Showing papers on "Biochip published in 2014"

Femtosecond laser 3D micromachining: a powerful tool for the fabrication of microfluidic, optofluidic, and electrofluidic devices based on glass.

Abstract: Femtosecond lasers have unique characteristics of ultrashort pulse width and extremely high peak intensity; however, one of the most important features of femtosecond laser processing is that strong absorption can be induced only at the focus position inside transparent materials due to nonlinear multiphoton absorption. This exclusive feature makes it possible to directly fabricate three-dimensional (3D) microfluidic devices in glass microchips by two methods: 3D internal modification using direct femtosecond laser writing followed by chemical wet etching (femtosecond laser-assisted etching, FLAE) and direct ablation of glass in water (water-assisted femtosecond laser drilling, WAFLD). Direct femtosecond laser writing also enables the integration of micromechanical, microelectronic, and microoptical components into the 3D microfluidic devices without stacking or bonding substrates. This paper gives a comprehensive review on the state-of-the-art femtosecond laser 3D micromachining for the fabrication of microfluidic, optofluidic, and electrofluidic devices. A new strategy (hybrid femtosecond laser processing) is also presented, in which FLAE is combined with femtosecond laser two-photon polymerization to realize a new type of biochip termed the ship-in-a-bottle biochip.

Hybrid femtosecond laser microfabrication to achieve true 3D glass/polymer composite biochips with multiscale features and high performance: the concept of ship‐in‐a‐bottle biochip

Abstract: True three-dimensionally (3D) integrated biochips are crucial for realizing high performance biochemical analysis and cell engineering, which remain ultimate challenges. In this paper, a new method termed hybrid femtosecond laser microfabrication which consists of successive subtractive (femtosecond laser-assisted wet etching of glass) and additive (two-photon polymerization of polymer) 3D microprocessing was proposed for realizing 3D “ship-in-a-bottle” microchip. Such novel microchips were fabricated by integrating various 3D polymer micro/nanostructures into flexible 3D glass microfluidic channels. The high quality of microchips was ensured by quantitatively investigating the experimental processes containing “line-to-line” scanning mode, improved annealing temperature (645°C), increased prebaking time (18 h for 1mm-length channel), optimal laser power (1.9 times larger than that on the surface) and longer developing time (6 times larger). The ship-in-a-bottle biochips show high capabilities to provide simultaneous filtering and mixing with 87% efficiency in a shorter distance and on-chip synthesis of ZnO microflower particles.

Microfluidic Systems with Ion-Selective Membranes

Abstract: When integrated into microfluidic chips, ion-selective nanoporous polymer and solid-state membranes can be used for on-chip pumping, pH actuation, analyte concentration, molecular separation, reactive mixing, and molecular sensing. They offer numerous functionalities and are hence superior to paper-based devices for point-of-care biochips, with only slightly more investment in fabrication and material costs required. In this review, we first discuss the fundamentals of several nonequilibrium ion current phenomena associated with ion-selective membranes, many of them revealed by studies with fabricated single nanochannels/nanopores. We then focus on how the plethora of phenomena has been applied for transport, separation, concentration, and detection of biomolecules on biochips.

Testing of Flow-Based Microfluidic Biochips: Fault Modeling, Test Generation, and Experimental Demonstration

Abstract: Recent advances in flow-based microfluidics have led to the emergence of biochemistry-on-a-chip as a new paradigm in clinical diagnostics and biomolecular recognition. However, a potential roadblock in the deployment of microfluidic biochips is the lack of test techniques to screen defective devices before they are used for biochemical analysis. Defective chips lead to repetition of experiments, which is undesirable due to high reagent cost and limited availability of samples. Prior work on fault detection in biochips has been limited to digital (“droplet”) microfluidics and other electrode-based technology platforms. The paper proposes the first approach for automated testing of flow-based microfluidic biochips that are designed using membrane-based valves for flow control. The proposed test technique is based on a behavioral abstraction of physical defects in microchannels and valves. The flow paths and flow control in the microfluidic device are modeled as a logic circuit composed of Boolean gates, which allows test generation to be carried out using standard automatic test pattern generation tools. The tests derived using the logic circuit model are then mapped to fluidic operations involving pumps and pressure sensors in the biochip. Feedback from pressure sensors can be compared to expected responses based on the logic circuit model, whereby the types and positions of defects are identified. We show how a fabricated biochip can be tested using the proposed method, and demonstrate experimental results for two additional fabricated chips.

