Numerical Studies of Electrokinetic Control of DNA Concentration in A Closed-End Microchannel

868 Yasaman Daghighi Dongqing Li
Department of Mechanical and Mechatronics Engineering, University of Waterloo, Waterloo, ON, Canada
Electrophoresis 2010, 31, 868878
Research Article
Numerical studies of electrokinetic control of DNA concentration in a closed-end microchannel

A major challenge in lab-on-a-chip devices is how to concentrate sample molecules from a dilute solution, which is critical to the effectiveness and the detection limit of on-chip bio-chemical reactions. A numerical study of sample concentration control by electrokinetic microuidic means in a closed-end microchannel is presented in this paper. The present method provides a simple and efcient way of concentration control by using electrokinetic trapping of a charged species of interest, controlling liquid ow and separating different sample molecules in the microchannel. The electrokinetic-concentration process and the controlled transport of the sample molecules are numerically studied. In this system, in addition to the electroosmotic ow and the electrophoresis, the closed-end of the chamber causes velocity variation at both ends of the channel and induces a pressure gradient and the associated uid movement in the channel. The combined effects determine the nal concentration eld of the sample molecules. The inuences of a number of parameters such as the channel dimensions, electrode size and the applied electric eld are investigated. Keywords: Closed-end microchannel / Concentration / Electrokinetics / Electrophoresis / Microuidics DOI 10.1002/elps.200900447
Received July 26, 2009 Revised September 29, 2009 Accepted October 18, 2009
1 Introduction
Biochemical detection in dilute solutions in microuidic devices is very important [1, 2]. The concentration of sample molecules directly affects the effectiveness of the biochemical reaction and the ability to detect the sample molecules in the solution. Often the technological challenge lies in detecting micro-bio-particles with a concentration of only a few particles per micro-liter, such as pre-concentration of viruses in aerosol samples. Concentrating the particles in one specic area will increase the chance and efciency of sampling the target particles in dilute solution. DNA detection has become a key technology for various biomedical applications. Currently, PCR has to be used to amplify the amount of DNA from the initial sample, before any DNA detection techniques can be applied. If the small amount of the DNA molecules from the initial sample can be concentrated and collected, this could enable many biomedical detection methods directly on a microuidic chip.
Correspondence: Professor Dongqing Li, Department of Mechanical and Mechatronics Engineering, University of Waterloo, Waterloo, ON, N2L 3G1 Canada E-mail: dongqing@mme.uwaterloo.ca Fax: 11-519-885-5862
Abbreviations: EDL, electrical double layer; FASS, eldamplied sample stacking
There are a number of papers reporting studies of sample concentrating processes in microchannels. Numerical simulation of DNA sample preconcentration in a microdevice by electrophoresis was introduced by Srivastava et al. [3]. This study presented a computational tool for understanding and designing sample injectors and electrophoretic protocols for DNA separation in a double-T injector. In another paper, electro-pre-concentration process in a microchannel was numerically simulated as a one-dimensional system by Plecis et al. [4]. They used Finite Element method to calculate catodic pre-concentration rate for different types of molecules and solutions. They investigated the pre-concentration of orescent dyes in low ionic strength solutions, and proteins in moderate ionic strength electrolyte solutions. Their study revealed the pre-concentration peak locations and its maximum rate of concentration as a function of time for different mobilities and various molecule charges. They claimed that their simulation is applicable to a wide range of microchannels and nanochannels but the one-dimensional assumption decreases the applicability of the method. Various stacking methods and focusing methods have been developed for concentrating samples by transport the sample to a local equilibrium state electrokinetically. IEF, which is also known as electrofocusing, is a technique for separating different molecules by their electric charge differences. This method uses pH gradients along a microchannel to focus charged samples at their pIs at which the
www.electrophoresis-journal.com
& 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
Microuidics and Miniaturization
869
