Quantitative microfluidic separation of DNA in self-assembled magnetic matrixes

Emerging on-chip electrokinetic based technologies for purification of circulating cancer biomarkers towards liquid biopsy: A review

Early detection of cancer can significantly reduce mortality and save lives. However, the current cancer diagnosis is highly dependent on costly, complex, and invasive procedures. Thus, a great deal of effort has been devoted to exploring new technologies based on liquid biopsy. Since liquid biopsy relies on detection of circulating biomarkers from biofluids, it is critical to isolate highly purified cancer-related biomarkers, including circulating tumor cells (CTCs), cell-free nucleic acids (cell-free DNA and cell-free RNA), small extracellular vesicles (exosomes), and proteins. The current clinical purification techniques are facing a number of drawbacks including low purity, long processing time, high cost, and difficulties in standardization. Here, we review a promising solution, on-chip electrokinetic-based methods, that have the advantage of small sample volume requirement, minimal damage to the biomarkers, rapid, and label-free criteria. We have also discussed the existing challenges of current on-chip electrokinetic technologies and suggested potential solutions that may be worthy of future studies.

Magnetic Polymers for Magnetophoretic Separation in Microfluidic Devices

Magnetophoresis offers many advantages for manipulating magnetic targets in microsystems. The integration of micro-flux concentrators and micro-magnets allows achieving large field gradients and therefore large reachable magnetic forces. However, the associated fabrication techniques are often complex and costly, and besides, they put specific constraints on the geometries. Magnetic composite polymers provide a promising alternative in terms of simplicity and fabrication costs, and they open new perspectives for the microstructuring, design, and integration of magnetic functions. In this review, we propose a state of the art of research works implementing magnetic polymers to trap or sort magnetic micro-beads or magnetically labeled cells in microfluidic devices.

Sorting polymers by size via an array of viscous posts

DNA fragments can be sorted according to size by forcing them through an array of nanoposts. Whereas previous studies have explored solid nanoposts, this work examines nanoposts constructed out of viscous inclusions. Langevin dynamics simulations are used to study the dynamics of polymers driven through arrays of these viscous nanoposts for a range of post viscosities. The results are compared to the solid post case. Increasing post viscosity causes a decrease in the mobility of polymers traversing the array. In the limit of high post viscosity, the mobility becomes lower than in the solid post arrays, rather than converging to it. Analysis of the distributions of event times also shows that the viscous case is fundamentally different from the solid post case. The decrease in mobility in the viscous case arises from slowing down the polymer as it interacts with or even moves through the nanoposts, whereas the solid post case exhibits wrapping and unwrapping dynamics, yielding escape-like statistics. This work suggests that it may be possible to use viscous inclusions within nanofluidic and microfluidic devices to sort biomolecules with high resolution.

Advancements in microfluidics for nanoparticle separation

Nanoparticles have been widely implemented for healthcare and nanoscience industrial applications. Thus, efficient and effective nanoparticle separation methods are essential for advancement in these fields. However, current technologies for separation, such as ultracentrifugation, electrophoresis, filtration, chromatography, and selective precipitation, are not continuous and require multiple preparation steps and a minimum sample volume. Microfluidics has offered a relatively simple, low-cost, and continuous particle separation approach, and has been well-established for micron-sized particle sorting. Here, we review the recent advances in nanoparticle separation using microfluidic devices, focusing on its techniques, its advantages over conventional methods, and its potential applications, as well as foreseeable challenges in the separation of synthetic nanoparticles and biological molecules, especially DNA, proteins, viruses, and exosomes.

Recent developments in nanowires for bio-applications from molecular to cellular levels

This review highlights the most promising applications of nanowires for bioanalytical chemistry and medical diagnostics. The materials discussed here are metal oxide and Si semiconductors, which are integrated with various microfluidic systems. Nanowire structures offer desirable advantages such as a very small diameter size with a high aspect ratio and a high surface-to-volume ratio without grain boundaries; consequently, nanowires are promising tools to study biological systems. This review starts with the integration of nanowire structures into microfluidic systems, followed by the discussion of the advantages of nanowire structures in the separation, manipulation and purification of biomolecules (DNA, RNA and proteins). Next, some representative nanowire devices are introduced for biosensors from molecular to cellular levels based on electrical and optical approaches. Finally, we conclude the review by highlighting some bio-applications for nanowires and presenting the next challenges that must be overcome to improve the capabilities of nanowire structures for biological and medical systems.

