Frequency-dependent laminar electroosmotic flow in a closed-end rectangular microchannel

This article presents an analysis of the frequency- and time-dependent electroosmotic flow in a closed-end rectangular microchannel. An exact solution to the modified Navier-Stokes equation governing the ac electroosmotic flow field is obtained by using the Green's function formulation in combination with a complex variable approach. An analytical expression for the induced backpressure gradient is derived. With the Debye-Hückel approximation, the electrical double-layer potential distribution in the channel is obtained by analytically solving the linearized two-dimensional Poisson-Boltzmann equation. Since the counterparts of the flow rate and the electrical current are shown to be linearly proportional to the applied electric field and the pressure gradient, Onsager's principle of reciprocity is demonstrated for transient and ac electroosmotic flows. The time evolution of the electroosmotic flow and the effect of a frequency-dependent ac electric field on the oscillating electroosmotic flow in a closed-end rectangular microchannel are examined. Specifically, the induced pressure gradient is analyzed under effects of the channel dimension and the frequency of electric field. In addition, based on the Stokes second problem, the solution of the slip velocity approximation is presented for comparison with the results obtained from the analytical scheme developed in this study.     

Investigation of heterogeneous electrochemical processes using multi-stream laminar flow in a microchannel

A multi-component microfluidic electrochemical cell is shown to be a useful analytical tool for probing complex coupled processes in electrolytic systems. We recently reported an enzymatic signal amplification phenomenon that may provide increased sensitivity when detecting bio-analytes (M. S. Hasenbank, E. Fu and P. Yager, Langmuir, 2006, 22, 7451-7453), but to fully harness this method requires an improved understanding of the underlying electrochemical and chemical processes. We use spatial control of electrolyte streams on patterned conductive substrates in a microfluidic platform to elucidate the coupling of homogeneous chemical steps to heterogeneous electrochemical charge transfer processes. Because the gold surface was observable using SPR imaging, electrochemical phenomena could be monitored optically in real time. Based on these and additional results, we propose a mechanism for the novel amplification phenomenon that involves direct electron transfer between surface-immobilized enzyme molecules and the gold surface. This improved understanding of the underlying mechanism should enable the future implementation of this phenomenon in signal amplification schemes for highly sensitive lab-on-a-chip biosensors.     

The change of activation energy in microchannel laminar flow as demonstrated by kinetic analysis of the DNA duplex-coil equilibrium

This paper presents the capability of changing the activation energy of chemical reactions using microchannel laminar flow. Kinetic parameters of the duplex-coil equilibrium of DNA oligomers were studied by measuring the hysteresis between denaturation-renaturation curves using an in-house temperature-controllable microchannel-type flow cell. For this study, DNA oligomers were used because they allow physicochemical analysis and theoretical discussion. Kinetic parameters of the duplex-coil equilibrium of DNA oligomers were obtained by measuring the denaturation-renaturation hysteresis curves. Both cooling and heating curves were shifted to the high-temperature side at higher flow rates. The renaturation reaction was influenced by a slower flow rate. The effect of the slower flow rate was more pronounced for renaturation than denaturation reactions. The magnitude of the activation energies of association decreased as the flow rate increased, but that of the activation energies of the dissociation increased as the flow rate increased. Overall, these results suggest that chemical reactions' change of activation energy depends on the flow rate and the DNA molecular size.     

Specific molecule localization in microchannel laminar flow and its application for non-immobilized-probe analysis

Microfluidic systems enable superior control of fluidics. We have developed a novel size-separation method utilizing secondary flow within a microchannel. Using confocal fluorescence microscopy and computer simulation, we confirmed that separation occurred as a result of specific molecular localization in the curving part of the microchannel. Maximum separation efficiency was achieved by optimizing microchannel design and flow rate for individual separation targets. In addition, more effective separation was achieved by use of plural microchannel curves. This method was used for sequence-selective DNA sensing. Double-stranded DNA formed by hybridization between target DNA and a complementary probe had different elution profiles from those of the single-stranded non-complementary sequence. Moreover, the response depends on the length of the DNA molecules. This method does not require immobilization of either probe or target DNA, because all reactions occurred in the solution phase. Such features may reduce experimental error and the difference between data from different operators.     

The effect of rib shape on the behavior of laminar flow of oil/MWCNT nanofluid in a rectangular microchannel

Journal of Thermal Analysis and Calorimetry - In this research, the laminar and forced flow and heat transfer of oil/multi-walled carbon nanotubes nanofluid in a microchannel have been numerically...     