electrophoretic force exerted on the samples vanishes. Cabrera and Yager used natural pH gradients without the use of an ampholyte to concentrate bacteria [5]. Huang and Pawliszyn used thermally driven pH gradients in a tapered microchannel to perform IEF [6]. Li et al. generated pH gradients using a commercially available carrier ampholytes [7]. It should be noted that IEF has also been used to separate samples according to their pI values [8]. Despite high resolution of IEF in discerning analytes, as ne as 0.01 pH, applications in biochemical analysis are limited, partially because of the low solubility of proteins at their pIs and because not all analytes have a specic pI. Field-amplied sample stacking (FASS) and ITP use two or more buffers with different conductivity to generate electric eld variation along a microchannel. A key to performing FASS or ITP is to inject a sample plug into the system without an electrokinetic injection bias. As a result, a hydrodynamic sample injection scheme is often used. Wainright et al. coupled ITP and zone electrophoresis on a microchip to concentrate and subsequently separate samples, resulting in an approximately 400fold improved sensitivity [9]. Jung et al. reported an 1100-fold signal increase on using FASS combined with a porous polymer structure for improved sample injection and ow control [10]. Beard et al. implemented FASS to detect 20-pM concentrations of biogenic amines [11]. Shaikh et al. [12] achieved simultaneous concentration, focusing and metering capabilities with current-generation sample-injection technology. They used microuidic chips incorporating arrays of individually addressable microfabricated electrodes, and demonstrate that DNA can be sequentially concentrated, focused into a narrow zone, metered, and injected into an analysis channel. Their technique transports charged biomolecules between active electrodes upon application of a small potential difference (1 V) and is capable of achieving orders of magnitude concentration increases within a small device footprint. The collected samples are highly focused, with sample zone size and shape dened solely by electrode geometry. Despite their good results, fabricating such chips is complicated and needs high accuracy. The integration of PCR with DNA separation on a single microchip was experimentally demonstrated by Lettieri et al. [13]. They described the trapping, pre-concentration and release of large DNA molecules in microuidic devices using controlled micro recirculating ows. Their method was used to extract and purify DNA from mixtures containing other substances. A convenient method capable of providing highly resolved, adequately sensitive and reproducible separation of DNA fragments was reported by Chen et al. [14]. They demonstrated an on-line pre-concentration and separation of DNA fragments by using uncoated capillaries together with UV detection. This technique involved a high degree of automation, used minimum quantities of the samples and reagents and was able to make reproducible separations of PCR products. The usefulness of this method was demonstrated by detecting exogenous genes in transgenic oilseed rape.
Svarnas et al. [15] presented the fabrication of a hybrid micro- and nanouidic device to study electro-preconcentration of biomolecules. In their study, they applied a bulklike machining method and developed a glass nanoporebased system in which four reservoirs are connected to four microchannels, respectively, in an H shaped channel network via nanochannel. The sharp contraction from a microchannel to a nanochannel creates a strong local electric eld. This eld is used for electrokinetic trapping of negatively charged molecules. They investigated concentration of charged molecules under the effect of concentration polarization. Huang and Yang [16] experimentally investigated the effect of concentration polarization using a hybrid microchannel and nanochannel interface. They controlled the ow by applying a two-step voltage. Their system contains two microchannels (one V-shape and one crossform) connected by a short nanochannel. They tried to produce a low-conductivity region within the loading channel by creating an ionic depletion effect at the anodic side of the nanochannel. In practical applications, manufacturing nanochannels is not simple and hence limits these methods. Du et al. [17] experimentally evaluated a microuidic device for trapping and concentrating a trace amount of DNA molecules. They used a quadrupole electrode platform to generate a nonlinear electroosmotic ow by charge polarization under high-frequency AC elds. Their trapping approach was validated over a large range of DNA concentrations. Using this method led to signicant and more efcient concentration enhancement within a few seconds. They could switch between trapping and release of DNA, showing potential in concentrating and transporting biomolecules in a continuous fashion. However, using such a quadrupole electrode device and high-frequency AC elds brings complexity to many applications of microuidic labon-a-chip devices. It is highly desirable to be able to concentrate and separate bio-molecules