An integrated microfluidic chip for immunocapture, preconcentration and separation of β-amyloid peptides

We present an integrated microfluidic chip for detection of β-amyloid (Aβ) peptides. Aβ peptides are major biomarkers for the diagnosis of Alzheimer's disease (AD) in its early stages. This microfluidic device consists of three main parts: (1) An immunocapture microcolumn based on self-assembled magnetic beads coated with antibodies specific to Aβ peptides, (2) a nano-porous membrane made of photopolymerized hydrogel for preconcentration, and (3) a microchip electrophoresis (MCE) channel with fluorescent detection. Sub-milliliter sample volume is either mixed off-chip with antibody coated magnetic beads and injected into the device or is injected into an already self-assembled column of magnetic beads in the microchannel. The captured peptides on the beads are then electrokinetically eluted and re-concentrated onto the nano-membrane in a few nano-liters. By integrating the nano-membrane, total assay time was reduced and also off-chip re-concentration or buffer exchange steps were not needed. Finally, the concentrated peptides in the chip are separated by electrophoresis in a polymer-based matrix. The device was applied to the capture and MCE analysis of differently truncated peptides Aβ (1-37, 1-39, 1-40, and 1-42) and was able to detect as low as 25 ng of synthetic Aβ peptides spiked in undiluted cerebrospinal fluid (CSF). The device was also tested with CSF samples from healthy donors. CSF samples were fluorescently labelled and pre-mixed with the magnetic beads and injected into the device. The results indicated that Aβ1-40, an important biomarker for distinguishing patients with frontotemporal lobe dementia from controls and AD patients, was detectable. Although the sensitivity of this device is not yet enough to detect all Aβ subtypes in CSF, this is the first report on an integrated or semi-integrated device for capturing and analyzing of differently truncated Aβ peptides. The method is less demanding and faster than the conventional Western blotting method currently used for research.

Three-dimensional Nanowire Structures for Ultra-Fast Separation of DNA, Protein and RNA Molecules

Separation and analysis of biomolecules represent crucial processes for biological and biomedical engineering development; however, separation resolution and speed for biomolecules analysis still require improvements. To achieve separation and analysis of biomolecules in a short time, the use of highly-ordered nanostructures fabricated by top-down or bottom-up approaches have been proposed. Here, we reported on the use of three-dimensional (3D) nanowire structures embedded in microchannels fabricated by a bottom-up approach for ultrafast separation of small biomolecules, such as DNA, protein, and RNA molecules. The 3D nanowire structures could analyze a mixture of DNA molecules (50-1000 bp) within 50 s, a mixture of protein molecules (20-340 kDa) within 5 s, and a mixture of RNA molecules (100-1000 bases) within 25 s. And, we could observe the electrophoretic mobility difference of biomolecules as a function of molecular size in the 3D nanowire structures. Since the present methodology allows users to control the pore size of sieving materials by varying the number of cycles for nanowire growth, the 3D nanowire structures have a good potential for use as alternatives for other sieving materials.

High-throughput DNA separation in nanofilter arrays

We numerically investigated the dynamics of short double-stranded DNA molecules moving through a deep-shallow alternating nanofilter, by utilizing Brownian dynamics simulation. We propose a novel mechanism for high-throughput DNA separation with a high electric field, which was originally predicted by Laachi et al. [Phys. Rev. Lett. 2007, 98, 098106]. In this work, we show that DNA molecules deterministically move along different electrophoretic streamlines according to their length, owing to geometric constraint at the exit of the shallow region. Consequently, it is more probable that long DNA molecules pass over a deep well region without significant lateral migration toward the bottom of the deep well, which is in contrast to the long dwelling time for short DNA molecules. We investigated the dynamics of DNA passage through a nanofilter facilitating electrophoretic field kinematics. The statistical distribution of the DNA molecules according to their size clearly corroborates our assumption. On the other hand, it was also found that the tapering angle between the shallow and deep regions significantly affects the DNA separation performance. The current results show that the nonuniform field effect combined with geometric constraint plays a key role in nanofilter-based DNA separation. We expect that our results will be helpful in designing and operating nanofluidics-based DNA separation devices and in understanding the polymer dynamics in confined geometries.