Parallel-stranded DNA: enhancing duplex stability by the 'G-clamp' and a pyrrolo-dC derivative

The new pyrrolo-dC derivative 4 tethered with an alkylamino side chain via a triazole linker was synthesized. Oligonucleotides containing the G-clamp 3 or the pyrrolo-dC derivative 4 were prepared. Oligonucleotide synthesis and deprotection under standard conditions led to unwanted side product formation. The side product was identified as an acrylonitrile adduct of the aminoalkyl side chain. Changing the synthesis and work-up conditions to fast-deprotection chemistry and performing β-elimination of the cyanoethyl group on the solid support yielded pure oligonucleotides. Oligonucleotide duplexes with parallel chain orientation were constructed incorporating dA·dT and isoG(d)·dC base pairs. Replacement of dC-residues by the G-clamp 3 led to extraordinarily stable duplexes (ΔT(m) = +11 °C for two incorporations) in ps DNA, while the pyrrolo-dC derivative 4 behaved like dC. Surprisingly, the G-clamp 3 forms an even more stable base pair with 2'-deoxyisoguanosine in DNA with parallel chain orientation than with 2'-deoxyguanosine in aps DNA.     

DNA separation by EFFF in a microchannel

This paper theoretically explores the application of electric field flow fractionation (EFFF) for the size-based separation of DNA strands in a microchannel. An axial electric field cannot separate DNA strands in solution because the electrical mobility of the strands is independent of the length. However, lateral electric fields coupled with an axial Poiseuille flow can separate the DNA strands of different sizes. By using regular perturbation analysis, we obtain the effective diffusivity and the mean velocity of the DNA molecules that are undergoing a pressure driven Poiseuille flow in a 2D channel in presence of a lateral electric field. The mean velocities and the dispersion coefficients are then utilized to determine the scaling for length of the channel and the time required for separation of DNA molecules in different parameter regimes. The results show that EFFF can separate DNA strands in the range of 10 kbp that differ in size by about 2.5 kbp in about half an hour in a 1 cm long channel. While DNA strands can be separated by EFFF, the performance of devices based on EFFF seems to be at best comparable to other techniques such as entropic trapping.     

DNA sequencing in a monolithic microchannel device

We present 50 cm long microchannels in a monolithic device for high resolution, long read-length DNA sequencing. These devices were fabricated and bonded in borofloat glass using unconventional photolithography techniques with 48-188 independent, straight microchannels. The microchannel DNA separation was tested with POP-6 polymer and a DNA sequencing ladder separated at room temperature and 200 V/cm. Single-base resolution greater than 600 bases was achieved and the sequence base called to 640 bases with 98% accuracy. Under the same experimental conditions, the performance of the microchip was identical to a fused-silica capillary with similar cross-sectional area.     

Electroosmotic flow velocity measurements in a square microchannel

Experiments were performed using a microparticle image velocimetry (MPIV) for 2D velocity distributions of electroosmotically driven flows in a 40-mm-long microchannel with a square cross section of 200×200 μm. Electroosmotic flow (EOF) bulk fluid velocity measurements were made in a range of streamwise electric field strengths from 5 to 25 kV/m. A series of seed particle calibration tests can be made in a 200×120×24,000-μm untreated polydimethyl siloxane (PDMS channel incorporating MPIV to determine the electrophoretic mobilities in aqueous buffer solutions of 1× TAE, 1× TBE, 10 mM NaCl, and 10 mM borate. A linear/nonlinear (due to Joule heating) flow rate increase with applied field was obtained and compared with those of previous studies. A parametric study, with extensive measurements, was performed with different electric field strength and buffer solution concentration under a constant zeta potential at wall for each buffer. The characteristics of EOF in square microchannels were thus investigated. Finally, a composite correlation of the relevant parameters was developed in the form of within ±1% accuracy for 99% of the experimental data.     

Aminoglycoside complexation with a DNA.RNA hybrid duplex: the thermodynamics of recognition and inhibition of RNA processing enzymes

