Fast and continuous-flow detection and separation of DNA complexes and DNA in nanofluidic chip format.

Fast separation of DNA and detection of protein/DNA complexes are important in many state-of-the-art molecular medicine technologies, like the production of gene vaccines or medical diagnostics. Here, we describe a nanofluidic chip-based technique for fast, efficient, and virtually label-free detection and separation of protein/DNA and drug/DNA complexes and topological DNA variants. The mechanism is based on a continuous-flow dielectrophoresis at a nanoslit and allows efficient separation of small DNA fragments (<7,000 base pairs) and fast detection of DNA complexes within 1 min.

Fast and continuous-flow separation of DNA-complexes and topological DNA variants in microfluidic chip format.

The efficient detection, separation and purification of topological and (protein-)complexed DNA variants is mandatory for many state-of-the-art molecular medicine technologies, like medical diagnostics, gene- and cancer-therapy as well as plasmid vaccination. Here, we present the proof-of-concept of a novel micro-nanofluidic device for a fast and efficient, continuous-flow, and virtually label-free detection/purification protocol that goes beyond the standard methods of electrophoretic mobility shift assays, capillary electrophoresis and affinity chromatography. Based on dielectrophoretic trapping, analyte mixtures of small linear DNA-fragments (2.868 kbp and 6.0 kbp), topological DNA variants like plasmids (6.766 kbp) and minicircle-DNA (2.257 kbp), or cytostatic- and protein-DNA complexes were separated in the vicinity of a channel-spanning bowed ridge (creating a nanoslit). One analyte is continuously deflected due to dielectrophoretic trapping at the ridge whereas other species pass the nanoslit unhindered, resulting in two molecule specific pathways with baseline separated resolution. This offers one-step real-time separation of low analyte volumes on a one-minute timescale at low-costs. The underlying dielectrophoretic mechanism was quantified by determining the electrical polarizabilities of the molecules. Additionally, we compared the continuous-flow detection of DNA-complexes with well-established electrophoretic mobility shift assays. Future analytical and preparative applications, such as for plasmid pharmaceuticals as well as continuous sample harvesting in parallel microchip format, are discussed.

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.

Microfluidic carbon-blackened polydimethylsiloxane device with reduced ultra violet background fluorescence for simultaneous two-color ultra violet/visible-laser induced fluorescence detection in single cell analysis.

In single cell analysis (SCA), individual cell-specific properties and inhomogeneous cellular responses are being investigated that is not subjected to ensemble-averaging or heterogeneous cell population effects. For proteomic single cell analysis, ultra-sensitive and reproducible separation and detection techniques are essential. Microfluidic devices combined with UV laser induced fluorescence (UV-LIF) detection have been proposed to fulfill these requirements. Here, we report on a novel microfluidic chip fabrication procedure that combines straightforward production of polydimethylsiloxane (PDMS) chips with a reduced UV fluorescence background (83%-reduction) by using PDMS droplets with carbon black pigments (CBP) as additives. The CBP-droplet is placed at the point of detection, whereas the rest of the chip remains transparent, ensuring full optical control of the chip. We systematically studied the relation of the UV background fluorescence at CBP to PDMS ratios (varying from 1:10 to 1:1000) for different UV laser powers. Using a CBP/PDMS ratio of 1:20, detection of a 100 nM tryptophan solution (S/N = 3.5) was possible, providing a theoretical limit of detection of 86 nM (with S/N = 3). Via simultaneous two color UV/VIS-LIF detection, we were able to demonstrate the electrophoretic separation of an analyte mixture of 500 nM tryptophan (UV) and 5 nM fluorescein (VIS) within 30 s. As an application, two color LIF detection was also used for the electrophoretic separation of the protein content from a GFP-labeled single Spodoptera frugiperda (Sf9) insect cell. Thereby just one single peak could be measured in the visible spectral range that could be correlated with one single peak among others in the ultraviolet spectra. This indicates an identification of the labeled protein γ-PKC and envisions a further feasible identification of more than one single protein in the future.

Continuous and reversible mixing or demixing of nanoparticles by dielectrophoresis.

Mixing and demixing (separation) are essential tasks in microfluidic devices, which seem to be contrary in nature. Accordingly, completely different strategies and devices are usually employed for their realization. We here present a microfluidic device which is capable of performing both these tasks as it can be operated in either mixing or demixing mode. The mixing and demixing processes are reversible and are accomplished by continuous operation of the device. An asymmetric S-shaped ridge extends over the full width of a microfluidic channel (200 µm) creating a constriction of 620 nm in height with an aspect ratio of 1 : 500. Appropriate AC and DC voltages generate electrodeless dielectrophoresis at the constriction as well as (linear) electrokinetic driving forces along the channel. These de/mixing parameters can be adapted in real time in such a way that continuous separation and mixing efficiencies of 85-100% can be achieved. As a proof of concept we demonstrate continuous mixing and demixing of polystyrene nanoparticles (20 and 100 nm). The experimental results are complemented by numerical simulations illustrating the particles' motion under the influence of the electrokinetic effects and thermal noise (diffusion). The monolithic one-step fabrication process by soft lithography (with PDMS in our case) will make integration and combination of several mixing and demixing functions into a more complex lab-on-a-chip device possible.

