Bioanalysis in structured microfluidic systems

Refinement of insulator-based dielectrophoresis

The ability to separate analytes with increasingly similar properties drives the field of separation science. One way to achieve such separations is using trapping and streaming dielectrophoresis (DEP), which directly exploits the subtle differences in the electrophysical properties of analytes. The non-uniform fields necessary for DEP can be formed using various insulator shapes in microchannels. Current insulator shapes include triangles, diamonds, circles, and rectangles. However, all of these insulators pose problems for trapping, streaming, and sorting (deflection) as the induced fields/gradients are not behaviorally consistent across the lateral dimension. This leads to analytes experiencing different forces depending on their pathline in the microchannel and result in low resolution separations. Based on an iterative process that explored approximately 40 different insulator shapes, a design was chosen that indicated improved particle streamlines, better trapping efficiency, and consistent electrical environments across the lateral dimension. The design was assessed by simulations where the electric field, gradient of the electric field squared, and the ratio of the two were plotted. The improved design includes a unique new multi-length scale element. The multi-length scale structure streamlines the analyte(s) and improves homogeneity in the lateral dimension, while still achieving high gradients necessary for analyte separation using DEP. The design is calculated to keep analytes on the centerline which should improve resolution, and eliminate extraneous trapping zones. Behaviors consistent with the features of the simulations were observed in proof of principle experiments using representative test probes.

Cell-Free Approaches in Synthetic Biology Utilizing Microfluidics

Synthetic biology is a rapidly growing multidisciplinary branch of science which aims to mimic complex biological systems by creating similar forms. Constructing an artificial system requires optimization at the gene and protein levels to allow the formation of entire biological pathways. Advances in cell-free synthetic biology have helped in discovering new genes, proteins, and pathways bypassing the complexity of the complex pathway interactions in living cells. Furthermore, this method is cost- and time-effective with access to the cellular protein factory without the membrane boundaries. The freedom of design, full automation, and mimicking of in vivo systems reveal advantages of synthetic biology that can improve the molecular understanding of processes, relevant for life science applications. In parallel, in vitro approaches have enhanced our understanding of the living system. This review highlights the recent evolution of cell-free gene design, proteins, and cells integrated with microfluidic platforms as a promising technology, which has allowed for the transformation of the concept of bioprocesses. Although several challenges remain, the manipulation of biological synthetic machinery in microfluidic devices as suitable 'homes' for in vitro protein synthesis has been proposed as a pioneering approach for the development of new platforms, relevant in biomedical and diagnostic contexts towards even the sensing and monitoring of environmental issues.

DNA dielectrophoresis: Theory and applications a review

Dielectrophoresis is the migration of an electrically polarizable particle in an inhomogeneous electric field. This migration can be exploited for several applications with (bio)molecules or cells. Dielectrophoresis is a noninvasive technique; therefore, it is very convenient for (selective) manipulation of (bio)molecules or cells. In this review, we will focus on DNA dielectrophoresis as this technique offers several advantages in trapping and immobilization, separation and purification, and analysis of DNA molecules. We present and discuss the underlying theory of the most important forces that have to be considered for applications with dielectrophoresis. Moreover, a review of DNA dielectrophoresis applications is provided to present the state-of-the-art and to offer the reader a perspective of the advances and current limitations of DNA dielectrophoresis.

Fabrication challenges and perspectives on the use of carbon-electrode dielectrophoresis in sample preparation

The focus of this review is to assess the current status of three-dimensional (3D) carbon-electrode dielectrophoresis (carbonDEP) and identify the challenges currently preventing it from its use in high-throughput applications such as sample preparation for diagnostics. The use of 3D electrodes over more traditional planar ones is emphasised here as a way to increase the throughput of DEP devices. Glass-like carbon electrodes are derived through the carbonisation of photoresist structures made using photolithography. These biocompatible carbon electrodes are not ideal electrical conductors but are more electrochemically stable than noble metals such as gold and platinum. They are also significantly less expensive than common electrode materials, both in terms of material cost and fabrication process. CarbonDEP has been demonstrated for the manipulation of microorganisms and biomolecules. This review is divided in three main sections: (i) carbonDEP fabrication process; (ii) applications using 3D carbonDEP; and (iii) challenges and perspectives on the use of carbonDEP for high-throughput applications.

Characterization of Chlorella vulgaris and Chlorella protothecoides using multi-pixel photon counters in a 3D focusing optofluidic system

A new type of multi-pixel photon counter was employed to miniaturize the device, lower its power consumption, and make it insensitive to magnetic fields.

