The electric field dependence of DNA mobilities in agarose gels: a reinvestigation

The electric field dependence of the electrophoretic mobility of linear DNA fragments in agarose gels was reinvestigated in order to correct the observed mobilities for the different temperatures actually present in the gel during electrophoresis in different electric field gradients. When corrected to a common temperature, the electrophoretic mobilities of DNA fragments less than or equal to 1 kilobase pairs (kbp) in size were independent of electric field strength at all field strengths from 0.6 to 4.6 V/cm if the gels contained less than or equal to 1.4% agarose. The mobilities of larger DNA fragments increased approximately linearly with electric field strength. If the agarose concentration was higher than 2%, the mobilities of all DNA fragments increased with increasing electric field strength. The electric field dependence of the mobility was larger in gels cast and run in Tris-borate buffer (TBE) than in gels cast and run in Tris-acetate buffer (TAE), and was more pronounced in gels without ethidium bromide incorporated in the matrix. Ferguson plots were constructed for the various DNA fragments, both with and without extrapolating the temperature-corrected mobilities to zero electric field strength. Linear Ferguson plots were obtained for all fragments less than or equal to 12 kbp in size in agarose gels less than or equal to 1.4% in concentration if the mobilities were first extrapolated to zero electric field strength. Concave upward curvature of the Ferguson plots was observed for DNA fragments greater than or equal to 2 kbp in size at finite electric field strengths. Convex downward curvature of the Ferguson plots was observed for DNA fragments greater than or equal to 1 kbp in size in agarose gels greater than or equal to 2% in concentration. The mobilities of the various DNA fragments, extrapolated to zero agarose concentration and zero electric field strength, decreased with increasing DNA molecular weight; extrapolating to zero molecular weight gave an "intrinsic" DNA mobility of 2.7 x 10(-4) cm2/Vs at 20 degrees C. The pore sizes of LE agarose gels cast and run in TAE and TBE buffers were estimated from the mobility of the DNA fragments.(ABSTRACT TRUNCATED AT 400 WORDS)     

一种直接测定微流控芯片电渗流速度的新方法

随着微芯片技术的成熟,越来越迫切地需要有一个准确而简洁的电渗流速度的检测方法。根据荧光物质罗丹明123（Rh123）在不同pH缓冲溶液中迁移时间的变化,推导出Rh123在pH 9和10条件下分别有中性分子存在,而中性分子的移动速度等于电渗流速度,因此建立了直接以Rh123中性分子为标记物测定电渗流速度的方法。通过直接检测Rh123中性分子的迁移时间,计算得出所用玻璃微流控芯片在pH 9.3和pH 10.1的电渗流速度为3.9×10-4 cm2/(s·V)和4.1×10-4 cm2/(s·V),与经典方法对照无明显差异。     

The free solution mobility of DNA in Tris-acetate-EDTA buffers of different concentrations,with and without added NaCl

The free solution mobility of a high-molecular-weight DNA, linear pUC19, and a 20-bp oligomer called dsA5 have been studied as a function of Tris-acetate-EDTA (TAE) buffer concentration, with and without added NaCl. The two DNAs migrate as separate peaks during capillary electrophoresis, because the mobility of linear pUC19 is higher than that of the 20-bp oligomer. In TAE buffers ranging from 10-400 mM in concentration, the migration times and peak areas of the two DNAs are independent of whether they are electrophoresed separately or in mixtures, indicating that DNA-DNA and DNA-buffer interactions are absent in these solutions. The migration times of the two DNAs vary and the peak areas are not additive when the TAE buffer concentration is reduced to 5 mM or below, indicating that DNA-DNA and DNA-buffer interactions are occurring at very low TAE buffer concentrations. The mobilities of linear pUC19 and dsA5 decrease slowly with increasing conductivity or ionic strength when the conductivity is increased by increasing the TAE buffer concentration. When the Tris buffer concentration is held constant and the conductivity is increased by adding various concentrations of NaCl to the solution, the mobilities of linear pUC19 and dsA5 first increase slightly, then become independent of solution conductivity (or ionic strength), and finally decrease when the NaCl concentration is increased above approximately 50 mM. The mobility variations observed in the various TAE and TAE-NaCl solutions are described qualitatively by Manning's theory, although quantitative agreement is not achieved. The free solution mobilities of single-stranded pUC19 and two 20-base oligonucleotides have also been measured. The free solution mobility of single-stranded pUC19 is approximately 15% lower than that of native pUC19, in agreement with other results in the literature. Somewhat surprisingly, the mobilities of the single- and double-stranded 20-mers are equal to each other in TAE buffers with and without added NaCl.     