Exact One-pass Synthesis of Digital Microfluidic Biochips

Abstract: With the advances of the microfluidic technology, the design of digital microfluidic biochips recently received significant attention. But thus far, the corresponding design tasks such as binding, scheduling, placement, and routing have usually been considered separately. Furthermore, often just heuristic results have been obtained. In this work, we present a one-pass synthesis scheme which directly realizes the desired functionality onto the chip and, at the same time, guarantees minimality with respect to area and/or timing. For this purpose, the deductive power of solvers for Boolean satisfiability is exploited. Experiments show how the approach leverages the design of the respective devices.

Design of a Microchannel-Nanochannel-Microchannel Array Based Nanoelectroporation System for Precise Gene Transfection

Abstract: A micro/nano-fabrication process of a nanochannel electroporation (NEP) array and its application for precise delivery of plasmid for non-viral gene transfection is described. A dip-combing device is optimized to produce DNA nanowires across a microridge array patterned on the polydimethylsiloxane (PDMS) surface with a yield up to 95%. Molecular imprinting based on a low viscosity resin, 1,4-butanediol diacrylate (1,4-BDDA), adopted to convert the microridge-nanowire-microridge array into a microchannel-nanochannel-microchannel (MNM) array. Secondary machining by femtosecond laser ablation is applied to shorten one side of microchannels from 3000 to 50 μm to facilitate cell loading and unloading. The biochip is then sealed in a packaging case with reservoirs and microfluidic channels to enable cell and plasmid loading, and to protect the biochip from leakage and contamination. The package case can be opened for cell unloading after NEP to allow for the follow-up cell culture and analysis. These NEP cases can be placed in a spinning disc and up to ten discs can be piled together for spinning. The resulting centrifugal force can simultaneously manipulate hundreds or thousands of cells into microchannels of NEP arrays within 3 minutes. To demonstrate its application, a 13 kbp OSKM plasmid of induced pluripotent stem cell (iPSC) is injected into mouse embryonic fibroblasts cells (MEFCs). Fluorescence detection of transfected cells within the NEP biochips shows that the delivered dosage is high and much more uniform compared with similar gene transfection carried out by the conventional bulk electroporation (BEP) method.

Microfluidic channels laser-cut in thin double-sided tapes: Cost-effective biocompatible fluidics in minutes from design to final integration with optical biochips

Abstract: A simple, reliable and cost-effective fluidic channel, fabricated by using double-sided pressure-sensitive tapes, is demonstrated here A laser-cutting method is applied to engrave structures in sheets of the tapes After peeling off the tape liners, the structures could be easily integrated at room temperature with label-free optical waveguide biochips without further modifications or additional processing steps It is shown that the well-defined and controllable height of the channels is advantageous for stopped-flow measurements of analyte binding The easy fabrication of a fully transparent integrated sensor unit – tape cuvette system is also demonstrated for parallel microscopic investigations The transparent unit was used to on-line monitor the surface adhesion of Salmonella cells on poly-l-lysine-coated biochip surfaces, followed by the straightforward microscopic visualization of the adhered bacterial cells The material of the double sided tape is stable in aqueous solutions Furthermore, its material is biocompatible, making it ideal for biological applications Excellent, stable and reversible bonding of the microstructured tapes to biocompatible plastic and glass is also demonstrated The simplicity of the fabrication at ambient temperatures makes the developed processes appealing for lab-on-a-chip applications, particularly if the bonded biochips are precious