Tilted post arrays for separating long DNA

Recent simulations by Chen and Dorfman [Electrophoresis 35, 405-411 (2014)] suggested that "tilting" the electric field with respect to the lattice vectors of a hexagonal post array would lead to a substantial improvement in electrophoretic DNA separations therein. We constructed such an array where the electric field is applied at an angle equidistant between the two lattice vectors. This tilted array leads to (i) baseline resolution of 20 kbp DNA and λ DNA (48.5 kbp) in a 4 mm channel and (ii) measurable separation resolutions for electric fields up to 50 V/cm, both of which are improvements over untilted post arrays of the same post density. The predicted time required to reach a resolution of unity is approximately 5 min, independent of electric field. The separations are more reproducible at higher fields.

Comparison of microfabricated hexagonal and lamellar post arrays for DNA electrophoresis

We used Brownian dynamics simulations to compare DNA separations in microfabricated post arrays containing either hexagonal or lamellar lattices. Contrary to intuition, dense hexagonal arrays with frequent DNA post collisions do not yield the optimal separation. Rather, hexagonal arrays with pore sizes commensurate with the radius of gyration of the DNA lead to increased separation resolution due to a molecular weight dependent collision probability that increases with molecular weight. However, when the hexagonal array is too sparse, this advantage is lost due to the low number of collisions. Lamellar lattices, such as the DNA nanofence, appear to be superior to a hexagonal array at the same post density, since the lamellar lattice combines regions for DNA relaxation with locally dense post regions for collisions. The relative advantages of different post arrays designs are explained in terms of the statistics for the number of collisions and the holdup time, providing guidelines for designing post arrays for separating long DNA.

Magnetic control of protein spatial patterning to direct microtubule self-assembly

Living systems offer attractive strategies to generate nanoscale structures because of their innate functional properties such as the dynamic assembly of ordered nanometer fibers, the generation of mechanical forces, or the directional transport mediated by molecular motors. The design of hybrid systems, capable of interfacing artificial building blocks with biomolecules, may be a key step toward the rational design of nanoscale devices and materials. Here, we have designed a bottom-up approach to organize cytoskeletal elements in space using the self-assembly properties of magnetic nanoparticles conjugated to signaling proteins involved in microtubule nucleation. We show that magnetic nanoparticles conjugated to signaling proteins involved in microtubule nucleation can control the positioning of microtubule assembly. Under a magnetic field, a self-organized pattern of biofunctionalized nanoparticles is formed and leads to the nucleation of a periodical network of microtubules in Xenopus laevis egg extract. Our method shows how bioactive nanoparticles can generate a biochemically active pattern upon magnetic actuation, which triggers the spatial organization of nonequilibrium biological structures.

Tilted hexagonal post arrays: DNA electrophoresis in anisotropic media

Using Brownian dynamics simulations, we show that DNA electrophoresis in a hexagonal array of micron-sized posts changes qualitatively when the applied electric field vector is not coincident with the lattice vectors of the array. DNA electrophoresis in such "tilted" post arrays is superior to the standard "un-tilted" approach; while the time required to achieve a resolution of unity in a tilted post array is similar to an un-tilted array at a low-electric field strengths, this time (i) decreases exponentially with electric field strength in a tilted array and (ii) increases exponentially with electric field strength in an un-tilted array. Although the DNA dynamics in a post array are complicated, the electrophoretic mobility results indicate that the "free path," i.e. the average distance of ballistic trajectories of point-sized particles launched from random positions in the unit cell until they intersect the next post, is a useful proxy for the detailed DNA trajectories. The analysis of the free path reveals a fundamental connection between anisotropy of the medium and DNA transport therein that goes beyond simply improving the separation device.