Characterization of SU-8 for electrokinetic microfluidic applications

The characterization of SU-8 microchannels for electrokinetic microfluidic applications is reported. The electroosmotic (EO) mobility in SU-8 microchannels was determined with respect to pH and ionic strength by the current monitoring method. Extensive electroosmotic flow (EOF), equal to that for glass microchannels, was observed at pH > or =4. The highest EO mobility was detected at pH > or =7 and was of the order of 5.8 x 10(-4) cm(2) V(-1) s(-1) in 10 mM phosphate buffer. At pH < or =3 the electroosmotic flow was shown to reverse towards the anode and to reach a magnitude of 1.8 x 10(-4) cm(2) V(-1) s(-1) in 10 mM phosphate buffer (pH 2). Also the zeta-potential on the SU-8 surface was determined, employing lithographically defined SU-8 microparticles for which a similar pH dependence was observed. SU-8 microchannels were shown to perform repeateably from day to day and no aging effects were observed in long-term use.     

Continuous microfluidic DNA and protein trapping and concentration by balancing transverse electrokinetic forces

Sample pre-concentration can be a critical element to improve sensitivity of integrated microchip assays. In this work a converging Y-inlet microfluidic channel with integrated coplanar electrodes was used to investigate transverse DNA and protein migration under uniform direct current (DC) electric fields to assess the ability to concentrate a sample prior to other enzymatic modifications or capillary electrophoretic separations. Employing a pressure-driven flow to perfuse the microchannel, negatively charged samples diluted in low and high ionic strength buffers were co-infused with a receiving buffer of the same ionic strength into a main daughter channel. Experimental results demonstrated that, depending of the buffer selection, different DNA migration and accumulation dynamics were seen. Charged analytes could traverse the channel width and accumulate at the positive bias electrode in a low electroosmotic mobility, high electrophoretic mobility, high ionic strength buffer or migrated towards an equilibrium position within the channel in a high electroosmotic mobility, high electrophoretic mobility, low ionic strength buffer. The various migration behaviours are the result of a balance between the electrophoretic force and a drag force induced by a recirculating electroosmotic flow generated across the channel width due to the bounding walls. Under continuous flow conditions, DNA samples were concentrated several-fold by balancing these transverse electrokinetic forces. The electrokinetic trapping technique presented here is a simple technique which could be expanded to concentrate or separate other analytes as a preconditioning step for downstream processes.     

Cationic polymer coatings for design of electroosmotic flow and control of DNA adsorption

A difficulty with the design and operation of an electrokinetically operated DNA hybridization microfluidic chip is the opposite direction of the electroosmotic flow and electrophoretic mobility of the oligonucleotides. This makes it difficult to simultaneously deliver targets and an appropriate hybridization buffer simultaneously to the probe sites. In this work we investigate the possibility of coating the inner walls of the microfluidic system with hexadimentrine bromide (polybrene, PB) and other cationic polymers in order to reverse the direction of electroosmotic flow so that it acts in the same direction as the electrophoretic transport of the oligonucleotides. The results indicated that the electroosmotic flow (EOF) in channels that were coated with the polymer could be reversed in 1× TBE buffer or 1× SSC buffer. Under these conditions, the DNA and EOF move in the same direction, and the flow can be used to deliver DNA to an area for selective hybridization within the channel. The effects of coating the surface of a nucleic acid microarray with polybrene were also studied to assess non-selective adsorption and stability. The polybrene coating significantly reduced the extent of non-selective adsorption of oligonucleotides in comparison to adsorption onto a glass surface, and the coating did not alter the extent of hybridization. The results suggest that use of the coating makes it possible to achieve semi-quantitative manipulation of nucleic acid oligomers for delivery to an integrated microarray or biosensor.     

Measurement of electroosmotic flow in plastic imprinted microfluid devices and the effect of protein adsorption on flow rate.

Several commercially available plastic materials were used as substrates in the fabrication of microfluid channels for biochemical analysis. Protocols for fabrication using the wire-imprinting method are reported for polystyrene, polymethylmethacrylate and a copolyester material. Channel sealing was accomplished by low-temperature bonding of a substrate of similar material; therefore, each channel was composed of a single material on all sides. The electroosmotic flow in 25-microm imprinted channels was evaluated for each substrate material. The copolyester material exhibited the highest electroosmotic flow mobility of 4.3 x 10(-4) cm2 V(-1) s(-1) which is similar to that previously reported for fused-silica capillaries. Polystyrene exhibited the lowest electroosmotic flow mobility of 1.8 x 10(-4) cm2 V(-1) s(-1). Plots of linear velocity versus applied electric field strength were linear from 100 V cm(-1) to 500 V cm(-1) indicating that heat dissipation is effective for all substrates in this range. Electroosmotic flow was reevaluated in the plastic channels following incubation in antibody solution to access the non-specific binding characteristics of a common biochemical reagent onto the substrate materials. All materials tested showed a high degree of non-specific adsorption of IgG as indicated by a decrease in the electroosmotic flow mobility in post-incubation testing.     