from a dilute solution in a simple microchannel using a simple process. In this study, a theoretical model of the electrokinetically driven concentration process in a straight, closed-end microchannel is developed. Numerical simulation is conducted by using FLUENT. The ow eld and the coupled time-dependent concentration eld in a closed-end microchannel are numerically studied. In this system, in addition to the electroosmotic ow and the electrophoresis, the closed-end of the channel causes velocity variation at both ends of the channel and induces pressure gradient and uid movement in the channel. Figure 1 shows the difference in the electroosmotic ow eld between an open microchannel and a microchannel with two closed ends. In the microchannel with closed ends, the combined effects of the electroosmotic ow and the induced pressuredriven ow determine the nal concentration eld of the sample molecules. The inuences of a number of parameters such as the initial concentration, chamber dimensions, electrode size and the applied electric eld are investigated in this work. In the second part of this paper, concentrating two
870
Y. Daghighi and D. Li
Figure 1. Schematic of a fully developed velocity prole of electroosmotic ow in (A) an open-end microchannel (B) a closed-end microchannel (the circle is a well at one end of the channel).
types of DNA molecules and then separating them are studied and effects of different parameters on such a process are investigated as well.
2 Theoretical model
Figure 2 illustrates the computational domain, which is used to study ow eld and the concentration eld in a closed-end microchannel system. The system consists of two reservoirs, A and B, each with a diameter of D, and one microchannel of width 2a and length L. Patankar and Hu [18] has proved that the velocity component in the z-direction is very small, one can apply a two-dimensional (the xy plane) study at any given height and reach a highly accurate ow eld with a lower computational cost. Therefore, we will perform the simulations in two dimensions (xy plane). The reservoirs and the channel are initially lled with a buffer solution. A dilute sample solution is added to Reservoir A. The liquid ows in the channel as soon as the electric led is applied between the electrodes and consequently through the microchannel. Three electrodes, E1, E2 and E3, are used in this system to control the electric eld in the different processes. Electrodes 1 and 3 are placed at the far end of Reservoirs A and B, respectively. Electrode 2 is mounted at the entrance of the microchannel from Reservoir A. First, we wish to concentrate on the negatively charged sample molecules in the dilute solution in Reservoir A by applying an electric eld. During the concentration process, an electric eld gradient is created between E1 and E2, so that the negatively charged sample
molecules will migrate to the vicinity of E2. In the meantime, an electric eld between E2 and E3 is produced to ensure zero net ow at the channel cross-section where E2 is located. After the sample molecules are concentrated in the region of E2, a different electric eld between E2 and E3 will be used to produce electrophoresis, i.e. to separate the different molecules in the concentrated sample plug while transporting the sample plug along the microchannel towards Reservoir B. Cartesian coordinate system for the numerical analysis is chosen, as indicated in Fig. 2. The liquid in the microchannel is assumed to be an incompressible and Newtonian, with symmetric electrolytes, constant density, r, and viscosity, m. The channel wall is uniformly charged with a zeta potential, z. The temperature is assumed to be uniform and constant.
3 Governing equations
Based on the assumption of a steady state, incompressible, laminar ow, the motion of the electrolyte solution under the application of an external electric eld, E, in the closedend microchannel can be described by the following equations.
3.1 The electric eld According to the theory of electrostatics, the applied electrical potential, f, in the reservoirs and in the
871
Figure 2. Two-dimensional (xy plane) illustration of the closed-end microchannel used in this study of sample concentration and separation.
microchannel can be described by Poisson equation H2 f 0 1
is subject to the following boundary conditions on the wall of system in the two-dimensional (xy plane) system: 0 xoD1b; D1b xo2D1L; Vslip mE12 Vslip mE32
Boundary conditions are required to solve this equation. We impose the insulation condition to all the walls of the reservoirs and the microchannel, and the specic values at each electrode. Once the electrical eld is known, the local electric eld strength can be calculated by ~ ~ E Hf
3.3 The concentration eld The distribution of the sample molecules or the concentration eld can be described by the mass concentration law in the form of transient mass transport equation
