On-chip pressure injection for integration of infrared-mediated DNA amplification with electrophoretic separation

Poly(dimethylsiloxane) (PDMS) membrane valves were utilized for diaphragm pumping on a PDMS-glass hybrid microdevice in order to couple infrared-mediated DNA amplification with electrophoretic separation of the products in a single device. Specific amplification products created during non-contact, infrared (IR) mediated polymerase chain reaction (PCR) were injected via chip-based diaphragm pumping into an electrophoretic separation channel. Channel dimensions were designed for injection plug shaping via preferential flow paths, which aided in minimizing the plug widths. Unbiased injection of sample could be achieved in as little as 190 ms, decreasing the time required with electrokinetic injection by two orders of magnitude. Additionally, sample stacking was promoted using laminar or biased-laminar loading to co-inject either water or low ionic strength DNA marker solution along with the PCR-amplified sample. Complete baseline resolution (Res = 2.11) of the 80- and 102-bp fragments of pUC-18 DNA marker solution was achieved, with partially resolved 257- and 267-bp fragments (Res = 0.56), in a separation channel having an effective length of only 3.0 cm. This resolution was deemed adequate for many PCR amplicon separations, with the added advantage of short separation time-typically complete in <120 s. Decreasing the amount of glass surrounding the PCR chamber reduced the DNA amplification time, yielding a further enhancement in analysis speed, with heating and cooling rates as high as 13.4 and -6.4 degrees C s(-1), respectively. With the time requirements greatly reduced for each step, it was possible to seamlessly couple IR-mediated amplification, sample injection, and separation/detection of a 278-bp fragment from the invA gene of <1000 starting copies of Salmonella typhimurium DNA in approximately 12 min on a single device, representing the fastest PCR-ME integration achieved to date.     

An automated capillary electrophoresis system for high-speed separation of DNA fragments based on a short capillary

A high-speed DNA fragment separation system was developed based on a short capillary and a slotted-vial array automated sample introduction system. The injection process of DNA sample in a short capillary was investigated systematically with three injection techniques including constant-field-strength, low-field-strength and translational spontaneous injections. Under the optimized conditions, picoliter-scale sample plugs (corresponding to ca. 20-μm plug length) were obtained, which ensure the high-speed and high-efficiency separation for DNA fragments with a short effective separation length. Other separation conditions including the sieving matrix concentration, separation field strength and effective separation length were also optimized. The present system was applied in the separation of ΦX174-Hae III digest DNA marker. With an effective separation length of 2.5 cm, the separation could be achieved in <100 s with plate heights ranging from 0.21 to 0.74 μm (corresponding to plate numbers from 4.86 × 10(6) to 1.36 × 10(6)/m). The repeatabilities for the migration time of the eleven fragments were between 0.4 and 1.1% RSD (n=8). By using the automated continuous injection method, the separation for four different DNA samples could be achieved within 250 s. The present system was further applied in the fast sizing of real DNA samples of PCR products.     

Calibration of migration times of variable salinity samples with internal standards in capillary electrophoresis

A practical approach is presented for identifying the analyte peaks stacked by transient ITP (TITP) in samples of uncontrolled salinity. For TITP with chloride ions acting as the leading electrolyte, the effect of matrix chloride of an unknown concentration was calibrated using multiple internal standards to predict the migration times of weakly acidic anionic analytes behaving as strong electrolytes to an accuracy of over 99.9%. The calibration equations for the migration time of an analyte are given as a function of the migration times of internal standards using the mobilities of the relevant ions as parameters. The effects of matrix chloride and various separation conditions such as the temperature, plug length, ionic strength, and pH of the BGE were completely eliminated from the calibration equations. In addition, the actual mobilities, determined for a standard saline sample under the working conditions, were used, and thus, there was no need to conduct supplementary experiments to determine the absolute mobilities at infinite dilution. The internal standards were dyes, which were easily identified in an auxiliary channel monitoring the absorbance at a longer wavelength. For five standard saline matrices containing 100-300 mM NaCl at intervals of 50 mM, the mean absolute error (MAE) in migration times calibrated with two internal standards was 0.4 s (n=5x13). For an electropherogram of a real standard reference urine sample, peaks of spiked analytes were identified with an MAE of 0.9 s (n=13) without conductivity normalizing or desalting of the sample.     