Continuous-flow separation of nanoparticles by electrostatic sieving at a micro-nanofluidic interface.

Continuous-flow separation of nanoparticles (NPs) (15 and 39 nm) is demonstrated based on electrostatic sieving at a micro-nanofluidic interface. The interface is realized in a poly(dimethylsiloxane) device with a nanoslit of 525 nm laterally spanning the microfluidic channel (aspect ratio of 540:1). Within this nanoslit, the Debye layers overlap and generate an electrostatic sieve. This was exploited to selectively deflect and sort NPs with a sorting purity of up to 97%. Because of the continuous-flow operation, the sample is continuously fed into the device, immediately separated, and the parameters can be adapted in real time. For bioanalytical purposes, we also demonstrate the deflection of proteins (longest axis 6.8 nm). The continuous operation mode and the general applicability of this separation concept make this method a valuable addition to the current Lab-on-a-Chip devices for continuous sorting of NPs and macromolecules.

Electrodeless dielectrophoresis for bioanalysis: theory, devices and applications.

Dielectrophoresis is a non-destructive, label-free method to manipulate and separate (bio-) particles and macromolecules. The mechanism is based on the movement of polarizable objects in an inhomogeneous electric field. Here, microfluidic devices are reviewed that generate those inhomogeneous electric fields with insulating posts or constrictions, an approach called electrodeless or insulator-based dielectrophoresis. Possible advantages compared to electrode-based designs are a less complex, monolithic fabrication process with low-cost polymeric substrates and no metal surface deterioration within the area of sample analysis. The electrodeless design has led to novel devices, implementing the functionality directly into the channel geometry and covering many areas of bioanalysis, like manipulation and separation of particles, cells, DNA, and proteins.

Dielectrophoretic trapping and polarizability of DNA: the role of spatial conformation.

Dielectrophoresis is a convenient tool for controlled manipulation of DNA with numerous applications, including DNA trapping, stretching, and separation. However, the mechanisms behind the dielectrophoretic properties of DNA are still under debate, and the role of conformation has not been addressed yet. Here, we quantify dielectrophoretic effects on DNA by determining its polarizability from microfluidic single molecule trapping experiments. We systematically study different DNA configurations (linear and supercoiled, 6-164 kbp) and demonstrate that the polarizability strongly depends on the specific conformation and size of the DNA molecules. The connection to its spatial extension is established by measuring diffusion coefficients and from that the radii of gyration; details about the spatial DNA structure are obtained from atomic force microscopy images. For linear and supercoiled DNA fragments, we found a power-law scaling for the polarizabilities and the diffusion coefficients. Our results imply a scaling of the polarizability with the radius of gyration, alpha approximately Rg0.9+/-0.1 and alpha approximately Rg1.6+/-0.2 for linear and supercoiled DNA, respectively. As an application, we demonstrate the separation of DNA topoisomers based on their dielectrophoretic properties, achieving baseline resolution within 210 s. Purified DNA samples of specific configuration may be of great importance for DNA nanoassembly or future DNA vaccines.

Space- and time-resolved protein dynamics in single bacterial cells observed on a chip.

Life cell imaging of bacterial cells over long times is very challenging because of the small dimensions and the need for a liquid environment assuring cell viability. In order to obtain space- and time-resolved information about protein dynamics, high resolution time-lapse fluorescence images (TLFI) of single bacterial cells were recorded in a poly(dimethylsiloxane) (PDMS) microfluidic chip. A new gradient coating technique was applied to ensure cell loading. As a proof-of-concept, we monitored the evenly distributed cytoplasmic protein GcrA as well as the asymmetric localization of the DivK protein in cells of S. meliloti over at least two division cycles. Localization of DivK was characterized by dividing each bacterial cell into 4 sections with dimensions closely above the optical limit of resolution. This approach of generating spatio-temporal resolved information of protein dynamics in single bacterial cells is applicable to many problems.

High resolution imaging of surface patterns of single bacterial cells.

We systematically studied the origin of surface patterns observed on single Sinorhizobium meliloti bacterial cells by comparing the complementary techniques atomic force microscopy (AFM) and scanning electron microscopy (SEM). Conditions ranged from living bacteria in liquid to fixed bacteria in high vacuum. Stepwise, we applied different sample modifications (fixation, drying, metal coating, etc.) and characterized the observed surface patterns. A detailed analysis revealed that the surface structure with wrinkled protrusions in SEM images were not generated de novo but most likely evolved from similar and naturally present structures on the surface of living bacteria. The influence of osmotic stress to the surface structure of living cells was evaluated and also the contribution of exopolysaccharide and lipopolysaccharide (LPS) by imaging two mutant strains of the bacterium under native conditions. AFM images of living bacteria in culture medium exhibited surface structures of the size of single proteins emphasizing the usefulness of AFM for high resolution cell imaging.

