Imaging of a band for DNA fragment migrating in microchannel on integrated microchip

Study of the peak broadening due to detection in the electrophoretic separation of DNA by CE and microchip CE and the application of image sensor for ultra-small detection cell length

Narrow peaks are important to high-resolution and high-speed separation of DNA fragments by capillary electrophoresis and microchip capillary electrophoresis. Detection cell length is one of the broadening factors, which is often ignored in experiments. However, is it always safe to neglect detection cell length under any condition? To answer this question, we investigated the influence of detection cell length by simulation and experiments. A parameter named as detection cell length ratio was proposed to directly compare the detection cell length and the spatial length of sample band. Electrophoretic peaks generated by various detection cell length ratios were analyzed. A simple rule to evaluate the peak broadening due to detection cell length was obtained. The current states of the detection cell length of detection system and their reliabilities in capillary electrophoresis and microchip capillary electrophoresis were analyzed. Microchip capillary electrophoresis detection with an ultra-small detection cell length of 0.36 μm was easily achieved by using an image sensor.

Accurate, predictable, repeatable micro-assembly technology for polymer, microfluidic modules

A method for the design, construction, and assembly of modular, polymer-based, microfluidic devices using simple micro-assembly technology was demonstrated to build an integrated fluidic system consisting of vertically stacked modules for carrying out multi-step molecular assays. As an example of the utility of the modular system, point mutation detection using the ligase detection reaction (LDR) following amplification by the polymerase chain reaction (PCR) was carried out. Fluid interconnects and standoffs ensured that temperatures in the vertically stacked reactors were within ± 0.2 C° at the center of the temperature zones and ± 1.1 C° overall. The vertical spacing between modules was confirmed using finite element models (ANSYS, Inc., Canonsburg, PA) to simulate the steady-state temperature distribution for the assembly. Passive alignment structures, including a hemispherical pin-in-hole, a hemispherical pin-in-slot, and a plate-plate lap joint, were developed using screw theory to enable accurate exactly constrained assembly of the microfluidic reactors, cover sheets, and fluid interconnects to facilitate the modular approach. The mean mismatch between the centers of adjacent through holes was 64 ± 7.7 μm, significantly reducing the dead volume necessary to accommodate manufacturing variation. The microfluidic components were easily assembled by hand and the assembly of several different configurations of microfluidic modules for executing the assay was evaluated. Temperatures were measured in the desired range in each reactor. The biochemical performance was comparable to that obtained with benchtop instruments, but took less than 45 min to execute, half the time.

Effective length calibration method for processing the fluorescence signal detected by charge-coupled device in capillary electrophoresis

A novel method named effective length calibration method has been developed to process the fluorescence signal detected by charge-coupled device during capillary electrophoresis. The new method treated each pixel as an individual point detector, and effectively binned a large number of pixels into a final electropherogram without losing the narrow detection window defined by a single pixel. Capillary electrophoresis separations of DNA were carried out and detected by charge-coupled device and conventional detector (photomultiplier tube). Detection properties including signal-to-noise ratio, peak width, detection frequency, and tilt of detector were investigated. It was found that the new method achieved much higher signal-to-noise ratio and smaller peak width than the conventional detector did. A Detection width of 0.5 μm was easily achieved.

Microfluidic biochip injection moulded using a patterned SU-8/Si mould insert

This paper presents the adaptation of a conventional injection moulding process to manufacture microfluidic components in thermoplastic polymers using alternative, exchangeable microstructured silicon-based mould inserts. The mould inserts consist of thick silicon wafers with microfeatures patterned in SU-8 epoxy photo-resist. This process allows changing the mould inserts according to the design, very easily and cost-effectively. The SU-8/Si mould inserts were robust enough to manufacture small series for laboratory purpose. More than a hundred replicas in thin polypropylene (PP) were produced successfully for a biochip designed for protein crystallisation and analysis.

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).

PMMA/PDMS valves and pumps for disposable microfluidics

Poly(methyl methacrylate) (PMMA) is gaining in popularity in microfluidic devices because of its low cost, excellent optical transparency, attractive mechanical/chemical properties, and simple fabrication procedures. It has been used to fabricate micromixers, PCR reactors, CE and many other microdevices. Here we present the design, fabrication, characterization and application of pneumatic microvalves and micropumps based on PMMA. Valves and pumps are fabricated by sandwiching a PDMS membrane between PMMA fluidic channel and manifold wafers. Valve closing or opening can be controlled by adjusting the pressure in a displacement chamber on the pneumatic layer via a computer regulated solenoid. The valve provides up to 15.4 microL s(-1) at 60 kPa fluid pressure and seals reliably against forward fluid pressure as high as 60 kPa. A PMMA diaphragm pump can be assembled by simply connecting three valves in series. By varying valve volume or opening time, pumping rates ranging from nL to microL per second can be accurately achieved. The PMMA based valves and pumps were further tested in a disposable automatic nucleic acid extraction microchip to extract DNA from human whole blood. The DNA extraction efficiency was about 25% and the 260 nm/280 nm UV absorption ratio for extracted DNA was 1.72. Because of its advantages of inexpensive, facile fabrication, robust and easy integration, the PMMA valve and pump will find their wide application for fluidic manipulation in portable and disposable microfluidic devices.

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.

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.

Microchip electrophoresis-based separation of DNA

Miniaturized instruments have developed very quickly in the last decade. This review is focused on the microchip electrophoresis-based separation of DNA. Fundamentals, including the chip format, substrates and fabrication technologies, fluid control, as well as various detection methods, are summarized. Array electrophoresis microchip and the on-chip integration of electrophoresis with other systems are introduced as well. In addition, the application of microchip electrophoresis in DNA sizing, genetic analysis and DNA sequencing are also presented in this paper.

Fluorescent derivatization of nitrite ions with 2,3-diaminonaphthalene utilizing a pH gradient in a Y-shaped microchannel

The on-chip derivatization of nitrite ions with 2,3-diaminonaphthalene (DAN) utilizing a pH gradient formed in a Y-shaped microchannel was investigated. Nitrite ions react with DAN at low pH, and strongly fluoresced at high pH. Therefore, a reaction at low pH followed by the addition of a strong alkaline solution is the usual procedure in a batch scheme. However, a strong alkaline solution, like an NaOH aqueous solution, erodes the wall of the microchannels in substrates made of glass or polymers, and has not been considered suitable for use in microchannels. We first investigated the derivatization reaction and fluorescent properties of nitrite ions with DAN. We found that the on-chip fluorescent derivatization reaction and detection without the addition of an alkaline solution is possible by controlling the pH values of the nitrite solution and the DAN solution to form a suitable pH gradient by utilizing a buffering effect of triethanolamine solution, which is used as an NO2 gas-absorption medium. These results have suggested the feasibility of novel reaction schemes which can provide the desired products due to a controlled pH gradient in the microchannels, as well as the possibility of an on-site monitoring microchip device for ambient NO2.