DNA electrophoresis in a sparse ordered post array

Micro/nanofluidic devices for DNA/RNA detection and separation

The development and research have ramped up at a greater speed than ever in the field of diseases diagnosis. Still there is struggle in developing early detection techniques which uses complex biomolecules like RNA, DNA and proteins in order to detect diseases caused by bacteria, viruses or fungi. Until now separation techniques used before detection rely on traditional techniques like electrophoresis etc. which often require centralized services. Although efforts are made in developing devices that is capable enough on carrying out separation and detection based on microfluidic (MF) and nanofluidic (NF) or lab on chip. Hence, in this chapter, we have discussed about the advancement, limitations and future steps that needs to be taken to flourish the field of NF and MF for the detection and separation of nucleic acid.

Separation Phenomena in Tailored Micro- and Nanofluidic Environments

Separations of bioanalytes require robust, effective, and selective migration phenomena. However, due to the complexity of biological matrices such as body fluids or tissue, these requirements are difficult to achieve. The separations field is thus constantly evolving to develop suitable methods to separate biomarkers and fractionate biospecimens for further interrogation of biomolecular content. Advances in the field of microfabrication allow the tailored generation of micro- and nanofluidic environments. These can be exploited to induce interactions and dynamics of biological species with the corresponding geometrical features, which in turn can be capitalized for novel separation approaches. This review provides an overview of several unique separation applications demonstrated in recent years in tailored micro- and nanofluidic environments. These include electrokinetic methods such as dielectrophoresis and electrophoresis, but also rather nonintuitive ratchet separation mechanisms, continuous flow separations, and fractionations such as deterministic lateral displacement, as well as methods employing entropic forces for separation.

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.

Nonmonotonic DNA-length-dependent mobility in pluronic gels

Two-dimensional electrophoresis was used to analyze the mobility of DNA fragments in micellar gels of pluronic F127 (EO_{100}PO_{70}EO_{100}) and pluronic P123 (EO_{20}PO_{70}EO_{20}). The 20-3500 base pair DNA fragments were separated by size first in agarose gels, and then in pluronic gels at room temperature. In agarose gels, the DNA mobility decreases monotonically with increasing DNA length. In pluronic gels, however, the mobility varies nonmonotonically according to fragment lengths that are strongly correlated with the diameter of the spherical micelles. Brownian dynamics (BD) simulations with short-ranged intra-DNA hydrodynamic interactions were performed to numerically calculate the length-dependent mobility in pluronic lattices. The rising and falling trends, as well as the oscillations of mobility, were captured by the coarse-grained BD simulations. Molecular dynamics simulations in pluronic F127, with explicitly modeled micelle coronas, justified that the hydrodynamic interactions mediated by the complex fluid of hydrated poly(ethylene oxide) are a possible reason for the initial rise of mobility with DNA length.

Capillary electrophoresis applied to DNA: determining and harnessing sequence and structure to advance bioanalyses (2009-2014)

This review of capillary electrophoresis methods for DNA analyses covers critical advances from 2009 to 2014, referencing 184 citations. Separation mechanisms based on free-zone capillary electrophoresis, Ogston sieving, and reptation are described. Two prevalent gel matrices for gel-facilitated sieving, which are linear polyacrylamide and polydimethylacrylamide, are compared in terms of performance, cost, viscosity, and passivation of electroosmotic flow. The role of capillary electrophoresis in the discovery, design, and characterization of DNA aptamers for molecular recognition is discussed. Expanding and emerging techniques in the field are also highlighted.

Stretching self-entangled DNA molecules in elongational fields

We present experiments of self-entangled DNA molecules stretching under a planar elongational field, and their stretching dynamics are compared to identical molecules without entanglements. Self-entangled molecules stretch in a stage-wise fashion, persisting in an "arrested" state for decades of strain prior to rapidly stretching, slowing down the stretching dynamics by an order of magnitude compared to unentangled molecules. Self-entangled molecules are shown to proceed through a transient state where one or two ends of the molecule are protruding from an entangled, knotted core. This phenomenon sharply contrasts with the wide array of transient configurations shown here and by others for stretching polymers without entanglements. The rate at which self-entangled molecules stretch through this transient state is demonstrably slower than unentangled molecules, providing the first direct experimental evidence of a topological friction. These experimental observations are shown to be qualitatively and semi-quantitatively reproduced by a dumbbell model with two fitting parameters, the values of which are reasonable in light of previous experiments of knotted DNA.

Ultrafast and wide range analysis of DNA molecules using rigid network structure of solid nanowires

Analyzing sizes of DNA via electrophoresis using a gel has played an important role in the recent, rapid progress of biology and biotechnology. Although analyzing DNA over a wide range of sizes in a short time is desired, no existing electrophoresis methods have been able to fully satisfy these two requirements. Here we propose a novel method using a rigid 3D network structure composed of solid nanowires within a microchannel. This rigid network structure enables analysis of DNA under applied DC electric fields for a large DNA size range (100 bp-166 kbp) within 13 s, which are much wider and faster conditions than those of any existing methods. The network density is readily varied for the targeted DNA size range by tailoring the number of cycles of the nanowire growth only at the desired spatial position within the microchannel. The rigid dense 3D network structure with spatial density control plays an important role in determining the capability for analyzing DNA. Since the present method allows the spatial location and density of the nanostructure within the microchannels to be defined, this unique controllability offers a new strategy to develop an analytical method not only for DNA but also for other biological molecules.