Acceleration of absolute negative mobility.

Recently, the counter intuitive migration phenomenon of absolute negative mobility (ANM) has been demonstrated to occur for colloidal particles in a suitably arranged post array within a microfluidic device [1]. This effect is based on the interplay of Brownian motion, nonlinear dynamics induced through microstructuring, and nonequilibrium driving, and results in a particle movement opposite to an applied static force. Simultaneously, the migration of a different particle species along the direction of the static force is possible [19], thus providing a new tool for particle sorting in microfluidic device format. The so far demonstrated maximum velocities for micrometer-sized spheres are slow, i. e., in the order of 10 nm per second. Here, we investigate numerically, how maximum ANM velocities can be significantly accelerated by a careful adjustment of the post size and shape. Based on this numerical analysis, a post design is developed and tested in a microfluidic device made of PDMS. The experiment reveals an order of magnitude increase in velocity.

Dielectrophoretic manipulation of DNA: separation and polarizability.

Although separation of polymers based on the combination of dielectrophoretic trapping and electrophoretic forces was proposed 15 years ago, experimental proof has not yet been reported. Here, we address this problem for long DNA fragments in a simple and easy-to-fabricate microfluidic device, in which the DNA is manipulated by electrophoresis and by electrodeless dielectrophoresis. By slowly increasing the strength of the dielectrophoretic traps in the course of the separation experiments, we are able to perform efficient and fast DNA separation according to length for two different DNA conformations: linear DNA (lambda (48.5-kbp) and T2 (164-kbp) DNA) and supercoiled covalently closed circular plasmid DNA (7 and 14 kbp). The underlying migration mechanism-thermally induced escape processes out of the dielectrophoretic traps in the direction of the electrophoretic force-is sensitive to different DNA fragments because of length-dependent DNA polarizabilities. This is analyzed in a second series of experiments, where the migration mechanism is exploited for the quantitative measurement of the DNA polarizabilities. This new and simple technique allows for the systematic characterization of the polarizability not only for DNA but also for other biomolecules like proteins. Furthermore, our results have direct implications to future biotechnological applications such as gene therapy and DNA vaccination.

Bioanalysis in structured microfluidic systems.

Microfluidic and lab-on-a-chip devices have attracted widespread interest in separation sciences and bioanalysis. Recent designs in microfluidic devices extend common separation concepts by exploiting new phenomena for molecular dynamics on a length scale of 10 mum and below, giving rise to novel manipulation tools and nonintuitive phenomena for microseparations. Here, we focus on three very recent developments for bioseparations based on tailored microfluidic systems: Single cell navigation, trapping and steering with subsequent on-chip lysis, protein separation and LIF detection (Section 3.1), then we report dielectrophoretic trapping and separation of large DNA fragments in structured microfluidic devices (Section 3.2). Finally, a paradoxial migration phenomenon based on thermal fluctuations, periodically arranged microchannels and a biased alternating current electric field is presented in Section 3.3.

Brownian motion: absolute negative particle mobility.

Noise effects in technological applications, far from being a nuisance, can be exploited with advantage - for example, unavoidable thermal fluctuations have found application in the transport and sorting of colloidal particles and biomolecules. Here we use a microfluidic system to demonstrate a paradoxical migration mechanism in which particles always move in a direction opposite to the net acting force ('absolute negative mobility') as a result of an interplay between thermal noise, a periodic and symmetric microstructure, and a biased alternating-current electric field. This counterintuitive phenomenon could be used for bioanalytical purposes, for example in the separation and fractionation of colloids, biological molecules and cells.

Poly(oxyethylene) based surface coatings for poly(dimethylsiloxane) microchannels.

Control of surface properties in microfluidic systems is an indispensable prerequisite for successful bioanalytical applications. Poly(dimethylsiloxane) (PDMS) microfluidic devices are hampered from unwanted adsorption of biomolecules and lack of methods to control electroosmotic flow (EOF). In this paper, we propose different strategies to coat PDMS surfaces with poly(oxyethylene) (POE) molecules of varying chain lengths. The native PDMS surface is pretreated by exposure to UV irradiation or to an oxygen plasma, and the covalent linkage of POE-silanes as well as physical adsorption of a triblock-copolymer (F108) are studied. Contact angle measurements and atomic force microscopy (AFM) imaging revealed homogeneous attachment of POE-silanes and F108 to the PDMS surfaces. In the case of F108, different adsorption mechanisms to hydrophilic and hydrophobic PDMS are discussed. Determination of the electroosmotic mobilities of these coatings in PDMS microchannels prove their use for electrokinetic applications in which EOF reduction is inevitable and protein adsorption has to be suppressed.