A spatially resolved nucleic acid biochip based on a gradient of density of immobilized probe oligonucleotide

The potential for a new biochip design based on a continuous gradient of density of immobilized single-stranded DNA oligonucleotide probes (ssDNA) is explored. This gradient resolved information platform (GRIP) can provide sequence identification based on the spatial location and extent of hybridization by a target sequence. Surfaces based on indium-tin oxide (ITO) on glass were first functionalized by 3-aminopropyltriethoxysilane (APTES) followed by attachment of glutaraldehyde, prior to immobilization of oligonucleotide probe that was terminated with amine. The use of Cy₃ and Cy₅ dye-labelled ssDNA probes and targets allowed estimation of density and correlation of the location of binding of labelled targets. Probe molecules of 20 mer lengths were loaded to produce density gradients in the range of 1.0-200 ng/mm². The biochips could resolve a mixture of fully complementary five base-pair mismatched targets by the location of binding on the surface. Thermal control provided additional selectivity. Thermal cycling and washing provided for regeneration of the surface, and the fluorescence intensities showed no deterioration in at least five cycles of hybridization reactions.     

Rapid discrimination of single-nucleotide mismatches using a microfluidic device with monolayered beads

A microfluidic device incorporating monolayered beads is developed for the discrimination of single-nucleotide mismatches, based on the differential dissociation kinetics between perfect match (PM) and mismatched (MM) duplexes. The monolayered beads are used as solid support for the immobilization of oligonucleotide probes containing a single-base variation. Target oligonucleotides hybridize to the probes, forming either PM duplexes or MM duplexes containing a single mismatch. Optimization studies show that PM and MM duplexes are easily discriminated based on their dissociation but not hybridization kinetics under an optimized buffer composition of 100 mM NaCl and 50% formamide. Detection of single-nucleotide polymorphism (SNP) using the device is demonstrated within 8 min using four probes containing all the possible single-base variants. The device can easily be modified to integrate multiplexed detection, making high-throughput SNP detection possible.     

Immobilized streptavidin gradients as bioconjugation platforms

Surface density gradients of streptavidin (SAV) were created on solid surfaces and demonstrated functionality as a bioconjugation platform. The surface density of immobilized streptavidin steadily increased in one dimension from 0 to 235 ng cm(-2) over a distance of 10 mm. The density of coupled protein was controlled by its immobilization onto a polymer surface bearing a gradient of aldehyde group density, onto which SAV was covalently linked using spontaneous imine bond formation between surface aldehyde functional groups and primary amine groups on the protein. As a control, human serum albumin was immobilized in the same manner. The gradient density of aldehyde groups was created using a method of simultaneous plasma copolymerization of ethanol and propionaldehyde. Control over the surface density of aldehyde groups was achieved by manipulating the flow rates of these vapors while moving a mask across substrates during plasma discharge. Immobilized SAV was able to bind biotinylated probes, indicating that the protein retained its functionality after being immobilized. This plasma polymerization technique conveniently allows virtually any substrate to be equipped with tunable protein gradients and provides a widely applicable method for bioconjugation to study effects arising from controllable surface densities of proteins.     

Joule heating effects on electrokinetic flows with conductivity gradients

Instability occurs in the electrokinetic flow of fluids with conductivity and/or permittivity gradients if the applied electric field is beyond a critical value. Understanding such an electrokinetic instability is significant for both improved transport (via the suppressed instability) and enhanced mixing (via the promoted instability) of liquid samples in microfluidic applications. This work presents the first study of Joule heating effects on electrokinetic microchannel flows with conductivity gradients using a combined experimental and numerical method. The experimentally observed flow patterns and measured critical electric fields under Joule heating effects to different extents are reasonably predicted by a depth-averaged numerical model. It is found that Joule heating increases the critical electric field for the onset of electrokinetic instability because the induced fluid temperature rise and in turn the fluid property change (primarily the decreased permittivity) lead to a smaller electric Rayleigh number.     

DNA mutation detection with chip-based temperature gradient capillary electrophoresis using a slantwise radiative heating system

A simple and robust chip-based temperature gradient capillary electrophoresis (TGCE) system was developed for DNA mutation/single-nucleotide polymorphism (SNP) analysis using a radiative heating system. Reproducible, stable and uniform temperature gradients were established along a 3 cm length of the electrophoretic separation channel using a single thermostated aluminium heater plate. The heater was slightly slanted relative to the plane of the glass chip at 0.2-1.3 degrees by inserting thin spacers between the plate and chip at one end to produce differences in radiative heating that created the temperature gradient. On-chip TGCE analyses of 4 mutant DNA model samples amplified from plasmid templates, each containing a single base substitution, with a wide range of melting temperatures, showed that mutations were successfully detected under a wide temperature gradient of 10 degrees C and within a short gradient region of about 3 cm (3.3 degrees C cm(-1) gradient). The radiative heating system was able to establish stable spatial temperature gradients along short microfluidic separation channels using simple peripheral equipment and manipulation while ensuring good resolution for detecting a wide range of mutations. Effectiveness of the system was demonstrated by the successful detection of K-ras gene mutations in 6 colon cancer cell lines.     

