PDMS Microfluidic Channel Research Articles

Rapid DNA Hybridization Analysis Using a PDMS Microfluidic Sensor and a Molecular Beacon

A rapid DNA analysis has been developed based on a fluorescence intensity change of a molecular beacon in a PDMS microfluidic channel. Recently, we reported a new analytical method of DNA hybridization involving a PDMS microfluidic sensor using fluorescence energy transfer (FRET). However, there are some limitations in its application to real DNA samples because the target DNA must be labelled with a suitable fluorescent dye. To resolve this problem, we have developed a new DNA microfluidic sensor using a molecular beacon. By monitoring the change in the restored fluorescence intensity along the channel length, it is possible to rapidly detect any hybridization of the molecular beacon to the target DNA. In this case, the target DNA does not need to be labelled. Our experimental results demonstrate that this microfluidic sensor using a molecular beacon is a promising diagnostic tool for rapid DNA hybridization analysis.

Fast and sensitive DNA analysis using changes in the FRET signals of molecular beacons in a PDMS microfluidic channel

A new DNA hybridization analytical method using a microfluidic channel and a molecular beacon-based probe (MB-probe) is described. A stem-loop DNA oligonucleotide labeled with two fluorophores at the 5' and 3' termini (a donor dye, TET, and an acceptor dye, TAMRA, respectively) was used to carry out a fast and sensitive DNA analysis. The MB-probe utilized the specificity and selectivity of the DNA hairpin-type probe DNA to detect a specific target DNA of interest. The quenching of the fluorescence resonance energy transfer (FRET) signal between the two fluorophores, caused by the sequence-specific hybridization of the MB-probe and the target DNA, was used to detect a DNA hybridization reaction in a poly(dimethylsiloxane) (PDMS) microfluidic channel. The azoospermia gene, DYS 209, was used as the target DNA to demonstrate the applicability of the method. A simple syringe pumping system was used for quick and accurate analysis. The laminar flow along the channel could be easily controlled by the 3-D channel structure and flow speed. By injecting the MB-probe and target DNA solutions into a zigzag-shaped PDMS microfluidic channel, it was possible to detect their sequence-specific hybridization. Surface-enhanced Raman spectroscopy (SERS) was also used to provide complementary evidence of the DNA hybridization. Our data show that this technique is a promising real-time detection method for label-free DNA targets in the solution phase. Figure FRET-based DNA hybridization detection using a molecular beacon in a zigzag-shaped PDMS microfluidic channel.

Geometry and surface-assisted micro flow discretization**A portion of this paper was presented at the 12th International Conference on Solid-State Sensors, Actuators, and Microsystems, June 2003, Boston, USA.

This paper presents a micro flow discretization system that autonomously digitizes continuous liquid flow into nanoliter segments. Powered by the interactions between liquid flow and micro-channels, the discretization process does not consume any electricity or require any external control. In the prototype demonstration, the discretizer is made of PDMS microfluidic channels with desired geometries and surface properties. Employing a novel self-aligned masking process followed by oxygen plasma treatment to pattern the three-dimensional channel surfaces, the areas exposed to plasma are converted from naturally hydrophobic into hydrophilic while the others covered by the mask remain hydrophobic. With the assistance of channel geometries and hydrophobic/hydrophilic surface patterns, continuous water flow has been split by interfacial forces into segments with controllable and pre-determined volumes from 15 to 35 nl. As such, this autonomous flow discretizer could serve a new class of metering and manipulation schemes for microfluidic applications including drug delivery and lab-on-a-chip.

Joule heating and its effects on electroosmotic flow in microfluidic channels

Joule heating is resulted from inevitable volumetric heating when an electric field is applied across conducting media and it would impose limitations to the performance of electrokinetic microfluidic devices. In this paper, the Joule heating and its effects on electroosmotic flow (EOF) in PDMS microfluidic channels are reported. 3D numerical simulation of the Joule heating induced temperature field and its effects on the EOF and electrophoretic transport of solutes in microchannels was performed. Experiments were carried out to verify the proposed models and the developed numerical code. A Rhodamine B based thermometry technique was used to measure the solution temperature distributions in PDMS microfluidic channels. The micro particle image velocimetry (micro-PIV) technique was used to characterize the velocity profiles of the EOF under the influence of Joule heating. The numerical simulations were compared with the experimental results, and reasonable agreement is found. Both the numerical simulations and the experimental results show that the presence of the Joule heating causes the EOF velocity to deviate from its normal ‘‘plug-like’’ profile; the EOF velocity exhibits a concaved shape in the hydrodynamically developing region and a convex (parabolic) pattern in the fully developed region.