Experimental study of the effect of disorder on DNA dynamics in post arrays during electrophoresis

We used top-down fabrication techniques to create both an ordered hexagonal array and a disordered array of 1 μm diameter cylindrical posts in a silicon dioxide microchannel with the same number of posts per unit area. The electrophoretic mobility and dispersion coefficient of λ DNA in each of the arrays were obtained as a function of the electric field using ensembles of DNA molecules in a double channel device that minimizes experimental artifacts. To deepen our understanding of the transport, we also used fluorescence microscopy to examine the dynamics of single DNA molecules as they interact with the arrays at a fixed value of the electric field. Based on the results of these two types of experiments, we conclude that the electrophoretic mobility is not dependent on the array order but that band broadening in the device is greater in the disordered array.

DNA electrophoresis in a nanofence array

We present the design and implementation of an oxidized silicon "nanofence array" for long DNA electrophoresis. The device consists of a periodic array of post-filled regions (the nanofences) alternating with empty channel regions. Even in this prototype version, the nanofence array provides the resolving power of a hexagonal nanopost array without requiring any direct-write nanopatterning steps such as electron-beam lithography. Through detailed single molecule investigations, we demonstrate that the origin of the resolving power of the nanofence array is not a reduction in band broadening, which might be expected from the theories for DNA electrophoresis in post arrays. Rather, the enhanced stretching of the hooked DNA by the uniform electric field between nanofences increases the efficiency of the collisions.

A systematic evaluation of the role of crystalline order in nanoporous materials on DNA separation

The role of order within a porous separation matrix on the separation efficiency of DNA was studied systematically. DNA separation was based on a ratchet mechanism. Monodisperse colloidal suspensions of nanoparticles were used to fabricate highly ordered separation media with a hexagonal close-packed structure. Doping with a second particle size yielded structures with different degrees of disorder, depending upon the volume fraction of each particle size. Radial distribution functions and orientational order parameters were calculated from electron micrographs to characterize the scale of disorder. The peak separation distance, band broadening, and separation resolution of DNA molecules was quantified for each structure. DNA separation parameters using pulsed fields and the ratchet effect showed a strong dependence on order within the porous nanoparticle array. Ordered structures gave large separation distances, smaller band broadening and better resolution than highly disordered, nearly random, porous structures. The effect dominated these three parameters when compared to the effect of pore size. However, the effect of order on separation performance was not monotonic. A small, but statistically significant improvement was seen in structures with short range order compared to those with long range order.

Microfluidic systems for single DNA dynamics

Recent advances in microfluidics have enabled the molecular-level study of polymer dynamics using single DNA chains. Single polymer studies based on fluorescence microscopy allow for the direct observation of non-equilibrium polymer conformations and dynamical phenomena such as diffusion, relaxation, and molecular stretching pathways in flow. Microfluidic devices have enabled the precise control of model flow fields to study the non-equilibrium dynamics of soft materials, with device geometries including curved channels, cross-slots, and microfabricated obstacles and structures. This review explores recent microfluidic systems that have advanced the study of single polymer dynamics, while identifying new directions in the field that will further elucidate the relationship between polymer microstructure and bulk rheological properties.

Ultrafast, efficient separations of large-sized dsDNA in a blended polymer matrix by microfluidic chip electrophoresis: a design of experiments approach

Double-stranded (ds) DNA fragments over a wide size range were successfully separated in blended polymer matrices by microfluidic chip electrophoresis. Novel blended polymer matrices composed of two types of polymers with three different molar masses were developed to provide improved separations of large dsDNA without negatively impacting the separation of small dsDNA. Hydroxyethyl celluloses with average molar masses of ∼27  kDa and ∼1  MDa were blended with a second class of polymer, high-molar mass (∼7  MDa) linear polyacrylamide. Fast and highly efficient separations of commercially available DNA ladders were achieved on a borosilicate glass microchip. A distinct separation of a 1-kb DNA extension ladder (200-40,000  bp) was completed in 2  min. An orthogonal design of experiments was used to optimize experimental parameters for DNA separations over a wide size range. We find that the two dominant factors are the applied electric field strength and the inclusion of a high concentration of low-molar mass polymer in the matrix solution. These two factors exerted different effects on the separations of small dsDNA fragments below 1  kbp, medium dsDNA fragments between 1 and 10  kbp, and large dsDNA fragments above 10  kbp.