* * @Ci 1H V 1V epi Ci Di HCi 0 @t
3.2 The ow eld The ow eld is dened by the continuity and momentum equations. HV 0 HP1F1m H2 V rV HV ~
* * * *
2 3
~ where V is the net velocity determined by both the electroosmotic ow and the induced pressure driven ow. P is the pressure, m is the kinematic viscosity of the uid and r is the density of the liquid. Assuming the gravity effect is negligible, then, the body force term will be the electric force, which is F Ex re x. Here re is the local net charge density and ~ is the electrical eld strength. Since the local E net charge density is not zero only in the electrical double layer (EDL), the driving force for the electroosmotic ow, ~ e , exists only in EDL. The electroosmotic ow velocity Er changes sharply in a thin layer of liquid near the wall, from zero at the channel wall surface to an approximately constant value at the outer edge of the EDL. For most onchip microuidic applications, buffer solutions have an ionic concentration of the order of mM, which results in a very thin EDL. For instance, a solution with a 10 mM concentration has a double layer thickness of approximately 10 nm, which is negligible in comparison with the microchannel size (e.g. 100 mm). Therefore, for the purpose of modeling the bulk liquid ow outside the EDL, the body force term ~ e in Eq. (2) will be dropped off and the Er electroosmotic effect is considered by the slip velocity 0 boundary condition: Vslip mslip Emslip eem B on the channel wall according to Smoluchowski equation. Equation (3)
where Ci is the concentration of the i-th species, Di is the ~ diffusion coefcient of the i-th sample molecules. V epi mepi E is the electrophoretic velocity of the i-th species, where mepi is the electrophoretic mobility. Equation (4) is subject to the following initial and boundary conditions for DNA concentration of the two solutions in the two-dimensional (xy plane) system: 0 xoD1b; D1b xo2D1L; x 2D1L Ci jt!0s 0 y 0 and x ! 0 At walls
@Ci jt!0s @n @Ci jt!0s @n
Ci jt0s C0 Ci jt0s 0
It should be realized that the above three equations are coupled together by the net ow velocity. Therefore, the process of concentrating the sample molecules in a closedend micro-chamber involves the electroosmotic ow, the counter ow caused by the induced pressure and the electrophoretic motion of the charged sample molecules.
4 Numerical method
The present numerical study is conducted by using FLUENT and employing a mesh-independent structure to make sure the results are unique and will not change if any
872
other grid distribution applies. The ow eld is solved as a steady-state ow and coupled to the transient concentration eld equation via the velocity term in Eq. (3). In order to discretize the solution domain the unstructured quadratic elements with various arbitrary geometrical complexities are applied. The solution domain is broken into quadratic nite elements in the way that elements fully cover the solution domain without overlapping. Figure 3 represents different types of mesh distributions in a half of the current domain. Different types of grid size, such as shown in Figs. 3A and B are examined for ensuring that the obtained results are independent of the grid size. Figure 3c shows the nonuniform domain discretization in a way that grid is much denser in the smaller microchannel section than that in the larger reservoirs. Higher accuracy is required to achieve reasonable results in the microchannel section as the size ratio of the microchannel to the reservoir is very small; therefore more and smaller grids should be applied to the microchannel section. Bigger meshes used in the reservoirs do not affect the result accuracy and were used to reduce the computing cost. In this study, the overall ow is driven by the electroosmotic ow along the microchannel walls. In order to verify the numerical method, the ow eld of a two-side
wall-driven ow in a cavity was solved and compared with the result published by Kalita et al. [19]. When the upper and lower walls of a closed chamber (cavity) are moving in the same direction with the same speed, two symmetric circulations are generated inside the cavity. Figure 4A represents the streamline patterns of such a cavity ow. Figure 4B shows the corresponding velocity vectors. The velocity vectors near the right wall are not the same as those on the left side of the cavity; this is because of the direction of the moving walls. The moving walls drag the ow to the stationary wall on the right side of the cavity. In the mean time, the induced pressure drives the liquid owing back towards the left side of the cavity, in order to satisfy the continuity requirement. The combination of the wall-driven ow and the induced pressure-driven ow makes the ow circulate. The ow eld results of our numerical study demonstrated excellent agreement with that of Kalita et al. [19], which veries our numerical method.
5 Results and discussion