Quantitative Determination of Nicotine in a PDMS Microfluidic Channel Using Surface Enhanced Raman Spectroscopy

Rapid and highly sensitive determination of nicotine in a PDMS microfluidic channel was investigated using surface enhanced Raman spectroscopy (SERS). A three-dimensional PDMS microfluidic channel was fabricated for this purpose. This channel shows a high mixing efficiency because the transverse and vertical dispersions of the fluid occur simultaneously through the upper and lower zig zag-type blocks. A higher efficiency of mixing could also be obtained by splitting each of the confluent streams into two sub-streams that then joined and recombined. The SERS signal was measured after nicotine molecules were effectively adsorbed onto silver nanoparticles by passing through the three-dimensional channel. A quantitative analysis of nicotine was performed based on the measured peak area at 1030 <TEX>$cm^{-1}$</TEX>. The detection limit was estimated to be below 0.1 ppm. In this work, the SERS detection, in combination with a PDMS microfluidic channel, has been applied to the quantitative analysis of nicotine in aqueous solution. Compared to the other conventional analytical methods, the detection sensitivity was enhanced up to several orders of magnitude.

Proteins modification of poly(dimethylsiloxane) microfluidic channels for the enhanced microchip electrophoresis

This report described proteins modification of poly(dimethylsiloxane) (PDMS) microfluidic chip based on layer-by-layer (LBL) assembly technique for enhancing separation efficiency. Two kinds of protein-coated films were prepared. One was obtained by successively immobilizing the cationic polyelectrolyte (chitosan, Chit), gold nanoparticles (GNPs), and protein (albumin, Albu) to the PDMS microfluidic channels surface. The other was achieved by sequentially coating lysozyme (Lys) and Albu. Neurotransmitters (dopamine, DA; epinephrine, EP) and environmental pollutants ( p-phenylenediamine, p-PDA; 4-aminophenol, 4-AP; hydroquinone, HQ) as two groups of separation models were studied to evaluate the effect of the functional PDMS microfluidic chips. The results clearly showed these analytes were efficiently separated within 140 s in a 3.7 cm long separation channel and successfully detected with in-channel amperometric detection mode. Experimental parameters in two protocols were optimized in detail. The detection limits of DA, EP, p-PDA, 4-AP, and HQ were 2.0, 4.7, 8.1, 12.3, and 14.8 μM (S/N = 3) on the Chit–GNPs–Albu coated PDMS/PDMS microchip, and 1.2, 2.7, 7.2, 9.8, and 12.2 μM (S/N = 3) on the Lys–Albu coated one, respectively. In addition, through modification, the more homogenous channel surface displayed higher reproducibility and better stability.

Fast and sensitive analysis of DNA hybridization in a PDMS micro-fluidic channel using fluorescence resonance energy transfer

Fluorescence resonance energy transfer has been used to illustrate its applicability to the sensitive detection of DNA hybridization reactions in a PDMS microfluidic channel.

On-Chip Transformation of Bacteria

On-chip transformation of Escherichia coli cells was accomplished for the first time using a microbial array chip. The continuous E. coli transformation procedures were performed on a chip in which the microcompartment was composed of PDMS microfluidic channels and a silicon substrate predeposited with different plasmid DNAs. The PDMS microfluidic device enabled the parallel transformation of E. coli cells with various plasmid DNAs by separating each transformation area. The phenotypic differences reflecting different plasmid DNAs were identified by various approaches such as colorimetry, fluorometry, and electrochemical methods. This microbial array chip could become a versatile tool for many cell biological applications.

Highly sensitive signal detection of duplex dye-labelled DNA oligonucleotides in a PDMS microfluidic chip: confocal surface-enhanced Raman spectroscopic study

Rapid and highly sensitive detection of duplex dye-labelled DNA sequences in a PDMS microfluidic channel was investigated using confocal surface enhanced Raman spectroscopy (SERS). This method does not need either an immobilization procedure or a PCR amplification procedure, which are essential for a DNA microarray chip. Furthermore, Raman peaks of each dye-labelled DNA can be easily resolved since they are much narrower than the corresponding broad fluorescence bands. To find the potential applicability of confocal SERS for sensitive bio-detection in a microfluidic channel, the mixture of two different dye-labelled (TAMRA and Cy3) sex determining Y genes, SRY and SPGY1, was adsorbed on silver colloids in the alligator teeth-shaped PDMS microfluidic channel and its SERS signals were measured under flowing conditions. Its major SERS peaks were observable down to the concentration of 10(-11) M. In the present study, we explore the feasibility of confocal SERS for the highly sensitive detection of duplex dye-labelled DNA oligonucleotides in a PDMS microfluidic chip.