Immunoglobulin G and bovine serum albumin streaming dielectrophoresis in a microfluidic device

Dielectrophoresis (DEP) has demonstrated to be a versatile tool to manipulate micro- and nanoparticles with applications for positioning, separation and fractionation. Recent developments of DEP have also shown that DEP can be used for the manipulation of biomolecules, such as DNA. Here, we focus on the manipulation of proteins using insulator-based dielectrophoresis (iDEP). We designed suitable post arrays in a microfluidic channel and use numerical simulations to calculate the electric field distribution as well as concentration of proteins according to a convection-diffusion model for both negative and positive DEP. Experimentally, we find DEP trapping of mainly protein aggregates in phosphate buffer. However, when adding a charged zwitterionic detergent, we observed DEP streamlining of immunoglobulin G (IgG) and bovine serum albumin (BSA). Our experimental observations are in excellent agreement with numerical simulations and indicate positive DEP behavior of IgG and BSA under the employed experimental conditions. Our results demonstrate DEP streaming of proteins in an iDEP device for the first time and indicate the potential of protein DEP for separation and fractionation.

Ring magnets for magnetic beads trapping in a capillary

This paper introduces the concept of ring magnets for magnetic beads (MBs) trapping in a capillary. Such magnets enable an easy insertion of a capillary simply like a pearl on a string. With this system, high magnetic forces are obtained thanks to the proximity between the magnet and the capillary, giving the opportunity to work at higher flow rates than with classical setups using two magnets with their magnetization perpendicular to the capillary. Moreover, by alternating magnets and non-magnetic spacers either in attraction or repulsion configuration, it is possible to form a chain and as a consequence to adapt the number of magnets to the desired number of plugs, thus controlling the surface available for molecule binding. Magnetic force mapping was first carried out by numerical simulations for a single ring magnet. The usefulness of this concept was then demonstrated with the achievement of an immunoassay and an online preconcentration experiment. To study the formation of multiplugs, the magnetic force was first simulated for a chain of four magnets in repulsion. This force was then introduced into a convection-diffusion model to understand the influence of the flow velocity on their size and position. The numerical simulations were qualitatively corroborated by microscopic visualizations, carried out in a capillary placed between rectangular magnets having a magnetization parallel to the capillary, and quantitatively by bead capture efficiency experiments.

Continuous-time random walk models of DNA electrophoresis in a post array: part II. Mobility and sources of band broadening

Using the two-state, continuous-time random walk model, we develop expressions for the mobility and the plate height during DNA electrophoresis in an ordered post array that delineate the contributions due to (i) the random distance between collisions and (ii) the random duration of a collision. These contributions are expressed in terms of the means and variances of the underlying stochastic processes, which we evaluate from a large ensemble of Brownian dynamics simulations performed using different electric fields and molecular weights in a hexagonal array of 1 μm posts with a 3 μm center-to-center distance. If we fix the molecular weight, we find that the collision frequency governs the mobility. On the contrary, the average collision duration is the most important factor for predicting the mobility as a function of DNA size at constant Péclet number. The plate height is reasonably well described by a single post rope-over-pulley model, provided that the extension of the molecule is small. Our results only account for dispersion inside the post array and thus represent a theoretical lower bound on the plate height in an actual device.

Microfluidic sorting and multimodal typing of cancer cells in self-assembled magnetic arrays