Microfluidic Single-Cell Analysis with Affinity Beads

A micrometer-sized affinity bead (red) is (i) taken up into a cell by phagocytosis, (ii) photochemically released from phagosomes, (iii) optically trapped by the cell, and (iv) isolated by cell lysis for subsequent analysis of captured intracellular analyte (green).

Microbial cell lysis and nucleic acid extraction via nanofluidic channel

This paper presents a microfluidic device with a nano-channel prepared by focused ion beam (FIB) milling for microbial cell lysis and nucleic acid extraction.

Supported Membranes Meet Flat Fluidics: Monitoring Dynamic Cell Adhesion on Pump-Free Microfluidics Chips Functionalized with Supported Membranes Displaying Mannose Domains

In this paper we demonstrate the combination of supported membranes and so-called flat microfluidics, which enables one to manipulate liquids on flat chip surfaces via “inverse piezoelectric effect”. Here, an alternating external electric field applied to the inter-digital transducers excites a surface acoustic wave on a piezoelectric substrate. Employing lithographic patterning of self-assembled monolayers of alkoxysilanes, we successfully confine a free-standing, hemi-cylindrical channel with the volume of merely 7 µL . The experimentally determined maximum flow velocity scales linearly with the acoustic power, suggesting that our current setup can drive liquids at the speed of up to 7 cm/s (corresponding to a shear rate of 280 s⁻¹) without applying high pressures using a fluidic pump. After the establishment of the functionalization of fluidic chip surfaces with supported membranes, we deposited asymmetric supported membranes displaying well-defined mannose domains and monitored the dynamic adhesion of E. Coli HB101 expressing mannose-binding receptors. Despite of the further technical optimization required for the quantitative analysis, the obtained results demonstrate that the combination of supported membranes and flat fluidics opens a large potential to investigate dynamic adhesion of cells on biofunctional membrane surfaces with the minimum amount of samples, without any fluidic pump.

Analysis of intracellular reducing levels in human hepatocytes on three-dimensional focusing microchip

A novel three-dimensional hydrodynamic focusing microfluidic device integrated with high-throughput cell sampling and detection of intracellular contents is presented. It has a pivotal role in maintaining the reducing environment in cells. Intracellular reducing species such as vitamin C and glutathione in normal and tumor cells were labeled by a newly synthesized 2,2,6,6-tetramethyl-piperidine-1-oxyl-based fluorescent probe. Hepatocytes are adherent cells, which are prone to attaching to the channel surface. To avoid the attachment of cells on the channel surface, a single channel microchip with three sheath-flow channels located on both sides of and below the sampling channel was developed. Hydrostatic pressure generated by emptying the sample waste reservoir was used as driving force of fluid on the microchip. Owing to the difference between the liquid levels of the reservoirs, the labeled cells were three-dimensional hydrodynamically focused and transported from the sample reservoir to the sample waste reservoir. Hydrostatic pressure takes advantage of its ease of generation on a microfluidic chip without any external pressure pump, which drives three sheath-flow streams to constrain a sample flow stream into a narrow stream to avoid blockage of the sampling channel by adhered cells. The intracellular reducing levels of HepG2 cells and L02 cells were detected by home-built laser-induced fluorescence detector. The analysis throughput achieved in this microfluidic system was about 59-68 cells/min.

Microfluidic devices for high-throughput proteome analyses

Over the last decades, microfabricated bioanalytical platforms have gained enormous interest due to their potential to revolutionize biological analytics. Their popularity is based on several key properties, such as high flexibility of design, low sample consumption, rapid analysis time, and minimization of manual handling steps, which are of interest for proteomics analyses. An ideal totally integrated chip-based microfluidic device could allow rapid automated workflows starting from cell cultivation and ending with MS-based proteome analysis. By reducing or eliminating sample handling and transfer steps and increasing the throughput of analyses these workflows would dramatically improve the reliability, reproducibility, and throughput of proteomic investigations. While these complete devices do not exist for routine use yet, many improvements have been made in the translation of proteomic sample handling and separation steps into microfluidic formats. In this review, we will focus on recent developments and strategies to enable and integrate proteomic workflows into microfluidic devices.