Impact of reservoir potentials on the analyte behavior in microchip electrophoresis: computer simulation and experimental validation for DNA fragments

Fundamental understanding of the impact of reservoir potentials on the analyte behavior on the microfluidic chips is an important issue in microchip electrophoresis (MCE) for suitable injection and separation of analytes, since the applied potentials may significantly affect the shape of sample plug, sample leakage from the injection channel to the separation channel, injected sample amount, and separation efficiency. This study addressed this issue for the case of a conventional cross-geometry microchip with four reservoirs using computer simulations, the results of which were verified by the analysis of DNA fragments. For the microchip with a definite structure and migration distance, the injected sample amount was shown to be the vital parameter for improving the limit of detection and resolution. During injection, the shape of the sample plug could be adjusted by varying the reservoir potentials. It was demonstrated that a "magnified injection" (applying high voltage on the three reservoirs to the sample reservoir) is useful to enhance the detection sensitivity depending on the analyte composition, although such injection was previously avoided because of introducing too large amounts of the analyte in comparison with two established modes, floating and pinched injection. Optimal magnified injection was proved to improve the sensitivity for about 4 times over that of pinched injection for the analysis of DNA step ladders using microchip gel electrophoresis (MCGE). Sample leakage of DNA fragments could be suppressed by applying a high positive voltage on injection channel during separation, but the voltage degraded the injected amount and resolution.     

Highly sensitive chemiluminescence detection of copper(II) in capillary electrophoresis with field-amplified sample injection

Field-amplified sample injection of copper(II) was investigated using capillary electrophoresis with chemiluminescence detection. The sensitivity of copper(II) has been improved markedly by the field-amplified sample injection technique and the detection limit reaches 2 x 10(-11) M. By injection of a short plug of water before sample introduction, the sensitivity can be further improved 5-fold and the detection limit reaches 4 x 10(-12) M. The relative standard deviations (n = 6) of the migration time and the peak height are 0.61% and 4.7% at 1.0 x 10(-9) M Cu(II), respectively. Parameters affecting the field-amplified sample injection, such as separation voltage and concentration of electrophoretic buffer, have been investigated.     

Pressure pinched injection of nanolitre volumes in planar micro-analytical devices

A new method for injecting and driving fluids by means of a multi-port injection valve and syringe pumps in a micro-channel network is described. A structure composed of two micro-channels arranged as a cross is connected with capillary tubes to an external multi-port injection valve. The fluid flows are driven by pressure and the multi-port valve controls the direction of the flow within the different sections of the structure. The first position of the multi-port valve allows the preparation of the loading of the sample, which is pinched in the cross section of the two micro-channels. The second position allows the precise injection of nL volumes. No dead volume exists between injection and separation modes. The system can be used to prepare a sample plug by pressure in order to perform chromatography with a broad range of buffered or non-buffered solutions. Thanks to the insensitivity to the ionic strength of the sample, this injection method is useful for the injection of complex biological samples in microchip analysis. In order to demonstrate the feasibility of the method, different solutions of ionic or fluorescent molecules were injected and detected in a photoablated planar polymer device.     

Optimization of injection technique in capillary ion electrophoresis for the determination of trace level anions in environmental samples

Capillary ion electrophoresis (Waters' trade name: Capillary Ion Analysis) offers several advantages compared to ion chromatography for the analysis of ionic solutes, primarily simplicity, matrix independence, and a different separation selectivity. The use of electromigration sample introduction leads to on-capillary enrichment of ionic analytes at the sample—buffer interface, permitting the determination of low ng/ml levels of anions in environmental samples of moderate ionic strength. This injection method allows improved sensitivity compared to hydrostatic injection; and is significantly more rapid than precolumn concentration ion chromatography. The analyte enrichment rate, hence peak response, is strongly dependent upon ionic strength and appropriate measures, such as standard addition or internal standard techniques, must be used to account for differences in standard and sample conductance.     

Effects of injector geometry and sample matrix on injection and sample loading in integrated capillary electrophoresis devices

The double-T injector design employed in many microchip capillary electrophoresis devices allows for the formation of very small (50-500 pL) sample plugs for subsequent analysis on-chip. In this study, we show that sample plugs formed at the channel junction can be geometrically defined. The channel width and injector symmetry prove to be of great importance to good performance. A unique pushback of solvent into the side channels can be induced when the side channels have a very low resistance to flow, and this helps to better define the injected sample plug. Samples and running buffers of differing ionic strength (e.g., 10 mM KCl buffer and 20 mM KCl sample) can yield widely variable results in terms of plug shape and amount injected (variations of 1.5 to 10x). Applying bias voltages to all the intersecting channels aids in controlling the plug shape. However, when the ionic strengths of buffer and sample are not matched, the actual amount injected (up to 10x variations) can be inconsistent with the appearance of the plug formed in the injector (up to only 30 % variations). Operating at constant pH and ionic strength produced the most consistent results. This report examines the effects of altering the injector geometry and solution ionic strengths, and presents the results of using bias voltages to control plug formation. The observed results should provide a benchmark for modeling of the fluid dynamics in channel intersections.     