For a large number of biomedical applications, preconcentration of sample molecules in a dilute solution is
Figure 3. Examples of different grid sizes and mesh distributions that were tested in this study.
Figure 4. (A) The streamline pattern and (B) the velocity vectors at Re 5 400 of the ow eld driven by the upper and bottom moving walls of a cavity.
873
very important, such as pre-concentration of viruses in aerosol samples and DNA molecules in a sample preparation process. Concentration of sample molecules on a microuidic lab-on-a-chip device is critical for the efciency of bio-chemical reaction and the subsequent detection of the bio-molecules. Therefore, the current study aims to rst concentrate DNA molecules in a dilute sample solution, and then transport the concentrated sample molecules along the microchannel. If there are more than one type of sample molecules, electrophoresis separation will be realized while transporting the sample plug in the channel. In the rst process, one electrical eld is applied between electrodes E1 and E2, so that the negatively charged sample molecules will move to a small region close to E2; while another electrical eld between electrodes E2 and E3 is setup in a way that at the end of electrode E2 position there is no liquid ow crossing that cross-section. This is to ensure the sample molecules migrating to the vicinity of E2 will not be carried away by the ow. In the second process, after the sample molecules are concentrated in the region of E2, a different electric eld between E2 and E3 will be used to produce electrophoresis, i.e. to separate the different molecules in the concentrated sample plug while transporting the plug along the microchannel towards Reservoir B. Figure 5 represents the electric elds required for the above-mentioned operation. The continuous line indicates the non-dimensional electric eld along the system during the rst concentration process. The dashed line shows the non-dimensional electric eld along the system during the second dispensing process. Table 1 below summarizes the quantitative information used in our simulation. There are several papers that describe characteristic parameters of DNA molecules such
as the electrophoretic mobility and diffusion coefcient [2022]. In this study, the parameter values of the buffer solution and the DNA molecules are the same as that of Stellwagen and Stellwagen [22]. Figure 6 illustrates the steady-state velocity eld in the reservoirs and in the microchannel for the concentrating and dispensing processes, respectively. It can be clearly seen that, in Fig. 6A, during the concentrating process, the ow is active in Reservoir A and in the microchannel entrance region where electrode E2 is placed. However, from the end of electrode E2 to Reservoir B, there is essentially no ow and hence no convective transfer of sample molecules. This is achieved by applying the electric eld as indicated by the continuous line in Fig. 5. Figure 6B reveals the velocity eld in the reservoirs and in the microchannel while the electric eld between electrodes E2 and E3 is increased (dashed line in Fig. 5). This change produces a net ow velocity, Vnet 5 Veo1Vp, from left to right. As the boundary condition of the momentum equation, the electroosmotic ow velocity at the wall is given by Vslip 5 m E23. One can see that increasing the electric eld E23 produces a larger slip velocity at the channel walls whose direction is from left to right. Meanwhile, the induced pressure-driven velocity also changes to satisfy the conservation of mass law. At a given channel cross-section, the averaged electroosmotic ow velocity Veo is 677.97 mm s1, and the averaged pressure-driven ow velocity Vp is 442.36 mm s1 (here the negative sign means the direction of the velocity is opposite to the x direction). Thus, the net ow velocity is Vnet 5 Veo1Vp 5 235.61 mm s1 and the net ow direction is from left to right.
5.1 Sample containing one type of DNA molecules Let us rst consider the case of the sample containing only one type of DNA molecules. The free solution mobility of DNA in a commonly used buffer, Tris-acetate-EDTA (TAE), is used here. As presented in Table 1, for this study small single-standard DNA is chosen (e.g. ssA5a oligomers). The mobility and diffusion coefcient of DNA molecules are 2.912 104 m2 V s1 and 1.52 106 cm2/s, respectively [22]. The initial concentration in Reservoir A at t 5 0 (s) is set to 1 104 mg/mL. Figure 7 shows the concentration process and the movement of the concentrated sample
Table 1. Parameters used in the simulation Dimensions of the channels Length of the electrode E2 Electric eld z Potential Buffer solution DNA molecules DNAs electrophoretic mobility DNAs diffusion coefcient DNAs molar concentration a 5 250 mm L 5 10 mm D 5 5 mm b 5 500 mm 50 V/cm 50 mV 40 mM TAE (Tris-Acetate-EDTA) Small single-stranded DNA 2.912 104 cm2 V1 s1 1.52 106 cm2/s 1 104 mg/mL
Figure 5. Applied voltage across the system during the concentrating and dispensing processes.
874
Figure 6. Velocity vector distributions in the reservoirs and along the microchannel during (A) concentrating and (B) dispensing processes, respectively.
molecules as a function of time. In this gure, the dark color, which lls the Reservoir B, indicates the pure buffer solution without the sample molecules. The light color of Reservoir A indicates the solution containing the sample molecules. The medium gray color, near to Electrode E2 region, indicates the concentrated sample molecules. The change in gray scale indicates the concentration change of the sample molecules. The rst four diagrams show the concentration process: The sample molecules are accumulated near the region of electrode E2 gradually, as indicated by the increasing area of the concentration and the change in gray scale from the initial light color to the nal dark color. In the meantime, as the result of sample molecules migrating from Reservoir A to the E2 region, the sample molecules concentration in Reservoir A becomes lower. That is why the gray color in Reservoir A becomes lighter and lighter as the process progresses. The last two diagrams show the movement of the concentrated molecules after changing the applied voltage of electrode E3. In this process, the electroosmotic ow goes from left to right while the pressure-driven ow (in the middle of the channel) goes from right to left. The negatively charged DNA molecules tend to move to the positive electrode E2 due to the electrophoresis; thus the DNA molecules tend to go from right to left. At a given channel cross-section, the averaged electroosmotic ow velocity Veo is 677.97 mm s1, and the averaged pressure-driven ow velocity Vp is 442.36 mm s1 (here the negative sign means the direction of the velocity is opposite to the x direction). Thus, the net ow velocity is
Vnet 5 Veo1Vp 5 235.61 mm s1 and the net ow direction is from left to right. The electrophoretic velocity of the DNA ~ molecules can be calculated by Vep mep E 145:6 mms1 . Clearly the net ow velocity Vnet is stronger than the electrophoretic velocity Vep, and hence the DNA samples plug moves from left to right with the net ow. Furthermore, the last two plots of Fig. 7 show the concentration distribution during the dispensing process. There is a bright color strip behind the concentrated moving sample plug and a light color strip before the concentrated moving plug. These are the effect of diffusion, i.e. the last term in the concentration eld equation, Equation (3). Generally, the concentrated sample plug size decreases with the increase of diffusion coefcient, as more sample molecules will diffuse into the buffer solution. In order to determine the efciency of the concentration process, the average concentration of the sample molecules is calculated for the E2 region and for Reservoir A at different times, and the ratio of these two averaged concentrations is used as an indicator of the efciency of the concentration process. As presented in Table 2, at t 5 125 s, the concentration of the sample molecules at the E2 region is 91 times of the initial concentration in Reservoir A.
5.2 Sample containing two types of DNA molecules Figure 8 shows the concentration process and the dispensing-separation process of a sample solution containing two