Electric potential induced dissociation of hybridized DNA with hairpin motif immobilized on silicon surface

DNA probes were immobilized on silicon surfaces through ester condensation between the -COOH group on the surface and the terminal -OH group in the oligonucleotide, and the surface density of DNA probes against the concentration of immobilization solution was measured by radioactive labeling. The dissociation of DNA duplex on the surface by an electric potential was studied with the scanning potential hairpin denaturation/dissociation (SPHD). The influence of the stem length in the hairpin probe on the SPHD curve was systematically investigated. It was found that the capability of discrimination on single nucleotide polymorphism (SNP) by a hairpin probe was related to the free energy of formation of the secondary structure in the probe (DeltaG(ss)). In our system, when DeltaG(ss) was around -3 kcal/mol, an optimal recognition of SNP was reached and the SPHD curve was sigmoid. In contrast, the equivalent SPHD curve from a linear probe was exponential-decay alike with a poor discrimination of SNP. The concentration dependent experiments showed good linearity between the melting potential and logarithm of target concentration in the range of 1 x 10(-9) to 5 x 10(-7) M.     

Magnetic force-based multiplexed immunoassay using superparamagnetic nanoparticles in microfluidic channel

This paper describes a novel microfluidic immunoassay utilizing binding of superparamagnetic nanoparticles to beads and deflection of these beads in a magnetic field as the signal for measuring the presence of analyte. The superparamagnetic 50 nm nanoparticles and fluorescent 1 microm polystyrene beads are immobilized with specific antibodies. When target analytes react with the polystyrene beads and superparamagnetic nanoparticles simultaneously, the superparamagnetic nanoparticles can be attached onto the microbeads by the antigen-antibody complex. In the poly(dimethylsiloxane)(PDMS) microfluidic channel, only the microbeads conjugated with superparamagnetic nanoparticles by analytes consequently move to the high gradient magnetic fields under the specific applied magnetic field. In this study, the magnetic force-based microfluidic immunoassay is successfully applied to detect the rabbit IgG and mouse IgG as model analytes. The lowest concentration of rabbit IgG and mouse IgG measured over the background is 244 pg mL(-1) and 15.6 ng mL(-1), respectively. The velocities of microbeads conjugated with superparamagnetic nanoparticles are demonstrated by magnetic field gradients in microfluidic channels and compared with the calculated magnetic field gradients. Moreover, dual analyte detection in a single reaction is also performed by the fluorescent encoded microbeads in the microfluidic device. Detection range and lower detection limit can be controlled by the microbeads concentration and the higher magnetic field gradient.     

A fluorescent molecular switch for room temperature operation based on oligonucleotide hybridization without labeling of probes or targets

A molecular switch was prepared by self-assembly. Neutravidin served as a template that allowed for a biotinylated probe oligonucleotide to be placed adjacent to a biotinylated long-chain linker that was terminated with thiazole orange (TO). Hybridization of probe oligonucleotide with target to form double-stranded DNA resulted in intercalation of the adjacent TO probe. This was a reversible process that could be tracked by fluorescence intensity changes. Formamide was used as a denaturant for double-stranded DNA, and could be used to depress thermal denaturation temperatures. In this work formamide had a dual function, providing for control of hybridization selectivity at room temperature, while concurrently ameliorating non-specific adsorption to improve signal-to-noise when using thiazole orange as a fluorescence signalling agent to determine oligonucleotide hybridization. Room temperature single nucleotide polymorphism (SNP) discrimination for oligonucleotide targets was achieved both in solution and for molecular switches that were immobilized onto optical fibers. In solution, a concentration of 18.5% formamide provided greater than 40-fold signal difference between single-stranded DNA and double-stranded DNA, in contrast to only a 2-fold difference in the absence of formamide. Selectivity for SNP determination in solution was demonstrated using targets of varying lengths including a 141-base PCR amplicon. The improved signal-to-noise achieved by use of formamide is likely due to preferential displacement of dye molecules that are otherwise electrostatically bound to the polyanionic nucleic acid backbone.     