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.     

Multiple-injection affinity capillary electrophoresis to estimate binding constants of receptors to ligands

Multiple-injection affinity capillary electrophoresis (MIACE) is used to determine binding constants (K _b) between receptors and ligands using as model systems vancomycin and teicoplanin from Streptomyces orientalis and Actinoplanes teichomyceticus, respectively, and their binding to D-Ala-D-Ala peptides and carbonic anhydrase B (CAB. EC 4.2.1.1) and the binding of the latter to arylsulfonamides. A sample plug containing a non-interacting standard is first injected followed by multiple plugs of sample containing the receptor and then a final injection of sample containing a second standard. Between each injection of sample, a small plug of buffer is injected which contains an increasing concentration of ligand to effect separation between the multiple injections of sample. Electrophoresis is then carried out in an increasing concentration of ligand in the running buffer. Continued electrophoresis results in a shift in the migration time of the receptor in the sample plugs upon binding to their respective ligand. Analysis of the change in the relative migration time ratio (RMTR) or electrophoretic mobility (μ) of the resultant receptor–ligand complex relative to the non-interacting standards, as a function of the concentration of ligand yields a value for K _b. The MIACE technique is a modification in the ACE method that allows for the estimation of binding affinities between biological interactions on a timescale faster than that found for standard ACE. In addition sample volume requirements for the technique are reduced compared to traditional ACE assays. These findings demonstrate the advantage of using MIACE to estimate binding parameters between receptors and ligands.     

Contactless conductivity detector array for capillary electrophoresis

A CE system featuring an array of 16 contactless conductivity detectors was constructed. The detectors were arranged along 70 cm length of a capillary with 100 cm total length and allow the monitoring of separation processes. As the detectors cannot be accommodated on a conventional commercial instrument, a purpose built set‐up employing a sequential injection manifold had to be employed for automation of the fluid handling. Conductivity measurements can be considered universal for electrophoresis and thus any changes in ionic composition can be monitored. The progress of the separation of Na⁺ and K⁺ is demonstrated. The potential of the system to the study of processes in CZE is shown in two examples. The first demonstrates the differences in the developments of peaks originating from a sample plug with a purely aqueous background to that of a plug containing the analyte ions in the buffer. The second example visualizes the opposite migration of cations and anions from a sample plug that had been placed in the middle of the capillary.     

Combination of cationic surfactant-assisted solid-phase extraction with field-amplified sample stacking for highly sensitive analysis of chlorinated acid herbicides by capillary zone electrophoresis

This report describes a novel online field-amplified sample stacking (FASS) procedure to analyze 16 chlorinated acid herbicides. By using a poly(vinyl alcohol) (PVA)-coated capillary to reduce electroosmotic flow and introducing a methanol-water plug before sample loading, the sample injection time could be very long without loss of sample and separation efficiency. Under the optimized condition, the FASS procedure could provide great sensitivity enhancement (5000-10 000-fold) and satisfactory reproducibility (relative standard deviations of migration times less than 2.4%, relative standard deviations of peak areas less than 8.0%). Combined with cationic surfactant-assisted solid-phase extraction (CSA-SPE), the limit of detection of the herbicides ranged from 0.269 to 20.3 ppt, which are two orders lower than those of the US Environmental Protection Agency standard method 515.1. The CSA-SPE-FASS-CE method was successfully applied to the analysis of local pond water.     

Integrated DNA purification, PCR, sample cleanup, and capillary electrophoresis microchip for forensic human identification

A fully integrated microdevice and process for forensic short tandem repeat (STR) analysis has been developed that includes sequence-specific DNA template purification, polymerase chain reaction (PCR), post-PCR cleanup and inline injection, and capillary electrophoresis (CE). Fragmented genomic DNA is hybridized with biotin-labeled capture oligos and pumped through a fluidized bed of magnetically immobilized streptavidin-coated beads in microchannels where the target DNA is bound to the beads. The bead-DNA conjugates are then transferred into a 250 nL PCR reactor for autosomal STR amplification using one biotin and one fluorescence-labeled primer. The resulting biotin-labeled PCR products are electrophoretically injected through a streptavidin-modified capture gel where they are captured to form a concentrated and purified injection plug. The thermally released sample plug is injected into a 14 cm long CE column for fragment separation and detection. The DNA template capture efficiency provided by the on-chip sequence-specific template purification is determined to be 5.4% using K562 standard DNA. This system can produce full 9-plex STR profiles from 2.5 ng input standard DNA and obtain STR profiles from oral swabs in about 3 hours. This fully integrated microsystem with sample-in-answer-out capability is a significant advance in the development of rapid, sensitive, and reliable micro-total analysis systems for on-site human identification.     