Spectroscopic and calorimetric techniques were employed to characterize and contrast the binding of the aminoglycoside paromomycin to three octamer nucleic acid duplexes of identical sequence but different strand composition (a DNA.RNA hybrid duplex and the corresponding DNA.DNA and RNA.RNA duplexes). In addition, the impact of paromomycin binding on both RNase H- and RNase A-mediated cleavage of the RNA strand in the DNA.RNA duplex was also determined. Our results reveal the following significant features: (i) Paromomycin binding enhances the thermal stabilities of the RNA.RNA and DNA.RNA duplexes to similar extents, with this thermal enhancement being substantially greater in magnitude than that of the DNA.DNA duplex. (ii) Paromomycin binding to the DNA.RNA hybrid duplex induces CD changes consistent with a shift from an A-like to a more canonical A-conformation. (iii) Paromomycin binding to all three octamer duplexes is linked to the uptake of a similar number of protons, with the magnitude of this number being dependent on pH. (iv) The affinity of paromomycin for the three host duplexes follows the hierarchy, RNA.RNA > DNA.RNA > DNA.DNA. (v) The observed affinity of paromomycin for the RNA.RNA and DNA.RNA duplexes decreases with increasing pH. (vi) The binding of paromomycin to the DNA.RNA hybrid duplex inhibits both RNase H- and RNase A-mediated cleavage of the RNA strand. We discuss the implications of our combined results with regard to the specific targeting of DNA.RNA hybrid duplex domains and potential antiretroviral applications.     

Diffusion based analysis in a sheath flow microchannel: the sheath flow T-sensor

This paper describes a microfluidic channel that allows for diffusion-based analysis of adsorbing species without passivation of the channel surfaces. The sheath flow configuration was used to measure the diffusion coefficient of fluorescently labeled species from their spatial distribution within the microchannel by analyzing the derivative of the intensity profile at the interface between two distinct core fluids. Measurements for both a small molecule (rhodamine B) and an intermediate-sized protein (wheat germ agglutinin) were made, demonstrating the utility of the sheath flow T-sensor.     

Transient analysis of electroosmotic flow in a slit microchannel

The transient aspects of electroosmotic flow in a slit microchannel are studied. Exact solutions for the electrical potential profile and the transient electroosmotic flow field are obtained by solving the complete Poisson-Boltzmann equation and the Navier-Stokes equation under an analytical approximation for the hyperbolic sine function. The characteristics of the transient electroosmotic flow are discussed under influences of the electric double layer and the geometric size of the microchannel.     

Quantification of electrical field-induced flow reversal in a microchannel

We characterize the electroosmotic flow in a microchannel with field effect flow control. High resolution measurements of the flow velocity, performed by micro particle image velocimetry, evidence the flow reversal induced by a local modification of the surface charge due to the presence of the gate. The shape of the microchannel cross-section is accurately extracted from these measurements. Experimental velocity profiles show a quantitative agreement with numerical results accounting for this exact shape. Analytical predictions assuming a rectangular cross-section are found to give a reasonable estimate of the velocity far enough from the walls.     

Influences of ribonucleotide on a duplex conformation and its thermal stability: study with the chimeric RNA-DNA strands

To understand the influences of the ribonucleotide on a duplex conformation and its stability, we systematically studied the CD spectra and the thermodynamics of nucleic acid duplexes formed by the chimeric RNA-DNA strand in which ribonucleotides and deoxyribonucleotides were covalently attached. It was found that the duplex stability was context-dependent and independent of the number of ribonucleotides in the chimeric strand, whereas the CD spectra showed less overall structural perturbation by the chimeric junctions. Combining the results of the CD and the thermodynamic data revealed a stability-structure relationship for the duplexes. Importantly, DeltaG(o)37 values estimated for the chimeric junction formation in the RNA-DNA/DNA and the RNA-DNA/RNA duplexes were close to those of RNA/DNA and RNA/RNA interactions, respectively. Furthermore, DeltaG(o)37s of the DNA-RNA/DNA and DNA-RNA/DNA-RNA junctions were similar to those of the DNA duplex, and the values of DNA-RNA/RNA-DNA were similar to those of the DNA/RNA. The thermodynamic analyses suggest that the 5'-nucleotide may be the crucial factor that determines the stability at the chimeric junction. Our results not only suggest influences of the ribonucleotide on a duplex conformation and its stability but also are useful for the design of RNA-DNA chimeric strands applicable to biotechnology.     

Unveiling the complex pattern of intermolecular interactions responsible for the stability of the DNA duplex

Herein, we provide new insights into the intermolecular interactions responsible for the intrinsic stability of the duplex structure of a large portion of human B-DNA by using advanced quantum mechanical methods. Our results indicate that (i) the effect of non-neighboring bases on the inter-strand interaction is negligibly small, (ii) London dispersion effects are essential for the stability of the duplex structure, (iii) the largest contribution to the stability of the duplex structure is the Watson–Crick base pairing – consistent with previous computational investigations, (iv) the effect of stacking between adjacent bases is relatively small but still essential for the duplex structure stability and (v) there are no cooperativity effects between intra-strand stacking and inter-strand base pairing interactions. These results are consistent with atomic force microscope measurements and provide the first theoretical validation of nearest neighbor approaches for predicting thermodynamic data of arbitrary DNA sequences.