Versatile method for electroosmotic flow measurements in microchip electrophoresis

A novel versatile method for the determination of low or high electroosmotic mobility values in microdevices of variable microchannel design is presented. The electroosmotic flow (EOF) calculation is based on the difference between the apparent and effective mobilities of a reference compound. The proposed method uses microchip frontal electrophoresis for the determination of these mobilities. This requires simple monochannel microchip design and demonstrates versatile and time-saving procedure when compared to conventional current monitoring method when measuring low EOF. It has been applied successfully to the characterization of different coating procedure in glass and poly(dimethylsiloxane) microchips.     

Success and failure with phthalate buffers in capillary zone electrophoresis

Phthalate buffers are currently used in capillary electrophoresis as robust electrolyte systems for indirect detection. This contribution demonstrates that these buffers show regularly not only successful regions of mobilities of analytes (sample window) but also regions of failure where the migration of analytes is strongly deteriorated due to the presence of a system zone. System zones in phthalate buffers may be easily detected by UV detection and manifest themselves as peaks or dips. Peak shape diagrams are advantageously used for the prediction of the migration behavior of system zones in phthalate background electrolyte (BGE) systems at various pH. It is shown that the mobility of the system zone varies strongly with pH, is practically zero at pH values below 4 and above 7, and shows a maximum at pH 5. Thus, the system peak may coincide either with the peaks of various analytes or with the electroosmotic flow (EOF) peak. Experiments are given showing the effects of such coincidences as, e.g., zigzag detection patterns, double EOF peaks, and/or unusually broad peaks/dips. The message of this contribution is to show how to understand the electrophoretic properties of phthalate BGEs that, regardless of possible failure regions, may be successfully used in the analytical practice of capillary zone electrophoresis (CZE).     

Indirect photomeric detection of anions in capillary electrophoresis using dyes as probes and electrolytes buffered with an isoelectric ampholyte

The use of highly absorbing anionic dyes as probes and isoelectric ampholytes as buffers in background electrolytes (BGEs) combined with the use of a light emitting diode (LED) as a light source has been studied for ultrasensitive indirect photometric detection in capillary electrophoresis (CE). Potential dyes and buffers were evaluated based on characteristics relevant to indirect photometric detection principles, such as the electrophoretic mobility of the probe dye, its solubility and adsorption behaviour, and the isoelectric point and buffering capacity of the ampholytic buffer. Two dyes, tartrazine and naphthol yellow S, and histidine as the ampholytic buffer, were selected for detailed investigation. Purification of the probes was vital to avoid anionic impurities interfering with the detection. For the electrolytes containing a purified probe (0.5 mM) and histidine as the isoelectric buffer (p/ 7.7), hydroxypropylmethyl cellulose (approximately 0.05%) was effective in suppression of the electroosmotic flow (EOF). Analytical method performance characteristics were determined. For both probes, experimentally determined mobilities were generally close to literature values, excellent peak shapes and separation efficiencies of up to 298 000 theoretical plates were obtained, and detection limits were generally at the sub-microM level. For the naphthol yellow S-histidine BGE, linearity and reproducibility were also evaluated, with excellent linearity being observed over a range of 5-500 microM, and reproducibility (relative standard deviation, RSD) less than 1% for migration times and 2-8% for normalised peak areas. The approach developed was applied successfully to several real samples including tap water, mineral waters, and beer.     