Multivariate evaluation of the separation performance in micellar electrokinetic capillary chromatography of peptides: Optimization

Summary A simultaneous optimization of resolution, efficiency and migration times of enkephalin-related peptides in micellar electrokinetic capillary chromatography (MEKC) was performed. Six experimental variables; the surfactant concentration, the percentage of organic modifier, the ionic strength of the buffer, the injected plug length, the applied temperature and the sample solution composition were studied via central composite design (CCD). Large differences in separation performance were observed at a commonly used level of organic modifier in the background electrolyte. Partial least squares regression of the responses revealed that the experimental domain was too large and complicated to be explained by the model. A new CCD model was obtained with improved prediction ability at narrower ranges of the experimental factors, especially of the organic modifier. A conflict between maximum resolution and efficiency within the shortest analysis time was observed. Therefore, constraints were set on maximal resolution and analysis time, while solving for maximum efficiency. Optimal operating conditions were found at 35 mM sodium dodecyl sulfate (SDS), 5% v/v of acetonitrile, 1.9 mm injected plug length, 35°C and sample solution with no added micelles, giving high efficiency and resolution at short analysis time. The value predicted by the model was found to agree very well to the observed values, at the optimal experimental conditions, even on a new capillary.     

A novel hybrid mode of sample injection to enhance CZE sensitivity for simultaneous determination of a pyridine-triphenylborane anti-fouling agent and its degradation products

We developed a novel hybrid sample injection mode (HSIM) that presents the combination of electrokinetic injection and vacuum injection to enhance detection sensitivity in CZE. Samples were introduced using both vacuum and electrokinetic injections simultaneously, with a water plug injected into the capillary prior to sample introduction (i.e. similarly to field-amplified sample injection, FASI). Using a sample mixture containing an anti-fouling agent applied to ship hulls, pyridine-triphenylborane and its degradation products (diphenylborinic acid, phenylboronic acid, and phenol) dissolved in ACN, the length of water plug, time, and voltage for sample introduction were optimized. The signal intensity (peak height) was found to be up to a 30-fold increased using HSIM by applying 4 kV for 4 s at the inlet end of the capillary as the cathode with supplementary vacuum in comparison with only vacuum injection for 4 s. The LODs (at a S/N of 3) for pyridine-triphenylborane, diphenylborinic acid, phenylboronic acid, and phenol were 0.88, 1.0, 21, and 23 μg/L, respectively. At the level of 0.04 mg/L, the RSDs (n=4, intra-day) for the above analytes were in the ranges of 1.9-11, 4.3-9.2, and 0.34-0.66% for peak area, peak height, and migration time, respectively. The HSIM is a simple and promising procedure useful for enhancing the sensitivity for both low-and high-mobility ions in CZE.     

Simplified capillary isoelectric focusing with chemical mobilization for intact protein analysis

We report a capillary isoelectric focusing system based on a sequential injection method for simplified chemical mobilization. This system was coupled to an ion trap mass spectrometer with an electrokinetically pumped nanoelectrospray interface. The nanoelectrospray emitter employed an acidic sheath electrolyte. To simplify focusing and mobilization, a plug of ammonium hydroxide was first injected into the capillary, followed by a section of mixed sample and ampholyte. During focusing, the NH₃H₂O section worked as catholyte. As focusing progressed, the NH₃H₂O section was titrated to lower pH by the acidic sheath electrolyte. Chemical mobilization started automatically once the ammonium hydroxide was consumed by the acidic sheath flow electrolyte, which then acted as the mobilization solution. In this report, the lengths of the NH₃H₂O section and sample were optimized. With a 1 m long capillary, a relative short plug of the NH₃H₂O section (3 cm) produced both fast migration and reasonable separation resolution. The simplified capillary isoelectric focusing mass spectrometry system produced base peak intensity relative standard deviation of 8.5% and migration time relative standard deviation ≤0.6% for myoglobin and cytochrome C in triplicate runs.     