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.

Simulations of DNA stretching by flow field in microchannels with complex geometry

Recently, we have reported the experimental results of DNA stretching by flow field in three microchannels (C. H. Lee and C. C. Hsieh, Biomicrofluidics 7(1), 014109 (2013)) designed specifically for the purpose of preconditioning DNA conformation for easier stretching. The experimental results do not only demonstrate the superiority of the new devices but also provides detailed observation of DNA behavior in complex flow field that was not available before. In this study, we use Brownian dynamics-finite element method (BD-FEM) to simulate DNA behavior in these microchannels, and compare the results against the experiments. Although the hydrodynamic interaction (HI) between DNA segments and between DNA and the device boundaries was not included in the simulations, the simulation results are in fairly good agreement with the experimental data from either the aspect of the single molecule behavior or from the aspect of ensemble averaged properties. The discrepancy between the simulation and the experimental results can be explained by the neglect of HI effect in the simulations. Considering the huge savings on the computational cost from neglecting HI, we conclude that BD-FEM can be used as an efficient and economic designing tool for developing new microfluidic device for DNA manipulation.

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.

Relationship between frequency and deflection angle in the DNA prism

The DNA prism is a modification of the standard pulsed-field electrophoresis protocol to provide a continuous separation, where the DNA are deflected at an angle that depends on their molecular weight. The standard switchback model for the DNA prism predicts a monotonic increase in the deflection angle as a function of the frequency for switching the field until a plateau regime is reached. However, experiments indicate that the deflection angle achieves a maximum value before decaying to a size-independent value at high frequencies. Using Brownian dynamics simulations, we show that the maximum in the deflection angle is related to the reorientation time for the DNA and the decay in deflection angle at high frequencies is due to inadequate stretching. The generic features of the dependence of the deflection angle on molecular weight, switching frequency, and electric field strength explain a number of experimental phenomena.

Stretching DNA by electric field and flow field in microfluidic devices: An experimental validation to the devices designed with computer simulations

We examined the performance of three microfluidic devices for stretching DNA. The first device is a microchannel with a contraction, and the remaining two are the modifications to the first. The modified designs were made with the help of computer simulations [C. C. Hsieh and T. H. Lin, Biomicrofluidics 5(4), 044106 (2011) and C. C. Hsieh, T. H. Lin, and C. D. Huang, Biomicrofluidics 6, 044105 (2012)] and they were optimized for operating with electric field. In our experiments, we first used DC electric field to stretch DNA. However, the experimental results were not even in qualitative agreement with our simulations. More detailed investigation revealed that DNA molecules adopt a globular conformation in high DC field and therefore become more difficult to stretch. Owing to the similarity between flow field and electric field, we turned to use flow field to stretch DNA with the same devices. The evolution patterns of DNA conformation in flow field were found qualitatively the same as our prediction based on electric field. We analyzed the maximum values, the evolution and the distributions of DNA extension at different Deborah number in each device. We found that the shear and the hydrodynamic interaction have significant influence on the performance of the devices.

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.

Separation of deformable particles in deterministic lateral displacement devices

Using numerical simulations, we study the separation of deformable bodies, such as capsules, vesicles, and cells, in deterministic lateral displacement devices, also known as bump arrays. These arrays comprise regular rows of obstacles such as micropillars whose arrangements are shifted between adjacent rows by a fixed amount. We show that, in addition to the zigzag and laterally displaced trajectories that have been observed experimentally, there exists a third type of trajectory which we call dispersive, characterized by seemingly random bumpings off the micropillars. These dispersive trajectories are observed only for large and rigid particles whose diameters are approximately more than half the gap size between micropillars and whose stiffness exceeds approximately 500 MPa. We then map out the regions in phase space, spanned by the row shift, row separation, particle diameter, and particle deformability, in which the different types of trajectories are expected. We also show that, in this phase space, it is possible to transition from zigzag to dispersive trajectories, bypassing lateral displacement. Experimentally, this is undesirable because it limits the ability of the device to sort particles according to size. Finally, we discuss how our numerical simulations may be of use in device prototyping and optimization.

Biophysics of knotting

Knots appear in a wide variety of biophysical systems, ranging from biopolymers, such as DNA and proteins, to macroscopic objects, such as umbilical cords and catheters. Although significant advancements have been made in the mathematical theory of knots and some progress has been made in the statistical mechanics of knots in idealized chains, the mechanisms and dynamics of knotting in biophysical systems remain far from fully understood. We report on recent progress in the biophysics of knotting-the formation, characterization, and dynamics of knots in various biophysical contexts.

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.