On-chip multiplexed solid-phase nucleic acid hybridization assay using spatial profiles of immobilized quantum dots and fluorescence resonance energy transfer

A microfluidic based solid-phase assay for the multiplexed detection of nucleic acid hybridization using quantum dot (QD) mediated fluorescence resonance energy transfer (FRET) is described herein. The glass surface of hybrid glass-polydimethylsiloxane (PDMS) microfluidic channels was chemically modified to assemble the biorecognition interface. Multiplexing was demonstrated using a detection system that was comprised of two colors of immobilized semi-conductor QDs and two different oligonucleotide probe sequences. Green-emitting and red-emitting QDs were paired with Cy3 and Alexa Fluor 647 (A647) labeled oligonucleotides, respectively. The QDs served as energy donors for the transduction of dye labeled oligonucleotide targets. The in-channel assembly of the biorecognition interface and the subsequent introduction of oligonucleotide targets was accomplished within minutes using a combination of electroosmotic flow and electrophoretic force. The concurrent quantification of femtomole quantities of two target sequences was possible by measuring the spatial coverage of FRET sensitized emission along the length of the channel. In previous reports, multiplexed QD-FRET hybridization assays that employed a ratiometric method for quantification had challenges associated with lower analytical sensitivity arising from both donor and acceptor dilution that resulted in reduced energy transfer pathways as compared to single-color hybridization assays. Herein, a spatial method for quantification that is based on in-channel QD-FRET profiles provided higher analytical sensitivity in the multiplexed assay format as compared to single-color hybridization assays. The selectivity of the multiplexed hybridization assays was demonstrated by discrimination between a fully-complementary sequence and a 3 base pair sequence at a contrast ratio of 8 to 1.     

Microfluidic DNA microarray analysis: a review

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 surface-to-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 pressure-driven 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.     

Mucin (MUC5AC) expression by lung epithelial cells cultured in a microfluidic gradient device

We have developed a microfluidic gradient device for controlling mucin gene expression of NCI-H292 epithelial cells derived from lung tissues. We hypothesized that gradient profiles would control mucin gene expression of lung epithelial cells. However, it was not possible to generate various stable gradient profiles using conventional culture methods. To address this limitation, we used a microfluidic gradient device to create various gradient profiles (i.e. non-linear, linear, and flat) in a temporal and spatial manner. NCI-H292 lung epithelial cells were exposed to concentration gradients of epidermal growth factor in a microfluidic gradient device with continuous medium perfusion. We demonstrated an effect of gradient profiles on mucin expression of lung epithelial cells cultured in the microfluidic gradient device. It was revealed that NCI-H292 lung epithelial cells exposed to the flat gradient profile of the epidermal growth factor exhibited high expression of mucin as compared with cells exposed to non-linear and linear gradient profiles. Therefore, this microfluidic gradient device could be a potentially useful tool for regulating the mucin expression of lung epithelial cells exposed to chemokine gradient profiles.     

DNA hole transport on an electrode: application to effective photoelectrochemical SNP typing

A useful feature of DNA is that long-range hole transport through DNA is readily achieved. Photostimulated long-range hole transport through DNA has prospective use in the development of a conceptually new electrochemical single-nucleotide polymorphism (SNP) typing method for use as a versatile platform for gene diagnostics and pharmacogenetics. We have applied artificial DNAs designed for photostimulated long-range hole transport through DNA to SNP typing. By hybridizing photosensitizer-equipped DNA probes, immobilized on gold working electrodes, with a target DNA strand containing an SNP site, we observed a cathodic photocurrent, which markedly changed depending on the nature of the base at the specific site. The use of a combination of hole-transporting bases constitutes a very powerful method for a single-step electrochemical assay applicable to SNP typing of all types of sequences.     

玻璃微流控通道中水凝胶固定寡核苷酸探针的方法及应用

核酸杂交是分子生物学研究中最常用和最基本的分析方法之一．杂交技术有多种,主要区别在于探针的固定．目前常用的是将探针直接固定在载体表面（尼龙膜或硅烷化的玻片）或用磁珠法和水凝胶法固定,其中水凝胶法兼有三维立体和简单实用的优势,其发展颇为引人注意．微流控芯片技术具有集成化和自动化的优势．将水凝胶和微流控技术相结合,将使核酸分析中的杂交、变性以及重新杂交等操作更为简单、快速、易行．     

Computer simulation study of probe-target hybridization in model DNA microarrays: effect of probe surface density and target concentration