Quantitative determination of clenbuterol, salbutamol and tulobuterol enantiomers by capillary electrophoresis

Enantiomers of clenbuterol, salbutamol and tulobuterol were directly separated and quantitated from a spiked sample by capillary electrophoresis (CE) using sulfaited beta-cyclodextrin (SCD) as chiral selector and phosphate as running buffer. The SCD and buffer concentration, pH and field strength were the parameters studied to optimize the separation. Optimal separation was obtained using 50 mM of phosphate monobasic at pH = 2.24, 0.25% (w/w) of sulfated cyclodextrin and a field strength of 10 kV, with 20 min total time analysis. Comparison between two different injection modes (hydrodynamic and electrokinetic) was made. In the hydrodynamic mode, repeatability (expressed as relative standard deviation, RSD) was less than 1.2% for migration times for all the analyte peaks and less than 2% for peak area percentages. With respect to reproducibility, RSD was less than 3.8% for migration time and less than 3% for peak area percentages. Calibration curves were set up for two different sample concentration ranges (1 to 10 microg mL(-1) and 160-800 ng mL(-1), of each of the racemates studied). Although the electrokinetic injection mode for an aqueous sample appeared to suffer from some enantiodiscrimination, calibration curves were linear in the range between 1 and 10 ng mL(-1) with regression coefficients ranging from 0.9996 to 0.9952. As in the case of hydrodynamic injection, the method was tested with a spiked sample.     

Mechanism of sequence-based separation of single-stranded DNA in capillary zone electrophoresis

Separation of DNA by length using CGE is a mature field. Separation of DNA by sequence, in contrast, is a more difficult problem. Existing techniques generally rely upon changes in intrinsic or induced differences in conformation. Previous work in our group showed that sets of ssDNA of the same length differing in sequence by as little as a single base could be separated by CZE using simple buffers at high ionic strength. Here, we explore the basis of the separation using circular dichroism spectroscopy, fluorescence anisotropy, and small angle X-ray scattering. The results reveal sequence-dependent differences among the same length strands, but the trends in the differences are not correlated to the migration order of the strands in the CZE separation. They also indicate that the separation is based on intrinsic differences among the strands that do not change with increasing ionic strength; rather, increasing ionic strength has a greater effect on electroosmotic mobility in the normal direction than on electrophoretic mobility of the strands in the reverse direction. This increases the migration time of the strands in the normal direction, allowing more time for the same-length strands to be teased apart based on very small differences in the intrinsic properties of the strands of different sequence. Regression analysis was used to model the intrinsic differences among DNA strands in order to gain insight into the relationship between mobility and sequence that underlies the separation.     

The impact of a plug of salts on the analysis of large volumes of dsDNA by capillary electrophoresis

A partially filling technique for the analysis of DNA markers and polymerase chain reaction (PCR) products by capillary electrophoresis in the presence of electroosmotic flow using polymer solutions is presented. Either after or prior to the sample injection, a plug of salts at high pH was hydrodynamically injected. During the separation, poly(ethylene oxide) (PEO) solution entered the capillary. We have found that the position, length, and composition of the plugs affect the sensitivity, resolution, and speed on the analysis of PhiX-174/HaeIII DNA restriction fragments or a DNA mixture (pBR 322/HaeIII digest, pBR 328/BglI digest and pBR 328/HinfI digest) with different degrees. Through careful evaluation of the impact of anions and cations on the analysis of DNA, we have suggested that the optimal condition is applying a plug consisting of 32 mM NaCl and 0.01 M NaOH at 30 cm height for 60 s after sample injection. In the presence of such a plug, PEO adsorption reduces, and thus the separation is faster, as well as the sensitivity improves. Using this condition, the analysis of a DNA mixture (injected at 30 cm for 360 s) containing ten different PCR products amplified after 17 cycles was complete in 25 min. About a 2000-fold improvement in the sensitivity was achieved when compared to that by a conventional method (10 s injection) without applying a plug.     

Optimization of a nano‐enzymatic reactor for on‐line tryptic digestion of polypeptide conjugates by capillary electrophoresis

This work aims at studying the optimization of an on‐line capillary electrophoresis (CE)‐based tryptic digestion methodology for the analysis of therapeutic polypeptides (PP). With this methodology, a mixture of surrogate peptide fragments and amino acid were produced on‐line by trypsin cleavage (enzymatic digestion) and subsequently analyzed using the same capillary. The resulting automation of all steps such as injection, mixing, incubation, separation and detection minimizes the possible errors and saves experimental time. In this paper, we first study the differents parameters influencing PP cleavage inside the capillary (plug length, reactant concentration, incubation time, diffusion and electrophoretic plugs mixing). In a second part, the optimization of the electrophoretic separation conditions of generated hydrolysis products (nature, pH and ionic strength (I) of the background electrolyte (BGE)) is described. Using the optimized conditions, excellent repeatability was obtained in terms of separation (migration times) and proteolysis (number of products from enzymatic hydrolysis and corresponding amounts) demonstrating the robustness of the proposed methodology.