Microfluidic approaches for epithelial cell layer culture and characterisation

Abstract: In higher eukaryotes, epithelial cell layers line most body cavities and form selective barriers that regulate the exchange of solutes between compartments. In order to fulfil these functions, the cells assume a polarised architecture and maintain two distinct plasma membrane domains, the apical domain facing the lumen and the basolateral domain facing other cells and the extracellular matrix. Microfluidic biochips offer the unique opportunity to establish novel in vitro models of epithelia in which the in vivo microenvironment of epithelial cells is precisely reconstituted. In addition, analytical tools to monitor biologically relevant parameters can be directly integrated on-chip. In this review we summarise recently developed biochip designs for culturing epithelial cell layers. Since endothelial cell layers, which line blood vessels, have similar barrier functions and polar organisation as epithelial cell layers, we also discuss biochips for culturing endothelial cell layers. Furthermore, we review approaches to integrate tools to analyse and manipulate epithelia and endothelia in microfluidic biochips; including methods to perform electrical impedance spectroscopy; methods to detect substances undergoing trans-epithelial transport via fluorescence, spectrophotometry, and mass spectrometry; techniques to mechanically stimulate cells via stretching and fluid flow-induced shear stress; and methods to carry out high-resolution imaging of vesicular trafficking using light microscopy. Taken together, this versatile microfluidic toolbox enables novel experimental approaches to characterise epithelial monolayers.

Fast Online Synthesis of Digital Microfluidic Biochips

Abstract: We introduce an online synthesis flow, focusing primarily on the virtual topology and operation binder, for digital microfluidic biochips, which will enable real-time response to errors and control flow. The objective of this flow is to facilitate fast assay synthesis while minimally compromising the quality of results. In particular, we show that a virtual topology, which constrains the allowable locations of assay operations such as mixing, dilution, sensing, etc., in lieu of traditional placement, can significantly speed up the synthesis process without significantly lengthening assay execution time. We present a base virtual topology and show how it can be leveraged to reduce algorithmic runtimes and guarantee rout ability. We later present several variations of the virtual topology and present experimental results demonstrating best-design practices. We present two binding solutions. The first is a left-edge binding algorithm, while the second is a more intelligent path-based binding algorithm that leverages spatial and temporal locality to produce superior results.

Multicolor and erasable DNA photolithography.

Abstract: The immobilization of DNA molecules onto a solid support is a crucial step in biochip research and related applications. In this work, we report a DNA photolithography method based on photocleavage of 2-nitrobenzyl linker-modified DNA strands. These strands were subjected to ultraviolet light irradiation to generate multiple short DNA strands in a programmable manner. Coupling the toehold-mediated DNA strand-displacement reaction with DNA photolithography enabled the fabrication of a DNA chip surface with multifunctional DNA patterns having complex geometrical structures at the microscale level. The erasable DNA photolithography strategy was developed to allow different paintings on the same chip. Furthermore, the asymmetrical modification of colloidal particles was carried out by using this photolithography strategy. This strategy has broad applications in biosensors, nanodevices, and DNA-nanostructure fabrication.

An Efficient Bi-criteria Flow Channel Routing Algorithm For Flow-based Microfluidic Biochips

Abstract: Rapid growth in capacity makes flow-based microfluidic biochips a promising candidate for biochemical analysis because they can integrate more complex functions. However, as the number of components grows, the total length of flow channels between components must increase exponentially. Recent empirical studies show that long flow channels are vulnerable due to blocking and leakage defects. Thus, it is desirable to minimize the total length of flow channels for robustness. Also, for timing-sensitive biochemical assays, increase in the longest length of flow channel will delay the assay completion time and lead to variation of fluid, thereby affecting the correctness of outcome. The increasing number of components, including the pre-placed components, on the chip makes the flow channel routing problem even more complicated. In this paper, we propose an efficient obstacle-avoiding rectilinear Steiner minimum tree algorithm to deal with flow channel routing problem in flow-based microfluidic biochips. Based on the concept of Kruskal algorithm and formulating the considerations as a bi-criteria function, our algorithm is capable of simultaneously minimizing the total length and the longest length of flow channel.

On-Chip Sample Preparation for Multiple Targets Using Digital Microfluidics

Abstract: In many biochemical protocols, sample preparation is an extremely important step for mixing multiple reagents in a given ratio. Dilution of a biochemical sample/reagent is the special case of mixing or solution preparation where only two fluids (sample and buffer) are mixed at a certain ratio corresponding to the desired concentration factor. Many bioassays often require multiple concentration values of the same sample/reagent, and implementing them efficiently on a digital microfluidic biochip is a challenge. In this paper, we present an algorithmic solution for the problem of producing a set of different target droplets in a minimum number of mix-split steps, and satisfying a given upper bound in concentration error. Unlike prior methods, this approach does not require any intermediate storage. We represent the underlying search space using a binary de Brujin graph and show that a shortest mix-split sequence can be obtained by solving an asymmetric traveling salesman problem therein. Simulation results over a large data set reveal that the proposed technique outperforms existing methods in terms of the number of mix-split steps, waste droplets, and reactant usage. The method is applicable in general scenarios of either one mixer or more mixers on the chip. A digital microfluidic platform can be easily designed to implement such a technique for rapid on-chip sample preparation.