Advanced electronic structure methods provide a new insight into the intermolecular interactions responsible for the intrinsic stability of the duplex structure of human DNA.     

Enzymatic degradation of p-chlorophenol in a two-phase flow microchannel system

Enzymatic degradation of p-chlorophenol was carried out in a two-phase flow in a microchannel (100 microm width, 25 microm depth) fabricated on a glass plate (70 mm x 38 mm). This is the first report on the enzymatic reaction in a two-phase flow on a microfluidic device. The surface of the microchannel was partially modified with octadecylsilane groups to be hydrophobic, thus allowing clear phase separation at the end-junction of the microchannel. The enzyme (laccase), which is surface active, was solubilized in a succinic aqueous buffer and the substrate (p-chlorophenol) was in isooctane. The degradation of p-chlorophenol occurred mainly at the aqueous-organic interface in the microchannel. We investigated the effects of flow velocity and microchannel shape on the enzymatic degradation of p-chlorophenol. Assuming that diffusion of the substrate (p-chlorophenol) is the rate-limiting step in the enzymatic degradation of p-chlorophenol in the microchannel, we proposed a simple theoretical model for the degradation in the microchannel. The calculated degradation values agreed well with the experimental data.     

Effective modulation of DNA duplex stability by reversible transition metal complex formation in the minor groove

Herein we describe the reversible changing of DNA duplex thermal stability by exploiting transition metal complexation phenomena. A terpyridine ligand was conjugated to the N2'-atoms of 2'-amino-2'-deoxyuridine and its locked counterpart 2'-amino-LNA, and these metal-complexing monomers were incorporated into oligodeoxyribonucleotides. Upon addition of varying amounts of transition metal ions, the thermal stability of DNA duplexes containing these terpyridine-functionalized units in different constitutions was affected to different degrees (DeltaTm values = -15.5 to +49.0 degrees C, relative to the unmodified duplex). The most pronounced effects were observed when two complexing monomers were positioned in opposite strands. Addition of 1 equiv of Ni2+ to such a system induced extraordinary duplex stabilization. Molecular modeling studies suggest, as an explanation for this phenomenon, formation of nickel-mediated interstrand linkages in the minor groove. Addition of an excess of metal ions resulted in largely decreased Tm values. Alternating addition of metal ions and EDTA demonstrated reversibility of metal ion-induced changes in hybridization strength, proving that the described approach provides an efficient method for duplex stability modulation.     

Focusing particles by induced charge electrokinetic flow in a microchannel

A novel method of sheathless particle focusing by induced charge electrokinetic flow in a microchannel is presented in this paper. By placing a pair of metal plates on the opposite walls of the channel and applying an electrical field, particle focusing is achieved due to the two pairs of vortex that constrain the flow of the particle solution. As an example, the trajectories of particles under different electrical fields with only one metal plate on one side channel wall were numerically simulated and experimentally validated. Other flow focusing effects, such as the focused width ratio (focused width/channel width) and length ratio (focused length/half‐length of metal plate) of the sample solution, were also numerically studied. The results show that the particle firstly passes through the gaps between the upstream vortices and the channel walls. Afterwards, the particle is focused to pass through the gap between the two downstream vortices that determine the focused particle position. Numerical simulations show that the focused particle stream becomes thin with the increases in the applied electrical field and the length of the metal plates. As regards to the focused length ratio of the focused stream, however, it slightly increases with the increase in the applied electrical field and almost keeps constant with the increase in the length of the metal plate. The size of the focused sample solution, therefore, can be easily adjusted by controlling the applied electrical field and the sizes of the metal plates.     

Analysis of electroosmotic flow of power-law fluids in a slit microchannel

Electroosmotic flow of power-law fluids in a slit channel is analyzed. The governing equations including the linearized Poisson-Boltzmann equation, the Cauchy momentum equation, and the continuity equation are solved to seek analytical expressions for the shear stress, dynamic viscosity, and velocity distribution. Specifically, exact solutions of the velocity distributions are explicitly found for several special values of the flow behavior index. Furthermore, with the implementation of an approximate scheme for the hyperbolic cosine function, approximate solutions of the velocity distributions are obtained. In addition, a generalized Smoluchowski velocity is introduced by taking into account contributions due to the finite thickness of the electric double layer and the flow behavior index of power-law fluids. Calculations are performed to examine the effects of kappaH, flow behavior index, double layer thickness, and applied electric field on the shear stress, dynamic viscosity, velocity distribution, and average velocity/flow rate of the electroosmotic flow of power-law fluids.