t=10 (s)
875
t=15 (s)
t=30 (s)
t=20 (s)
t=55 (s)
t=40 (s)
t=85 (s)
t=75 (s)
t=125 (s)
t=115 (s)
t=168 (s)
t=153 (s)
t=242 (s)
t=211 (s)
Figure 7. An example of concentration and dispensing processes of one type of DNA molecules as a function of time at E 5 50 V/cm. The dark color, which lls the Reservoir B, indicates the pure buffer solution without the sample molecules. The light color of Reservoir A indicates the solution containing the sample molecules. The medium gray color, near to Electrode E2 region, indicates the concentrated sample molecules. Figure 8. An example of the concentration and dispensing processes of a sample containing two types of DNA molecules as a function of time at E 5 50 V/cm. The dark color, which lls the Reservoir B, indicates the pure buffer solution without the sample molecules. The light color of Reservoir A indicates the solution containing the sample molecules. The medium gray color, near to Electrode E2 region, indicates the concentrated sample molecules.
Table 2. The change of the sample concentration at electrode

E2 region
Time (s) t 5 15 t 5 30 t 5 55 T 5 85 t 5 125

The initial sample C0 5 1 104 mg/mL. concentration in
CE2 t C0 (times)
8 21 38 64 91
Reservoir A is
different DNA molecules. One type of DNA molecules is the same DNA molecules used in the last section. The electrophoretic mobility and the diffusion coefcient are the same as listed in Table 1. In order to study the separation of two types of DNA molecules, the second type of DNA molecules is considered as the same DNA molecules but with a 20% larger mobility and a 20% larger diffusion coefcient. The assumed mobility value will not affect the qualitative results of this study. For comparison, the initial concentration in Reservoir A at t 5 0(s) is set to 1 104 mg/mL, which consists of 50% of type 1 DNA molecules and 50% of type 2 DNA molecules. In other word, the type 1 DNA and the type 2 DNA have the same concentration. Similar to Fig. 7, in the concentration
process, the DNA molecules migrate from Reservoir A to the region of electrode E2 gradually, under an applied electric eld similar to what shown in Fig. 5. The concentration process is slightly faster in comparison with that shown in Fig. 7, because we deal with two types of molecules with the same total number of molecules and one type of the molecules is identical to that in the previous case. The applied electric eld is the same as that used in the previous case. While the type 1 DNA molecules are concentrated at the same rate, the type 2 DNA molecules migrate to E2 region faster because of its larger mobility. During the dispensing process, the concentrated sample plugs move toward Reservoir B. Due to the different electrophoretic mobility values, the two types of DNA molecules are gradually separated into two bands, as clearly shown in Fig. 8. Through the dispensing process, the direction of electroosmotic velocity, Veof, is from left to right, while the direction of the electrophoresis velocity, Veph, and the pressure-driven ow velocity, VP, are from right to left. Considering this fact, the total velocity (VTot 5 VeofVPVeph) of type 2 DNA (with a larger Veph) is smaller than the total velocity of type 1 DNA (with a smaller Veph). Therefore, the second concentrated region (closer to Reservoir B) represents the concentrated region of type 1 DNA molecules. Furthermore, because the type 2 DNA molecules
876
Figure 9. Non-dimensionalized concentration along the microchannel during the concentration and dispensing-separation processes.