Biochip Synthesis and Dynamic Error Recovery for Sample Preparation Using Digital Microfluidics

Abstract: Recent advances in digital microfluidic biochips have led to a promising future for miniaturized laboratories, with the associated advantages of high sensitivity and reconfigurability. Since sample preparation plays an important front-end role in assays and laboratories in biochemical applications, and most of the analysis time is associated with sample collection, transportation, and preparation, it is important to minimize the time required for this key step in bioassays. Moreover, it is also critical to ensure the correctness of intermediate steps and recover from errors efficiently during sample preparation. We describe an optimization algorithm and the associated chip design method for sample preparation, including architectural synthesis and layout synthesis. We also present the first dynamic error recovery procedure for use during sample preparation. The proposed algorithm is evaluated on both real-life biochemical applications and synthetic test cases to demonstrate its effectiveness and efficiency. Compared to prior work, the proposed algorithm can achieve up to 50% reduction in sample preparation time, and the optimized chip layout can achieve over 40% reduction in sample preparation time.

Configurable Low‐Cost Plotter Device for Fabrication of Multi‐Color Sub‐Cellular Scale Microarrays

Abstract: The construction and operation of a low-cost plotter for fabrication of microarrays for multiplexed single-cell analyses is reported. The printing head consists of polymeric pyramidal pens mounted on a rotation stage installed on an aluminium frame. This construction enables printing of microarrays onto glass substrates mounted on a tilt stage, controlled by a Lab-View operated user interface. The plotter can be assembled by typical academic workshops from components of less than 15,000 Euro. The functionality of the instrument is demonstrated by printing DNA microarrays on the area of 0.5 cm2 using up to three different oligonucleotides. Typical feature sizes are 5 μm diameter with a pitch of 15 μm, leading to densities of up to 10(4)-10(5) spots/mm2. The fabricated DNA microarrays are used to produce sub-cellular scale arrays of bioactive epidermal growth factor peptides by means of DNA-directed immobilization. The suitability of these biochips for cell biological studies is demonstrated by specific recruitment, concentration, and activation of EGF receptors within the plasma membrane of adherent living cells. This work illustrates that the presented plotter gives access to bio-functionalized arrays usable for fundamental research in cell biology, such as the manipulation of signal pathways in living cells at subcellular resolution.

DNA Molecular Beacon-Based Plastic Biochip: A Versatile and Sensitive Scanometric Detection Platform

Abstract: In this paper, we report a novel DNA molecular beacon (MB)-based plastic biochip platform for scanometric detection of a range of analytical targets. Hairpin DNA strands, which are dually modified with amino and biotin groups at their two ends are immobilized on a disposable plastic (polycarbonate) substrate as recognition element and gold nanoparticle-assisted silver-staining as signal reading protocol. Initially, the immobilized DNA probes are in their folded forms; upon target binding the hairpin secondary structure of the probe strand is “forced” open (i.e., converted to the unfolded state). Nanogold-streptavidin conjugates can then bind the terminal biotin groups and promote the deposition of rather large silver particles which can be either directly visualized or quantified with a standard flatbed scanner. We demonstrate that with properly designed probe sequences and optimized preparation conditions, a range of molecular targets, such as DNA strands, proteins (thrombin) and heavy metal ions (Hg2+),...

