdevices, 2014
We report a microfluidic device and measurement method to perform real-time PCR (or qPCR) in a miniaturized configuration for on-chip implementation using reaction volumes of less than 20 μL. The qPCR bioreactor is designed as a module to be embedded in an automated sample-in/profile-out system for rapid DNA biometrics or human identification. The PCR mixture is excited with a 505 nm diode-pumped solid-state laser (DPSSL) and the fluorescence build-up is measured using optical fibers directly embedded to the sidewalls of the microfluidic qPCR bioreactor. We discuss manufacturing and operating parameters necessary to adjust the internal surface conditions and temperature profiles of the bioreactor and to optimize the yield and quality of the PCR reaction for the amplification of 62 bp hTERT intron fragments using the commercial Quantifiler® kit (Life Technologies, Carlsbad, CA) commonly accepted for genotyping analysis. We designed a microfluidic device suitable for continuously proc...
Microfluidics in Bioanalytical Instrumentation
2013
Portable and field deployable analytical instruments are attractive in many fields, including medical diagnostics where point-of-care and on-site diagnostics systems capable of providing rapid quantitative results have the potential to improve the productivity and quality of medical care. A major limitation and impediment to the usage of portable and field deployable microfluidic chip based analytical instruments in solving real world analytical problems has been the scarcity of commercially available portable or field deployable platforms, which are fully flexible for research. The bench-top analytical instrument , the Agilent Bioanalyzer 2100 used in this research is a microfluidic chip-based platform with fluorescence detection system, available on the market since 1999. Originally, this instrument was capable of electrophoretic analysis of deoxyribonucleic acids (DNA) and ribonucleic acids (RNA), with user-tailored application solutions including chips, reagents and pre-develope...