Chiral particle separation by a nonchiral microlattice

We conceived a model experiment for a continuous separation strategy of chiral molecules (enantiomers) without the need of any chiral selector structure or derivatization agents: Microparticles that only differ by their chirality are shown to migrate along different directions when driven by a steady fluid flow through a square lattice of cylindrical posts. In accordance with our numerical predictions, the transport directions of the enantiomers depend very sensitively on the orientation of the lattice relative to the fluid flow.

Sampling techniques for single-cell electrophoresis

Cells are extraordinarily complex, containing thousands of different analytes with concentrations spanning at least nine orders of magnitude. Analyzing single cells instead of tissue homogenates provides unique insights into cell-to-cell heterogeneity and aids in distinguishing normal cells from pathological ones. The high sensitivity and low sample consumption of capillary and on-chip electrophoresis, when integrated with fluorescence, electrochemical, and mass spectrometric detection methods, offer an ideal toolset for examining single cells and even subcellular organelles; however, the isolation and loading of such small samples into these devices is challenging. Recent advances have addressed this issue by interfacing a variety of enhanced mechanical, microfluidic, and optical sampling techniques to capillary and on-chip electrophoresis instruments for single-cell analyses.

Suspension flow in microfluidic devices--a review of experimental techniques focussing on concentration and velocity gradients

Microfluidic devices are an emerging technology for processing suspensions in e.g. medical applications, pharmaceutics and food. Compared to larger scales, particles will be more influenced by migration in microfluidic devices, and this may even be used to facilitate segregation and separation. In order to get most out of these completely new technologies, methods to experimentally measure (or compute) particle migration are needed to gain sufficient insights for rational design. However, the currently available methods only allow limited access to particle behaviour. In this review we compare experimental methods to investigate migration phenomena that can occur in microfluidic systems when operated with natural suspensions, having typical particle diameters of 0.1 to 10 μm. The methods are used to monitor concentration and velocity profiles of bidisperse and polydisperse suspensions, which are notoriously difficult to measure due to the small dimensions of channels and particles. Various methods have been proposed in literature: tomography, ultrasound, and optical analysis, and here we review and evaluate them on general dimensionless numbers related to process conditions and channel dimensions. Besides, eleven practical criteria chosen such that they can also be used for various applications, are used to evaluate the performance of the methods. We found that NMR and CSLM, although expensive, are the most promising techniques to investigate flowing suspensions in microfluidic devices, where one may be preferred over the other depending on the size, concentration and nature of the suspension, the dimensions of the channel, and the information that has to be obtained. The paper concludes with an outlook on future developments of measurement techniques.

Dielectrophoretic mobility determination in DC insulator-based dielectrophoresis

Insulator-based dielectrophoresis (iDEP) is a powerful tool for separating and characterizing particles, yet it is limited by a lack of quantitative characterizations. Here, this limitation is addressed by employing a method capable of quantifying the DEP mobility of particles. Using streak-based velocimetry the particle properties are deduced from their motion in a microfluidic channel with a constant electric field gradient. From this approach, the DEP mobility of 1 μm polystyrene particles was found to be -2±0.4 10(-8)  cm4 /(V2  s). In the future, such quantitative treatment will allow for the elucidation of unique insights and rational design of devices.

Dielectric and dielectrophoretic properties of DNA

The physical properties of DNA are quite important for molecular genetics as well as for its nanotechnological applications. Studying the interactions of alternating current (AC) electric fields with deoxyribonucleic acid (DNA) allows one to draw conclusions about these properties. These interactions are usually investigated in two different ways. In dielectric spectroscopy, a DNA solution is placed in a homogeneous AC field and electronic parameters are measured over several frequency decades in the Hz to GHz range. These electronic data are then interpreted on the basis of physico-chemical models as a result of certain phenomena on the molecular level. In dielectrophoretic studies, a DNA solution is exposed to an inhomogeneous AC field and the spatial response of few or single molecules is monitored by optical or scanning force microscopy. This response can involve translation, elongation and orientation of the molecular strings. In this review, a survey is given of the literature dealing with the dielectric and dielectrophoretic properties of DNA as well as with applications of DNA dielectrophoresis.