A surface functionalized nanoporous titania integrated microfluidic biochip

Abstract: We present a novel and efficient nanoporous microfluidic biochip consisting of a functionalized chitosan/anatase titanium dioxide nanoparticles (antTiO2-CH) electrode integrated in a polydimethylsiloxane (PDMS) microchannel assembly. The electrode surface can be enzyme functionalized depending on the application. We studied in detail cholesterol sensing using the cholesterol esterase (ChEt) and cholesterol oxidase (ChOx) functionalized chitosan supported mesoporous antTiO2-CH microfluidic electrode. The available functional groups present in the nanoporous antTiO2-CH surface in this microfluidic biochip can play an important role for enzyme functionalization, which has been quantified by the X-ray photoelectron spectroscopic technique. The Brunauer-Emmett-Teller (BET) studies are used to quantify the specific surface area and nanopore size distribution of titania nanoparticles with and without chitosan. Point defects in antTiO2 can increase the heterogeneous electron transfer constant between the electrode and enzyme active sites, resulting in improved electrochemical behaviour of the microfluidic biochip. The impedimetric response of the nanoporous microfluidic biochip (ChEt-ChOx/antTiO2-CH) shows a high sensitivity of 6.77 kΩ (mg dl(-1))(-1) in the range of 2-500 mg dl(-1), a low detection limit of 0.2 mg dl(-1), a low Michaelis-Menten constant of 1.3 mg dl(-1) and a high selectivity. This impedimetric microsystem has enormous potential for clinical diagnostics applications.

Methods for Forming Lipid Bilayers on Biochips

Abstract: This disclosure provides a biochip comprising a plurality of wells The biochip includes a membrane that is disposed in or adjacent to an individual well of the plurality of wells The membrane comprises a nanopore, and the individual well comprises an electrode that detects a signal upon ionic flow through the pore in response to a species passing through or adjacent to the nanopore The electrode can be a non-sacrificial electrode A lipid bilayer can be formed over the plurality of wells using a bubble

Control-layer optimization for flow-based mVLSI microfluidic biochips

Abstract: Recent advantages in flow-based microfluidic biochips have enabled the emergence of lab-on-a-chip devices for bimolecular recognition and point-of-care disease diagnostics. However, the adoption of flow-based biochips is hampered today by the lack of computer-aided design tools. Manual design procedures not only delay product development but they also inhibit the exploitation of the design complexity that is possible with current fabrication techniques. In this paper, we present the first practical problem formulation for automated control-layer design in flow-based microfluidic VLSI (mVLSI) biochips and propose a systematic approach for solving this problem. Our goal is to find an efficient routing solution for control-layer design with a minimum number of control pins. The pressure-propagation delay, an intrinsic physical phenomenon in mVLSI biochips, is minimized in order to reduce the response time for valves, decrease the pattern set-up time, and synchronize valve actuation. Two fabricated flow-based devices and five synthetic benchmarks are used to evaluate the proposed optimization method. Compared with manual control-layer design and a baseline approach, the proposed approach leads to fewer control pins, better timing behavior, and shorter channel length in the control layer.

Reliability-Driven Pipelined Scan-Like Testing of Digital Microfluidic Biochips

Abstract: A digital micro fluidic biochip (DMFB) is an attractive platform for immunoassays, point-of-care clinical diagnostics, DNA sequencing, and other laboratory procedures in biochemistry. Effective testing methods are required to ensure robust DMFB operation and high confidence in the outcome of biochemical experiments. Prior work on DMFB testing does not address the problem of designing the test to minimize reliability degradation during test application. It also ignores physical constraints arising from fluidic behavior and the physics of electro wetting-on-dielectric. We develop a practical and realistic testing method by first systematically analyzing the influence of actuation voltage and actuation frequency on the distribution of the electric field, and its resulting effect on dielectric degradation. Next, we use this analysis to choose appropriate parameter settings for testing, and proposes a new pipelined scan-like testing method. Both static and dynamic fluidic constraints are considered in the new testing method, and a diagnosis technique is presented to easily locate defects. Finally, simulation results are presented to demonstrate the effectiveness of the proposed testing approach in minimizing test-completion time.

Sample preparation with multiple dilutions on digital microfluidic biochips

Abstract: Digital microfluidic (DMF) biochips offer a versatile platform for implementing several laboratory based biochemical protocols. These tiny chips can electrically control the dynamics of nanoliter volume of discrete fluid droplets on an electrode array by application of actuation patterns. One important step in biochemical sample preparation is dilution, where the objective is to prepare a fluid with a desired concentration factor. The protocols implemented on DMF biochips may require several different concentration values of a sample. In this study, the authors propose a scheme to produce such target droplets from a supply of an input sample and a buffer solution. Simulation results show a significant amount of savings in the number of mix-split steps and waste droplets in comparison to other methods for generating multiple concentration factors.