We use lattice Monte Carlo simulations to study the thermodynamics of hybridization of single-stranded "target" genes in solution with complementary "probe" DNA molecules immobilized on a microarray surface. The target molecules in our system contain 48 segments and the probes tethered on a hard surface contain 8-24 segments. The segments on the probe and target are distinct, with each segment representing a sequence of nucleotides that interacts exclusively with its unique complementary target segment with a single hybridization energy; all other interactions are zero. We examine how surface density (number of probes per unit surface area) and concentration of target molecules affect the extent of hybridization. For short probe lengths, as the surface density increases, the probability of binding long stretches of target segments increases at low surface density, reaches a maximum at an intermediate surface density, and then decreases at high surface density. Furthermore, as the surface density increases, the target is less likely to bind completely to one probe; instead, it binds simultaneously to multiple probes. At short probe lengths, as the target concentration increases, the fraction of targets binding completely to the probes (specificity) decreases. At long probe lengths, varying the target concentration does not affect the specificity. At all target concentrations as the probe length increases, the fraction of target molecules bound to the probes by at least one segment (sensitivity) increases while the fraction of target molecules completely bound to the probes (specificity) decreases. This work provides general guidelines to maximizing microarray sensitivity and specificity. Our results suggest that the sensitivity and specificity can be maximized by using probes 130-180 nucleotides long at a surface density in the range of 7 x 10(-5)- 3 x 10(-4) probe molecules per nm(2).     

Recirculating flow accelerates DNA microarray hybridization in a microfluidic device

A recirculating microfluidic device fabricated by laminating Mylar and glass was developed for the analysis of hybridization of oligonucleotides to DNA microarrays. The device is part of a system that provides controlled hybridization to DNA probes immobilized in a microarray of polyacrylamide gel pads using recirculation and temperature control. The system was used to obtain real-time kinetics of DNA hybridization and more accurate melting profiles of target-probe duplexes than possible using a static hybridization format. Recirculation shortened the time of perfect match target-probe hybridization from 6 hours to 2 hours and shifted the Td by 1.54 degrees C, relative to static conditions. The experimental results were consistent with a three-dimensional simulation of hybridization using a recirculating buffer system.     

Microfluidic nanoplasmonic-enabled device for multiplex DNA detection

We describe a rapid, quantitative, multiplex, self-labelled, and real-time DNA biosensor employing Ag nanoparticle-bound DNA hairpin probes immobilized in a microfluidic channel. Capture of complementary target DNAs by the microarrayed DNA hairpin probes results in a positive fluorescence signal via a conformational change of the probe molecules, signalling the presence of target DNAs. The device's capability for quantitative analyses was evaluated and a detection time as low as 6 min (with a target flow rate of 0.5 μl min(-1)) was sufficient to generate significant detection signals. This detection time translates to merely 3 μl of target solution consumption. An unoptimized sensitivity of 500 pM was demonstrated for this device.     

Simple replication methods for producing nanoslits in thermoplastics and the transport dynamics of double-stranded DNA through these slits

Mixed-scale nano- and microfluidic networks were fabricated in thermoplastics using simple and robust methods that did not require the use of sophisticated equipment to produce the nanostructures. High-precision micromilling (HPMM) and photolithography were used to generate mixed-scale molding tools that were subsequently used for producing fluidic networks into thermoplastics such as poly(methyl methacrylate), PMMA, cyclic olefin copolymer, COC, and polycarbonate, PC. Nanoslit arrays were imprinted into the polymer using a nanoimprinting tool, which was composed of an optical mask with patterns that were 2-7 μm in width and a depth defined by the Cr layer (100 nm), which was deposited onto glass. The device also contained a microchannel network that was hot embossed into the polymer substrate using a metal molding tool prepared via HPMM. The mixed-scale device could also be used as a master to produce a polymer stamp, which was made from polydimethylsiloxane, PDMS, and used to generate the mixed-scale fluidic network in a single step. Thermal fusion bonding of the cover plate to the substrate at a temperature below their respective T(g) was accomplished by oxygen plasma treatment of both the substrate and cover plate, which significantly reduced thermally induced structural deformation during assembly: ～6% for PMMA and ～9% for COC nanoslits. The electrokinetic transport properties of double-stranded DNA (dsDNA) through the polymeric nanoslits (PMMA and COC) were carried out. In these polymer devices, the dsDNA demonstrated a field-dependent electrophoretic mobility with intermittent transport dynamics. DNA mobilities were found to be 8.2 ± 0.7 × 10(-4) cm(2) V(-1) s(-1) and 7.6 ± 0.6 × 10(-4) cm(2) V(-1) s(-1) for PMMA and COC, respectively, at a field strength of 25 V cm(-1). The extension factors for λ-DNA were 0.46 in PMMA and 0.53 in COC for the nanoslits (2-6% standard deviation).     