Suppression of electroosmotic flow and its application to determination of electrophoretic mobilities in a poly(vinylpyrrolidone)-coated capillary

A hydrophilic polymer, poly(vinylpyrrolidone) (PVP), was employed for suppressing the electroosmotic flow (EOF). A capillary was filled with aqueous PVP solution for coating the capillary wall with PVP; the PVP solution was then replaced by a migration buffer solution containing no PVP. Three types of PVP with different molecular weights were examined. The EOF was suppressed more effectively as the molecular weight of PVP increased. The EOF in the coated capillary was approximately 10-fold smaller than that of a bare capillary and was constant in the pH range of 6-8. The suppressed EOF was stable even when no PVP was added to the migration buffer. However, the EOF increased significantly when sodium dodecyl sulfate was added into the migration buffer. The method was applied for determining the electrophoretic mobilities of inorganic anions that have negative electrophoretic mobilities larger than the electroosmotic mobility of the bare capillary. A novel method for determining the electrophoretic mobilities was proposed based on the linear relationship between electric current and electrophoretic mobility. The electrophoretic mobility was proportional to the electric current. Therefore, the intercept of the regression equation represents the electrophoretic mobility at room temperature. The electrophoretic mobilities were in good agreement with the absolute electrophoretic mobilities.     

Photoluminescence Stability of Colloidal CdTe Quantum Dots in Various Buffer Solutions

Mercaptoacetic acid-capped CdTe quantum dots (QDs) are potential luminescent markers for biological analysis. The photoluminescence (PL) stability of the QDs in buffer solutions determines their practicability as markers in electrophoresis. The stability of the QDs was thus investigated in electrophoresis buffers including tris–borate–ethylenediaminetetraacetic acid (TBE) and tris–acetate–ethylenediaminetetraacetic acid (TAE). The QDs were completely unstable in high-concentrated buffers (≥0.1×). In the case of low concentrations (≤0.07× for TAE, ≤0.035× for TBE), the PL intensity of the QDs in two kinds of buffers decreased with increasing buffer concentrations. A red-shifted PL peak wavelength and PL intensity fluctuation were observed after dispersing the QDs in diluted TAE buffer solutions with concentrations of ≤0.07× for long time. According to the Stern–Volmer plots of PL degradation, the factors leading to the degradation were complicated, which was attributed to the actions of the components including tris, borate or acetic acid, and ethylenediaminetetraacetic acid as well as their mutual effects.     

Capillary electrochromatography using a fluoropolymer as the chromatographic support material

Fused-silica capillary columns were packed with ethylene chlorotrifluoroethylene (ECTFE) particles for use in capillary electrochromatography (CEC). Electroosmotic flow (EOF) was generated in these columns using acetonitrile-water mixtures as the mobile phase. Electroosmotic mobilities of 1.6 x 10(-4) cm2 V(-1) s(-1) (linear velocities of 1 mm s(-1)) were observed using a mobile phase without an electrolyte present. The EOF in the ECTFE-packed columns is enhanced when using trifluoroacetic acid (TFA) as a mobile phase additive; electroosmotic mobilities of 3.65 x 10(-4) cm2 (V-1) s(-1) (linear velocity of 2.5 mm s(-1)) were observed. This enhancement of EOF is attributed to dynamic coating of the ECTFE particles by TFA. Other electrolytes (i.e., Tris/Tris-HCl buffer and H3PO4) in the mobile phase did not have such an enhancement of EOF. However, a slight enhancement of EOF is observed, for example, if small quantities of TFA are added to the mobile phase containing Tris buffer. The potential of ECTFE for CEC is demonstrated by separating a mixture of amino acids.     

Determination of electroosmotic flow mobility with a pressure-mediated dual-ion technique for capillary electrophoresis with conductivity detection using organic solvents

A method is described for the indirect determination of the mobility of the electroosmotic flow (EOF), which can be carried out within a few minutes even for very low mobilities. It is independent of the direction of the EOF. It is based on the comparison of the measured mobilities of two oppositely charged reference ions (tetraphenylphosphonium and tetraphenylborate) with given mobilities in different organic solvents (methanol, acetonitrile, N,N-dimethylformamide, N,N-dimethylacetamide, propylene carbonate) at ionic strengths between 5 and 50 mM. The method is based on the sequential movement of the reference ions in a three-step process: first by a laminar flow to a certain position in the separation capillary, followed by electromigration due to application of voltage, and pressurised migration towards the detector. In this way the total mobilities of the reference ions can be determined from their residence times, and the difference to their known actual mobilities gives the mobility of the EOF. The method avoids misinterpretations caused by system- and eigen-peaks, which often bias the results especially when a conductivity detector is used. The method is suitable for all solvents, and is an advantage especially for organic and mixed aqueous–organic background electrolytes with high UV absorbance.     