Test generation and design-for-testability for flow-based mVLSI microfluidic biochips

Abstract: Advances in flow-based microfluidic biochips offer tremendous potential for biochemical analyses and clinical diag-nostics. However, the adoption of flow-based biochips is hampered by defects that are especially common for chips fabricated using soft lithography techniques. Recently published work on fault detection in flow-based biochips is based on logic-circuit modeling of the microfluidic channels and control valves, followed by classical test generation for digital circuits. However, this approach is not applicable to realistic designs because the circuit model is generated manually and many real defects are mapped to undetectable faults in the logic-circuit model. We present a technique for automated and hierarchical generation of the logic-circuit model from the layout of a flow-based microfluidic chip. Moreover, based on the analysis of untestable faults in the logic-circuit model, we present a design-for-testability (DfT) technique that can achieve 100% fault coverage. Two microfluidic VLSI (mVLSI) chips, each containing over 1500 valves, are used to demonstrate the automated model generation and DfT solutions.

A Low-Cost Field-Programmable Pin-Constrained Digital Microfluidic Biochip

Abstract: This paper introduces a field-programmable pin-constrained digital microfluidic biochip (FPPC-DMFB), which offers general-purpose assay execution at a lower cost than general-purpose direct addressing DMFBs and highly optimized application-specific pin-constrained DMFBs. One of the key cost drivers for DMFBs is the number of printed circuit board (PCB) layers, onto which the device is mounted. We demonstrate a scalable single-layer PCB wiring scheme for several FPPC-DMFB variations, for PCB technology with orthogonal routing capacity of at least three; for PCB technology with orthogonal capacity of two, more PCB layers are required, but the FPPC-DMFB retains its cost advantage. These results offer new insights on the relationship between PCB layer count, pin count, and cost. Additionally, to reduce the execution time of assays on the FPPC-DMFB, we present efficient algorithms for droplet routing, with and without contamination removal via wash droplets.

Correctness Checking of Bio-chemical Protocol Realizations on a Digital Microfluidic Biochip

Abstract: Recent advances in digital micro fluidic (DMF) technologies offer a promising platform for a wide variety of bio-chemical applications, such as DNA analysis, automated drug discovery, and toxicity monitoring. For on-chip implementation of complex bioassays, automated synthesis tools are now being used in order to meet the increasing design challenges. Currently, the synthesis tools cycle through a number of complex design steps to realize a given bio-chemical protocol on a target DMF architecture. Thus, several design errors are likely to creep into the synthesis process. Before deploying a DMF biochip on a safety critical system, it is becoming mandatory to ensure that the desired bio-chemical protocol has been correctly implemented, i.e., the synthesized output (actuation sequences for the biochip) is free from any design or realization errors. In this paper, we propose a symbolic constraint-based analysis and verification framework for checking the correctness of a synthesized bio-chemical protocol with respect to the original design specification. The proposed framework detects realization errors and generates diagnostic feedback to indicate the possible sources of design rule violations. We have developed a tool that implements our strategy and we present some experimental results on the polymerase chain reaction (PCR).

Wash optimization for cross-contamination removal in flow-based microfluidic biochips

Abstract: Recent advances in flow-based microfluidics have enabled the emergence of biochemistry-on-a-chip as a new paradigm in drug discovery and point-of-care disease diagnosis. However, these applications in biochemistry require high precision to avoid erroneous assay outcomes, and therefore are vulnerable to contamination between two fluidic flows with different biochemistries. Moreover, to wash contaminated sites, the buffer solution in flow-based biochips has to be guided along pre-etched channel networks. This constraint makes washing in flow-based microfluidics even harder. In this paper, we propose the first approach for automated wash optimization for contamination removal in flow-based microfluidic biochips. The proposed approach targets the generation of washing pathways to clean all contaminated microchannels with minimum execution time. A path dictionary is first established by pre-searching physically implementable paths in a given chip layout. When wash targets and occupied microchannels are defined, the proposed methods determine an optimized path set with the least washing time by calculating the priorities of wash targets. Two fabricated biochips are used to evaluate the proposed washing method. Compared to an ad hoc baseline method, the proposed approach leads to more efficient washing in all cases.