Microfluidic single-cell analysis of intracellular compounds

Biological analyses traditionally probe cell ensembles in the range of 103-106 cells, thereby completely averaging over relevant individual cell responses, such as differences in cell proliferation, responses to external stimuli or disease onset. In past years, this fact has been realized and increasing interest has evolved for single-cell analytical methods, which could give exciting new insights into genomics, proteomics, transcriptomics and systems biology. Microfluidic or lab-on-a-chip devices are the method of choice for single-cell analytical tools as they allow the integration of a variety of necessary process steps involved in single-cell analysis, such as selection, navigation, positioning or lysis of single cells as well as separation and detection of cellular analytes. Along with this advantageous integration, microfluidic devices confine single cells in compartments near their intrinsic volume, thus minimizing dilution effects and increasing detection sensitivity. This review overviews the developments and achievements of microfluidic single-cell analysis of intracellular compounds in the past few years, from proof-of-principle devices to applications demonstrating a high biological relevance.

Characterization and use of laser-based lysis for cell analysis on-chip

We demonstrate the use of a pulsed laser microbeam for cell lysis followed by electrophoretic separation of cellular analytes in a microfluidic device. The influence of pulse energy and laser focal point within the microchannel on the threshold for plasma formation was measured. The thickness of the poly(dimethylsiloxane) (PDMS) layer through which the beam travelled was a critical determinant of the threshold energy. An effective optical path length, Leff, for the laser beam can be used to predict the threshold for optical breakdown at different microchannel locations. A key benefit of laser-based cell lysis is the very limited zone (less than 5 microm) of lysis. A second asset is the rapid cell lysis times (approx. microseconds). These features enable two analytes, fluorescein and Oregon Green, from a cell to be electrophoretically separated in the channel in which cell lysis occurred. The resolution and efficiency of the separation of the cellular analytes are similar to those of standards demonstrating the feasibility of using a pulsed laser microbeam in single-cell analysis.

Versatile control of multiphase laminar flow for in-channel microfabrication

We have improved the multiphase laminar flow based in-channel fabrication method to overcome diffusion-induced broadening. A sheathing phase with protecting molecules confines metal wire deposition and allows for flexible control of the location, width, and uniformity of deposited metal wires. Two-layered T-junctions are introduced to form vertically stacked multiphase laminar flow. Combining these techniques, we fabricate quadrupole silver electrodes on the four sidewalls of rectangular polydimethylsiloxane (PDMS) microchannels that are 3 cm in length.

Single cell analysis in full body quartz glass chips with native UV laser-induced fluorescence detection

In order to investigate the individual and inhomogenous cellular response, e.g. to external stimuli, single cell analysis is mandatory and may provide new cognitions in proteomics as well as in other fields of systems biology in the future. Here, we report on novel chip architectures for single cell analysis based on full body quartz glass microfluidic chips (QG chips) that extend our previous studies in polydimethylsiloxane (PDMS) chips, and enhance the detection sensitivity of native UV laser-induced fluorescence (UV-LIF) detection. Detection of a 10nM tryptophan solution with an S/N ratio of 11.9, which gives a theoretical limit of detection of 2.5 nM (with S/N=3), was possible. With these optimizations the three proteins alpha-chymotrypsinogen A, ovalbumin and catalase each at a concentration of 100 microg/mL (equal to 4 microM, 0.4 microM and 2.2 microM) were injected electrokinetically and could be separated with nearly baseline resolution. Furthermore, fluorescence spectra (excitation wavelength, lambda(ex) = 266 nm) clearly demonstrate the favourable properties like the very high UV transparency and the nearly vanishing background fluorescence of the QG chips as compared to PDMS chips and to PDMS quartz window (PQW) chips. Finally we exploit the improved sensitivity for single cell electropherograms of Spodoptera frugiperda (Sf9) insect cells.

Chemical cytometry on microfluidic chips

Chemical cytometry, referring to the analysis of the chemical contents in individual cells, has been in intensive study since Kennedy's first work that was published in Science. The early researches relied on fine-tip capillaries to capture the cells and do the analyses, which were lab- and time-intensive and required high skills of operation. The emergence of microfluidics has greatly spurred this research field and a great number of research papers have been published in the last decades. Highly integrated microfluidic chips have been developed to capture multiple single cells, lyse them, perform chemical reactions in enclosed microchambers, separate contents by CE and detect chemical species in individual cells. This review focuses on the development of relevant components and their integration for on-chip chemical cytometry.

Single beam optical tweezers setup with backscattered light detection for three-dimensional measurements on DNA and nanopores

We introduce a versatile and high precision three-dimensional optical tweezers setup with minimal optical interference to measure small forces and manipulate single molecules in the vicinity of a weak reflective surface. Our tweezers system integrates an inverted optical microscope with a single IR-laser beam that is spatially filtered in an appropriate way to allow force measurements in three dimensions with remarkably high precision when operated in backscattered light detection mode. The setup was tested by overstretching a lambda-DNA in x and z directions (perpendicular and along the optical axis), and by manipulating individual lambda-DNA molecules in the vicinity of a nanopore that allowed quantitative single molecule threading experiments with minimal optical interference.