have a larger electrophoretic velocity in the opposite direction to the electroosmotic ow, the sample band is longer than that of type 1 DNA molecules. Figure 9 shows the non-dimensionalized concentration of DNA molecules against the axial position in the microchannel at different times. It can be seen that during the concentration process, DNA molecules are gathered close to electrode E2 over a period of 115 s, as indicated by the increasing concentration prole. After the concentration process is complete when a desired concentration is achieved, the electric eld is adjusted, as illustrated in Fig. 5, and the collected sample molecules move to the downstream of the channel. During the transporting process, the electrophoresis separation of the two types of DNA molecules occurs, together with the molecular diffusion. As seen in Fig. 9, at t 5 153 s, the width of the sample plug becomes much bigger than that during the concentration process. This is the combined effect of the electrophoresis separation of the two types of DNA molecules and the diffusion. Eventually, due to the different electrophoretic mobilities, the two types of DNA molecules are separated into two individual plugs. This is shown by the two separate dashed curves (i.e. the concentration proles) at t 5 211 s. The wider spans at the bottom of these two dashed curves again indicate the diffusion effect.
Figure 10. Effect of electric eld on the required time for concentrating DNA molecules to 91 times of the initial concentration at electrode E2 region.
5.3 Effects of other parameters The applied electric eld has at least two effects on the concentration process. It drives the negatively charged sample molecules to move to the positive electrode, E2. It also creates the ow eld as shown in Fig. 6A, which affects the migration of the sample molecules to the E2 region and the keeping of the sample molecules in the E2 region. The effect of the electrical eld on the speed of the concentration process is plotted in Fig. 10 using the parameters listed in Table 1. In all these cases we compare the time required to reach the same nal concentration at the E2 region, i.e. 91 times of the original concentration in Reservoir A. As it can be seen, increasing the electric led strength decreases the time needed for concentrating the sample. However, this is
Figure 11. The size effect of electrode E2 on the required time for concentrating DNA molecules to 91 times of the initial concentration at electrode E2 region under the electric eld of E 5 50 V/cm.
not a linear relationship: Doubling the applied electric eld does not necessarily reduce the required time by half when the electric eld is above 100 V/cm. The size of electrode E2 directly affects the electric eld near E2 and hence the concentration process. Figure 11 represents the required time for the concentration process
877
Figure 12. Effect of the aspect ratio on the required time for concentrating DNA molecules to 91 times of the initial concentration at electrode E2 region under the electric eld of E 5 50 V/cm; (A) changing the diameter of reservoir A with a xed microchannel width; (B) changing the microchannel width with a xed diameter of the reservoir A.
under a constant applied electric led strength and a constant initial sample concentration. As seen clearly from this gure, the dependence of the concentration time is not a linear function of the electrode size. When the electrode size is b, the concentration process is complete in approximately 115 s. Reducing the electrode size by half, b/2, slows down the concentration process almost two times, to about 210 s in order to reach the same concentration. Doubling the electrode size to 2b does not reduce the concentration time by half. Figure 12 represents the effect of the ratio of the diameter of Reservoir A to the microchannel width on the concentration process. Again we consider the required time for concentrating the DNA molecules to 91 times of the initial concentration at E 5 50 V/cm. In a larger Reservoir A, DNA molecules have to travel a longer distance to reach electrode E2 region, and hence the required concentration time will increase. Figure 12A shows that doubling the reservoir diameter leads to an increase of the required concentration time by about three times. Figure 12B reveals the dependence of the concentration time on the microchannel width, while keeping the reservoirs diameter constant. Clearly, increasing the size of the microchannel results faster concentrating process. This is because more negatively charged DNA molecules have a chance to move to the region close to the positive electrode E2.