We propose a unique method for cell sorting, "Ephesia," using columns of biofunctionalized superparamagnetic beads self-assembled in a microfluidic channel onto an array of magnetic traps prepared by microcontact printing. It combines the advantages of microfluidic cell sorting, notably the application of a well controlled, flow-activated interaction between cells and beads, and those of immunomagnetic sorting, notably the use of batch-prepared, well characterized antibody-bearing beads. On cell lines mixtures, we demonstrated a capture yield better than 94%, and the possibility to cultivate in situ the captured cells. A second series of experiments involved clinical samples--blood, pleural effusion, and fine needle aspirates--issued from healthy donors and patients with B-cell hematological malignant tumors (leukemia and lymphoma). The immunophenotype and morphology of B-lymphocytes were analyzed directly in the microfluidic chamber, and compared with conventional flow cytometry and visual cytology data, in a blind test. Immunophenotyping results using Ephesia were fully consistent with those obtained by flow cytometry. We obtained in situ high resolution confocal three-dimensional images of the cell nuclei, showing intranuclear details consistent with conventional cytological staining. Ephesia thus provides a powerful approach to cell capture and typing allowing fully automated high resolution and quantitative immunophenotyping and morphological analysis. It requires at least 10 times smaller sample volume and cell numbers than cytometry, potentially increasing the range of indications and the success rate of microbiopsy-based diagnosis, and reducing analysis time and cost.

Onset of channeling during DNA electrophoresis in a sparse ordered post array

The "channeling hypothesis" of DNA electrophoresis in sparse, ordered arrays of posts predicts that the DNA will move through the array relatively unhindered if (i) the spacing between the posts is larger than the DNA coil and (ii) the electric field lines are straight. We tested this hypothesis by studying the electrophoretic separation of a small plasmid DNA (pUC19, 2686 base pairs) and a large, linear DNA (lambda-DNA, 48 500 base pairs) in a hexagonal array of 1 mum diameter posts with a pitch of 7 mum. At low electric field strengths, these DNAs are separated due to the long-lived, rope-over-pulley collisions of lambda-DNA with the posts. The resolution is lost as the electric field increases due to the onset of channeling by the lambda-DNA. Using a diffusive model, we show that channeling arises at low electric fields due to the finite size of the array. This channeling is not intrinsic to the system and is attenuated by increasing the size of the array. Higher electric fields lead to intrinsic channeling, which is attributed to the disparate time scales for a rope-over-pulley collision and transverse diffusion between collisions. The onset of channeling is a gradual process, in agreement with extant Brownian dynamics simulation data. Even at weak electric fields, the electrophoretic mobility of lambda-DNA in the array is considerably higher than would be expected if the DNA frequently collided with the posts.

Electrophoretic separation of DNA in gels and nanostructures

The development of nanostructure devices has opened the door to new DNA separation techniques and fundamental investigations. With advanced nanotechnologies, artificial gels (e.g. nanopillar arrays, nanofilters) can be manufactured with controlled and ordered geometries. This contrast with gels, where the pores are disordered and the range of available pore sizes is limited by the level of cross-linking and the mechanical properties of the gel. In this review, we recall the theories developed for free-solution and gel electrophoresis (extended Ogston model, biased reptation and entropic trapping) and from this perspective, suggestions for future concepts for fast DNA separation using nanostructures will be given.

Magnetic forces produced by rectangular permanent magnets in static microsystems

Finite element numerical simulations were carried out in 2D geometries to map the magnetic field and force distribution produced by rectangular permanent magnets as a function of their size and position with respect to a microchannel. A single magnet, two magnets placed in attraction and in repulsion have been considered. The goal of this work is to show where magnetic beads are preferentially captured in a microchannel. These simulations were qualitatively corroborated, in one geometrical case, by microscopic visualizations of magnetic bead plug formation in a capillary. The results show that the number of plugs is configuration dependent with: in attraction, one plug in the middle of the magnets; in repulsion, two plugs near the edges of the magnets; and with a single magnet, a plug close to the center of the magnet. The geometry of the magnets (h and l are the height and length of the magnets respectively) and their relative spacing s has a significant impact on the magnetic flux density. Its value inside a magnet increases with the h/l ratio. Consequently, bar magnets produce larger and more uniform values than flat magnets. The l/s ratio also influences the magnetic force value in the microchannel, both increasing concomitantly for all the configurations. In addition, a zero force zone in the middle appears in the attraction configuration as the l/s ratio increases, while with a single magnet, the number of maxima and minima goes from one to two, producing two focusing zones instead of only one.