Study of the selectivity of inorganic anions in hydro-organic solvents using indirect capillary electrophoresis

In capillary electrophoresis (CE) analysis of small inorganic anions, the ability to control the electroosmotic flow (EOF) and the ability to alter the electrophoretic mobility of the ions are essential to improve resolution and separation speed. In this work, a CE method for separation of small inorganic anions using indirect detection in mixed methanol/water buffers is presented. The suitability of different UV absorbing probes commonly used for indirect detection including chromate, iodide, phthalate, benzoate, trimellitate, and pyromellitate, in mixed methanol/water buffers is examined. The effect of the electrolyte buffer system, including the pH, buffer concentration and the organic solvent on the electrophoretic mobility of the probes and analytes are also investigated. The EOF was reversed using cationic surfactant, cetyltrimethylammonium bromide (CTAB) so ions were separated under co-EOF mode. The organic solvent alters the electrophoretic mobility of the probes and the analytes differently and hence choice of the appropriate probe is essential to achieve high degree of detection sensitivity. Separations of six anions in less than 2.5 min were accomplished in buffers containing up to 30% MeOH. Adjustment of the methanol content helps to improve the selectivity and resolution of inorganic anions. Limit of detection, reproducibility and application of the method for quantification of anions in water samples will also be discussed.     

DNA microelectrophoresis using double focus fluorescence correlation spectroscopy

Double focus fluorescence correlation spectroscopy (dfFCS) was used to determine electrophoretic mobilities of short double-stranded DNA (dsDNA)-fragments (75 base pairs (bp) -1019 bp) in microfluidic channels. The electrokinetic flow profile across a microchannel was measured with 1 microm spatial resolution and separated in electroosmotic and electrophoretic contributions. Experiments show that the free solution mobility is independent of DNA length. The diffusion constant is additionally determined by FCS and follows a length dependent rod-diffusion model. We interpret the electrophoretic mobilities using a modified Nernst Einstein relation, which additionally takes Manning condensation and counterion induced hydrodynamic retardation forces into account. In 3% w/v polyethylene oxide (PEO)-network (M(r) 3 .10(5) Dalton) the electrophoretic velocities become size-dependent with a power-law exponent be-tween 0.28 and 0.31. Mixtures of dsDNA-fragments exhibit distinguishable peaks in the dfFCS cross-correlation function. The potential of dfFCS for realtime micro-analysis in terms of speed and spatial resolution is discussed.     

Hydrodynamic suppression of the electroosmotic flow in capillary electrophoresis with indirect spectrophotometric detection

A version of capillary electrophoresis with indirect spectrophotometric detection and the hydrodynamic suppression of electroosmotic flow is studied. It is shown that, to improve the reliability of ion identification, one should calculate electrophoretic mobilities of ions or migration times corrected with regard to the electroosmotic flow rate. Correlations between electrophoretic peak areas of ions and their electrophoretic mobilities are derived. In the studied version of capillary electrophoresis, the accuracy of measuring anion concentrations can be improved using the internal standard method.     

A split microchannel design and analytical model to compensate for electroosmotic instabilities in micro-separations

Organic polymers offer many advantages as materials for the construction of microfluidic devices but suffer frequently from the limitation that the electrodynamic flow they support can exhibit considerable instability. This article describes a split-channel microfluidic device that can be used to compensate for changes in electroosmotic flow. The design of the separation system divides an analyte plug after injection between two separation channels of differing length. The two channels are later recombined for single point detection, eliminating the need for a scanning optical detection system. The utility of this simple design lies in the fact that the migration time of any analyte can be referenced to its twin in the parallel separation channel. This eliminates the need for a separate electroosmotic marker and allows mobilities measured in multiple devices to be compared quantitatively. Using a model adopted from the literature, the data from the split channel system can be used to precisely account for the drift that characterizes electrophoretic separations made in a polymer chip. The relative standard deviations of the analyte mobilities measured for replicate runs on multiple devices were reduced from values as high as 20% to ca. 1% RSD. This internal standardization procedure also appears to address other sources of drift in the electroosmotic flow (EOF) supported by the polymer microchannel, eliminating the need for careful monitoring of either the temperature or reservoir pH between separation runs.     

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.     

A method for determining electrophoretic and electroosmotic mobilities using AC and DC electric field particle displacements

We have developed a method for measuring the electrophoretic mobility of submicrometer, fluorescently labeled particles and the electroosmotic mobility of a microchannel. We derive explicit expressions for the unknown electrophoretic and the electroosmotic mobilities as a function of particle displacements resulting from alternating current (AC) and direct current (DC) applied electric fields. Images of particle displacements are captured using an epifluorescent microscope and a CCD camera. A custom image-processing code was developed to determine image streak lengths associated with AC measurements, and a custom particle tracking velocimetry (PTV) code was devised to determine DC particle displacements. Statistical analysis was applied to relate mobility estimates to measured particle displacement distributions.