with different mobilities can be separated while being transported to downstream along the microchannel. Increasing the applied electric eld and the size of electrode E2 will shorten the concentration process. Increasing size of Reservoir A, while keeping other parameters constant, will increase the concentration time. The proposed method does not require any nanochannel structure and complicated AC eld and may lead to develop a simple and practical microuidic chip for sample concentration and separation in dilute solutions. The authors have declared no conict of interest.
7 References
[1] Gao, Y., Hu, G., Lin, F. Y., Sherman, P. M., Li, D., Biomed. Microdevices 2005, 7, 301312. [2] Murray, K., Wang, T. H., Rebello, K., Crookston, J., Miragliotta, J., IEEE/NLM Life Science Systems and Applications Workshop 2006, 12. [3] Srivastava, A., Metaxas, A. C., So, P., Matsudaira, P., Ehrlich, D., Georghiou, G. E., Electrophoresis 2005, 26, 11301143. [4] Plecis, A., Nanteuil, C., Haghiri-Gosnet, A. M., Chen, Y., Anal. Chem. 2008, 80, 95429550. [5] Cabrera, C. R., Yager, P., Electrophoresis 2001, 22, 355362.
6 Concluding remarks
A simple electrokinetic method for concentrating DNA molecules from a dilute solution in a straight microchannel with two closed ends is proposed. The sample concentration process and the subsequent sample dispensing and separation process can be controlled by simple DC eld via three electrodes. The numerical simulations performed in this study show that 91 times concentration increase can be achieved in about 115 s. The concentrated sample molecules
[6] Huang, T., Pawliszyn, J., Electrophoresis 2002, 23, 35043510. [7] Li, Y., DeVoe, D. L., Lee, C. S., Electrophoresis 2003, 24, 193199. [8] Cui, H., Horiuchi, K., Dutta, P., Ivory, C. F., Anal. Chem. 2005, 77, 13031309. [9] Wainright, A., Stephen, J. W., Ciambrone, G., Xue, Q. F., Wei, J., Harris, D., J. Chromatogr. A 2002, 979, 6980. [10] Jung, B., Bharadwaj, R., Santiago, J. G., Electrophoresis 2003, 24, 34763483.
878
[11] Beard, N. J., Zhang, C. X., deMello, A. J., Electrophoresis 2003, 24, 732739. [12] Shaikh, F. A., Ugaz, V. M., Proc. Natl. Acad. Sci. USA 2006, 103, 48254830. [13] Lettieri, G. L., Ceriotti, L., Rooij, N. F., Verpoorte, E., OnChip DNA trapping and pre-concentration employing recirculating ow devices, 7th lnternational Conference on Miniaturized Chemical and Blochemlcal Analysts Systems, October 59 (2003) Squaw Valley, Callfornla USA. [14] Chen, H., Wu, Y. H., Song, D. Y., Zhang, W., Dong, X. Y., Li, P. W., Lu, C. M., Microchem. J. 2007, 86, 1722. [15] Svarnas, P., Plecis, A., Nanteuil, C., Duong, D., David, C., Muller, M., Chen, Y., Eur. Phys. J. Appl. Phys. 2008, 44, 245253. [16] Huang, K. D., Yang, R. J., Electrophoresis 2008, 29, 48624870.
[17] Du, J. R., Juang, Y. J., Wu, J. T., Wei, H. H., Biomicrouidics 2008, 2, 044103_3044103_10. [18] Patankar, N. A., Hu, H. H., Anal. Chem. 1998, 70, 18701881. [19] Kalita, J. C., Kumar, N., Dass, A. K., HOC computation of two-sided lid-driven cavity ow, Proceedings of the Second International Conference on Computational Mechanics and Simulation, IIT Guwahati, India. December, 2006, 1, 941948. [20] Stellwagen, N. C., Gel, C., Righetti, P. G., Biopolymers 1998, 42, 687703. [21] Brahmasandra, S. N., Burke, D. T., Mastrangelo, C. H., Burns, M. A., Electrophoresis 2001, 22, 10461062. [22] Stellwagen, E., Stellwagen, N. C., Electrophoresis, 2002, 23, 27942803.

Numerical Studies of Electrokinetic Control of DNA Concentration in A Closed-End Microchannel

Enviado por

Dados do documento

Título original

Direitos autorais

Formatos disponíveis

Compartilhar este documento

Compartilhar ou incorporar documento

Opções de compartilhamento

Você considera este documento útil?

Este conteúdo é inapropriado?

Direitos autorais:

Formatos disponíveis

Numerical Studies of Electrokinetic Control of DNA Concentration in A Closed-End Microchannel

Enviado por

Direitos autorais:

Formatos disponíveis

868 Yasaman Daghighi Dongqing Li

Electrophoresis 2010, 31, 868878