Microfluidic cell disruption system employing a magnetically actuated diaphragm

A microfluidic cell lysis chip equipped with a micromixer and SPE unit was developed and used for quantitative analysis of intracellular proteins. This miniaturized sample preparation system can be employed for any purpose where cell disruption is needed to obtain intracellular constituents for the subsequent analysis. This system comprises a magnetically actuated micromixer to disrupt cells, a hydrophobic valve to manipulate the cell lysate, and a packed porous polymerized monolith chamber for SPE and filtering debris from the cell lysate. Using recombinant Escherichia coli expressing intracellular enhanced green fluorescent protein (EGFP) and lipase as model bacteria, we optimized the cell disruption condition with respect to the lysis buffer composition, mixing time, and the frequency of the diaphragm in the micromixer, which was magnetically actuated by an external magnetic stirrer in the micromixer chamber. The lysed sample prepared under the optimal condition was purified by the packed SPE in the microfluidic chip. At a frequency of 1.96 Hz, the final cell lysis efficiency and relative fluorescence intensity of EGFP after the cell disruption process were greater than 90 and 94%, respectively. Thus, this microfluidic cell disruption chip can be used for the efficient lysis of cells for further analysis of intracellular contents in many applications.

Chemical analysis of single cells

Chemical analysis of single cells requires methods for quickly and quantitatively detecting a diverse array of analytes from extremely small volumes (femtoliters to nanoliters) with very high sensitivity and selectivity. Microelectrophoretic separations, using both traditional capillary electrophoresis and emerging microfluidic methods, are well suited for handling the unique size of single cells and limited numbers of intracellular molecules. Numerous analytes, ranging from small molecules such as amino acids and neurotransmitters to large proteins and subcellular organelles, have been quantified in single cells using microelectrophoretic separation techniques. Microseparation techniques, coupled to varying detection schemes including absorbance and fluorescence detection, electrochemical detection, and mass spectrometry, have allowed researchers to examine a number of processes inside single cells. This review also touches on a promising direction in single cell cytometry: the development of microfluidics for integrated cellular manipulation, chemical processing, and separation of cellular contents.

Analysis of single mammalian cells on-chip

A goal of modern biology is to understand the molecular mechanisms underlying cellular function. The ability to manipulate and analyze single cells is crucial for this task. The advent of microengineering is providing biologists with unprecedented opportunities for cell handling and investigation on a cell-by-cell basis. For this reason, lab-on-a-chip (LOC) technologies are emerging as the next revolution in tools for biological discovery. In the current discussion, we seek to summarize the state of the art for conventional technologies in use by biologists for the analysis of single, mammalian cells, and then compare LOC devices engineered for these same single-cell studies. While a review of the technical progress is included, a major goal is to present the view point of the practicing biologist and the advances that might increase adoption by these individuals. The LOC field is expanding rapidly, and we have focused on areas of broad interest to the biology community where the technology is sufficiently far advanced to contemplate near-term application in biological experimentation. Focus areas to be covered include flow cytometry, electrophoretic analysis of cell contents, fluorescent-indicator-based analyses, cells as small volume reactors, control of the cellular microenvironment, and single-cell PCR.

Analysis of subcellular surface structure, function and dynamics

Analytics of single biological cells allows quantitative investigation from a structural, functional and dynamical point of view and opens novel possibilities to an unamplified subcellular analysis. In this article, we report on three different experimental methods and their applications to single cellular systems with a subcellular sensitivity down to the single molecule level. First, the subcellular surface structure of living bacteria (Corynebacterium glutamicum) was investigated with atomic force microscopy (AFM) at the resolution of individual surface layer (S-layer) proteins; discrimination of bacterial strains that lack the expression of hexagonally packed surface layer proteins was possible. Second, quantitative measurement of individual recognition events of membrane-bound receptors on living B-cells was achieved in single cell manipulation and probing experiments with optical tweezers (OT) force spectroscopy. And third, intracellular dynamics of translocating photoactivatable GFP in plant protoplasts (Nicotiana tabacum BY-2) was quantitatively monitored by two-photon laser scanning microscopy (2PLSM).