DNA electrophoresis in a sparse ordered post array

We present a study of the electrophoresis of long DNA in a strong electric field through a hexagonal array of cylindrical microscale posts spaced such that the pore size is commensurate with equilibrium coil size of the DNA. Experimental mobility, dispersivity, and videomicroscopy data indicate that the DNA frequently collide with the posts, contradicting previous Brownian dynamics studies using a uniform electric field. We demonstrate via simulations that the frequent collisions, which are essential to separations in these devices, are due to the nonuniform electric field, highlighting the importance of accounting for electric-field gradients when modeling DNA transport in microfluidic devices.

DNA unhooking from a single post as a deterministic process: insights from translocation modeling

Using stochastic methods developed for DNA translocation through nanopores, we study the unhooking of a long DNA chain from an isolated stationary micropost. Such methods quickly and efficiently furnish both the full probability distribution of the unhooking time and the ensuing moments for a wide range of chain and field parameters. The results compare favorably to more realistic but computationally intense Brownian dynamics simulations. For typical chain lengths and applied electric fields used in experiments, the unhooking process is effectively deterministic; diffusive fluctuations make a negligible contribution to the first and second moments of the unhooking time. This result lends credence to continuous-time random-walk models of the overall transport process that treat the unhooking as a convective process.

Simulation of electrophoretic stretching of DNA in a microcontraction using an obstacle array for conformational preconditioning

Recently our group has reported experiments using an obstacle array to precondition the conformations of DNA molecules to facilitate their stretch in a microcontraction. Based upon previous successes simulating electrophoretic stretching in microcontractions without obstacles, we use our simulation model to study the deformation of DNA chains in a microcontraction preceded by an array of cylindrical obstacles. We compare our data to the experimental results and find good qualitative, and even quantitative, agreement concerning the behavior of the chains in the array; however, the simulations overpredict the mean stretch of the chains as they leave the contraction. We examine the amount of stretch gained between leaving the array and reaching the end of the contraction and speculate that the differences seen are caused by nonlinear electrokinetic effects that become important in the contraction due to a combination of field gradients and high field strengths.

Electrophoretic separations on microfluidic chips

This review presents a brief outline and novel developments of electrophoretic separation in microfluidic chips. Distinct characteristics of microchip electrophoresis (MCE) are discussed first, in which sample injection plug, joule heat, channel turn, surface adsorption and modification are introduced, and some successful strategies and recognized conclusions are also included. Important achievements of microfluidic electrophoresis separation in small molecules, DNA and protein are then summarized. This review is aimed at researchers, who are interested in MCE and want to adopt MCE as a functional unit in their integrated microsystems.

Label-free sequence-specific DNA sensing using copper-enhanced anodic stripping of purine bases at boron-doped diamond electrodes

Stripping voltammetric determination of purine bases in the presence of copper ions at mercury, amalgam, or carbon-based electrodes has recently been utilized in analysis of DNA or synthetic oligodeoxynucleotides (ODNs). Here we report on copper-enhanced label-free anodic stripping detection of guanine and adenine bases in acid-hydrolyzed DNA at anodically oxidized boron-doped diamond electrode (AO-BDDE). The AO-BDDE was successfully applied in a three-electrode microcell in which an approximately 50 microL drop of the analyte solution can be efficiently stirred during the accumulation step by streaming of an inert gas. Accelerated mass transport due to the solution motion in the presence of copper resulted in enhancement of the guanine oxidation signal by about 2 orders of magnitude (compared to accumulation of the analyte from still solution not containing copper), allowing an easy detection of approximately 25 fmol of the ODNs. The proposed technique is shown to be suitable for a determination of purine (particularly guanine) content in DNA samples. Applications of the technique in magnetic bead-based DNA assays (such as hybridization with DNA sequences exhibiting asymmetrical distribution of purine/pyrimidine nucleotides between the complementary strands or monitoring of amplification of specific DNA fragments in a duplex polymerase chain reaction) are demonstrated.

Relaxation of stretched DNA in slitlike confinement

We experimentally observe two separate time scales governing the entropic recoil in the linear force-extension regime of single double-stranded DNA in slit confinement. We demonstrate the existence of two distinct relaxation regimes at different extensions during relaxation. Contrary to bulk measurements, the true longest relaxation time may only be probed very close to equilibrium. A simple model of the relaxation mechanism leads to a scaling analysis that correctly predicts the extension at the crossover between the two regimes.