Ultra-sensitive trace analysis of cyanide water pollutant in a PDMS microfluidic channel using surface-enhanced Raman spectroscopy

Rapid and highly sensitive trace analysis of cyanide water pollutant in an alligator teeth-shaped PDMS microfluidic channel was investigated using surface-enhanced Raman spectroscopy. Compared with previously reported analytical methods, the detection sensitivity was enhanced by several orders of magnitude.

Analysis of Passive Mixing Behavior in a Poly(Dimethylsiloxane) Microfluidic Channel Using Confocal Fluorescence and Raman Microscopy

Confocal fluorescence microscopy (CFM) and confocal Raman microscopy (CRM) have been applied to monitor the laminar flow mixing behavior in a poly(dimethylsiloxane) (PDMS) microfluidic channel. Two passive PDMS micromixing devices were fabricated for this purpose: a two-dimensional round-wave channel and a three-dimensional serpentine channel. The microscale laminar flow mixing of ethanol and isopropanol was evaluated using the CFM and CRM at various flow rates. The mixing behavior of confluent streams in the microchannel was assessed by determining the degree of color change in Rhodamine 6G dye on mixing using the CFM. However, it was also possible to quantitatively evaluate the mixing process without employing a fluorescence label using the CRM. The results show a strong potential for CRM as a highly sensitive detection tool to measure fundamental fluid mixing processes and to provide detailed information on chemical changes of non-fluorescent reaction mixtures in a PDMS microfluidic channel.

Formation of droplets of alternating composition in microfluidic channels and applications to indexing of concentrations in droplet-based assays.

For screening the conditions for a reaction by using droplets (or plugs) as microreactors, the composition of the droplets must be indexed. Indexing here refers to measuring the concentration of a solute by addition of a marker, either internal or external. Indexing may be performed by forming droplet pairs, where in each pair the first droplet is used to conduct the reaction, and the second droplet is used to index the composition of the first droplet. This paper characterizes a method for creating droplet pairs by generating alternating droplets, of two sets of aqueous solutions in a flow of immiscible carrier fluid within PDMS and glass microfluidic channels. The paper also demonstrates that the technique can be used to index the composition of the droplets, and this application is illustrated by screening conditions of protein crystallization. The fluid properties required to form the steady flow of the alternating droplets in a microchannel were characterized as a function of the capillary number Ca and water fraction. Four regimes were observed. At the lowest values of Ca, the droplets of the two streams coalesced; at intermediate values of Ca the alternating droplets formed reliably. At even higher values of Ca, shear forces dominated and caused formation of droplets that were smaller than the cross-sectional dimension of the channel; at the highest values of Ca, coflowing laminar streams of the two immiscible fluids formed. In addition to screening of protein crystallization conditions, understanding of the fluid flow in this system may extend this indexing approach to other chemical and biological assays performed on a microfluidic chip.

Tailoring the Surface Properties of Poly(dimethylsiloxane) Microfluidic Devices

Poly(dimethylsiloxane) (PDMS) is an attractive material for microelectrophoretic applications because of its ease of fabrication, low cost, and optical transparency. However, its use remains limited compared to that of glass. A major reason is the difficulty of tailoring the surface properties of PDMS. We demonstrate UV grafting of co-mixed monomers to customize the surface properties of PDMS microfluidic channels in a simple one-step process. By co-mixing a neutral monomer with a charged monomer in different ratios, properties between those of the neutral monomer and those of the charged monomer could be selected. Mixtures of four different neutral monomers and two different charged monomers were grafted onto PDMS surfaces. Functional microchannels were fabricated from PDMS halves grafted with each of the different mixtures. By varying the concentration of the charged monomer, microchannels with electrophoretic mobilities between +4 x 10(-4) cm2/(V s) and -2 x 10(-4) cm2/(V s) were attainable. In addition, both the contact angle of the coated surfaces and the electrophoretic mobility of the coated microchannels were stable over time and upon exposure to air. By carefully selecting mixtures ofmonomers with the appropriate properties, it may be possible to tailor the surface of PDMS for a large number of different applications.