Accurate Zygote‐Specific Discrimination of Single‐Nucleotide Polymorphisms Using Microfluidic Electrochemical DNA Melting Curves

We report the first electrochemical system for the detection of single‐nucleotide polymorphisms (SNPs) that can accurately discriminate homozygous and heterozygous genotypes using microfluidics technology. To achieve this, our system performs real‐time melting‐curve analysis of surface‐immobilized hybridization probes. As an example, we used our sensor to analyze two SNPs in the apolipoprotein E (ApoE) gene, where homozygous and heterozygous mutations greatly affect the risk of late‐onset Alzheimer’s disease. Using probes specific for each SNP, we simultaneously acquired melting curves for probe–target duplexes at two different loci and thereby accurately distinguish all six possible ApoE allele combinations. Since the design of our device and probes can be readily adapted for targeting other loci, we believe that our method offers a modular platform for the diagnosis of SNP‐based diseases and personalized medicine.     

Fabrication of DNA microarrays on nanoengineered polymeric ultrathin film prepared by self-assembly of polyelectrolyte multilayers

Microarray-based technology is in need of flexible and cost-effective chemistry for fabrication of oligonucleotide microarrays. We have developed a novel method for the fabrication of oligonucleotide microarrays with unmodified oligonucleotide probes on nanoengineered three-dimensional thin films that are deposited on glass slides by consecutive layer-to-layer adsorption of polyelectrolytes. Unmodified oligonucleotide probes were spotted and immobilized on these multilayered polyelectrolyte thin films (PET) by electrostatic adsorption and entrapment on the porous structure of the PET film. The PET provides higher probe binding capacity and thus higher hybridization signal than that of the traditional two-dimensional aminosilane and poly-L-lysine coated slides. Immobilized probe densities of 3.4 x 10(12)/cm2 were observed for microarray spots on PET with unmodified 50-mer oligonucleotide probes, which is comparable to the immobilized probe densities of alkyamine-modified 50-mer probes end-tethered on an aldehyde-functionalized slide. The study of hybridization efficiency showed that 90% of immobilized probes on PET film are accessible to target DNA to form duplex format in hybridization. The DNA microarray fabricated on PET film has wider dynamic range (about 3 orders of magnitude) and lower detection limit (0.5 nM) than the conventional amino- and aldehyde-functionalized slides. Oligonucleotide microarrays fabricated on these PET-coated slides also had consistent spot morphology. In addition, discrimination of single nucleotide polymorphism of 16S rRNA genes was achieved with the PET-based oligonucleotide microarrays. The PET microarrays constructed by our self-assembly process is cost-effective, versatile, and well suited for immobilizing many types of biological active molecules so that a wide variety of microarray formats can be developed.     

Profiling pH gradients across nanocapillary array membranes connecting microfluidic channels

Nanocapillary array membranes (NCAMs), comprised of thin (d approximately 5-10 microm) nuclear track-etched polycarbonate sheets containing approximately 10(8) cm(-2) nearly parallel nanometer-diameter capillaries, may act to gate fluid transport between microfluidic channels to effect, for example, sample collection. There is interest in H+-transport across these NCAMs because there is significant practical interest in being able to process analyte-containing samples under different pH conditions in adjacent layers of an integrated microfluidic circuit and because protons, with their inherently high mobility, present a challenge in separating microfluidic environments with different properties. To evaluate the capability of NCAMs to support pH gradients, the proton transport properties of NCAMs were studied using laser scanning confocal fluorescence microscopy (LSCFM). Spatiotemporal maps of [H+] in microfluidic channels adjacent to the NCAMs yield information regarding diffusive and electrokinetic transport of protons. The NCAMs studied here are characterized by a positive zeta potential, zeta > 0, so at small nanocapillary diameters, the overlap of electrical double layers associated with opposite walls of the nanocapillary establish an energy barrier for either diffusion or electrokinetic transport of cations through the nanometer-diameter capillaries due to the positive charge on the nanocapillary surface. Proton transfer through an NCAM into microchannels is reduced for pore diameters, d < or = 50 nm and ionic strengths I < or = 50 mM, while for large pore diameters or solution ionic strengths, the incomplete overlap of electric double layer allows more facile ionic transfer across the membranes. These results establish the operating conditions for the development of multilevel integrated nanofluidic/microfluidic architectures which can support multidimensional chemical analysis of mass-limited samples requiring sequential operations to be implemented at different pH values.