Effect of ionic strength, pH and polymer concentration on the separation of DNA fragments in the presence of electroosmotic flow

Controlling the droplet cell environment in scanning electrochemical cell microscopy (SECCM) via migration and electroosmotic flow

Scanning electrochemical cell microscopy (SECCM) is a powerful nanoscale electrochemical technique that advances our understanding of heterogeneity at the electrode-electrolyte interface. In SECCM, dual-channel nanopipettes can serve as the probe, and a voltage bias between the channels can control the local electrolyte environment inside the droplet cell via migration and electroosmotic flow (EOF) between the channels, enabling applications including controlled electrodeposition of bimetallic nanoparticles with variable compositions. Herein, we show quantitatively how the voltage bias between the channels modulates the local electrolyte environment via experiment and finite element modeling. Experimentally, redox molecules of different charges (e.g., ferrocene derivatives and Ruthenium(III) hexamine) were filled in separate channels, where their limiting currents at the substrate electrode were used to distinguish the contribution of migration and EOF. Furthermore, EOF was visualized by fluorescence imaging. Finite element models were developed to further validate the experimental results quantitively. We showed that migration is affected by the charge number of the redox molecule. Meanwhile, EOF is affected by the surface charge on the wall of the nanopipette and the location of the slipping plane inside the electrical double layer, which can be tuned by the solution pH and the ionic strength of the electrolyte, respectively. The experimentally validated model can guide the precise modulation of droplet cell environment in SECCM, potentially enabling new scanning modes in SECCM.

Selective Extraction of Biomolecules Using a Bidirectional Flow Filter

We present a microfluidic device for selective separation and extraction of molecules based on their diffusivity. The separation relies on electroosmotically driven bidirectional flows in which high-diffusivity species experience a net-zero velocity and lower diffusivity species are advected to a collection reservoir. The device can operate continuously and is suitable for processing low sample volumes. Using several model systems, we show that the extraction efficiency of the system is maintained at more than 90% over tens of minutes with a purity of more than 99%. We demonstrate the applicability of the device to the extraction of genomic DNA from short DNA fragments.

Separation detection of hemoglobin and glycated hemoglobin fractions in blood using the electrochemical microfluidic channel with a conductive polymer composite sensor

Separation and detection of hemoglobin (Hb) and glycated hemoglobin fractions (HbA1c, HbAld₁₊₂, HbAle, HbAld3a, HbAl_a+b, HbA2, and HbAld3b) was performed using an electrochemical AC field modulated separation channel (EMSC) coupled with a sensor probe. The sensor was fabricated based on immobilization of a redox mediator on the poly(2,2':5',5″-terthiophene-3'-p-benzoic acid, pTTBA) and N,S-doped porous carbon (NSPC) nanocomposite. The different types of catalytic redox mediators such as Nile Blue (NB), toluidine blue O (TBO), and Neutral Red (NR) were evaluated to achieve the efficient detection. Of these, the NB-based sensor showed the best analytical signal for Hb and HbA1c, thus it was characterized using various electrochemical and surface analysis methods. After that, the sensor was coupled with the EMSC to achieve the separation detection of the Hb family. The frequency and amplitude of the AC electrical field applied onto the EMSC walls were the main driving forces for the separation and sensitive detection of the analytes. Under optimized conditions, linear dynamic ranges for Hb and HbA1c among their fractions were obtained between 1.0 × 10^-6 to 3.5 mM and 3.0 × 10^-6 to 0.6 mM with the detection limit of 8.1 × 10^-7 ± 3.0 × 10^-8 and 9.2 × 10^-7 ± 5 × 10^-8 mM, respectively. Interference effects of other biomolecules were also investigated and the clinical applicability of the device was evaluated by the determination of total Hb and % HbA1c in real human blood samples.

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.

Analysis of DNA complexes with small solutes by CE with LIF detection

In this article, we describe the analysis of aptamers for Hg(2+) ions through CE with LIF (CE-LIF) detection using 2% poly(ethylene oxide) solutions containing OliGreen (fluorophore). In the presence of an EOF, DNA strands migrating against the EOF were detected at the cathode end. Four DNA strands - T(33), T(5)C(28), T(5)C(5)T(23), and T(15)C(5)T(13) - could not be separated through CE-LIF in the absence of Hg(2+). At 0.3 mM Hg(2+), however, all four were partially separated within 20 min, with SDs of the migration times all being less than 2.5%. From the CE, fluorescence, and ellipticity data, we concluded that the conformations of these four DNA strands all changed from random-coil to folded structures as a result of T-Hg(2+)-T bonding. In addition, we found that this CE approach provided different electropherograms patterns for T(7), T(15), and T(33) in the absence and presence of Hg(2+), indicating various interactions of the DNA strands with Hg(2+). Using this simple, high-resolution CE approach, we also demonstrated that adenosine triphosphate has a stronger interaction with the adenosine triphosphate aptamer than with either the platelet-derived growth factor aptamer or T(33). This CE approach holds great potential for screening aptamers for small solutes, studying the catalytic activity of DNAzymes, and evaluating the biological functions of microRNA.

Using electrospray ionization mass spectrometry to explore the interactions among polythymine oligonucleotides, ethidium bromide, and mercury ions

We have used electrospray ionization mass spectrometry (ESI-MS) and fluorescence and circular dichroism (CD) spectroscopy to explore the binding of ethidium bromide (EthBr) to non-self-complementary polythymine (polyT) strands in the absence and presence of Hg2+ ions. In the gas phase, ESI-MS revealed that Hg2+ ions have greater affinity, through T-Hg2+-T coordination, toward polyT strands than do other metal ions. These findings are consistent with our fluorescence and CD results obtained in solution; they revealed that more T33-EthBr-Hg2+ complexes existed upon increasing the concentrations of Hg2+ ions (from 0 to 50 microM). Surprisingly, the ESI-MS data indicated that the Hg2+ concentration dependence of the interaction between T33 and EthBr is biphasic. Our ESI-MS data revealed that the T33-EthBr-Hg2+ complexes formed with various stoichiometries depending on their relative concentrations of the components and the length of the DNA strand. When the concentrations of T33/EthBr/Hg2+ were 5/5/2.5 microM and 5/10/7.5 microM, 1:1:1 and 1:1:2 T33-EthBr-Hg2+ complexes were predominantly formed, respectively. Thus, Hg2+-induced DNA conformational changes clearly affect the interactions between DNA and EthBr.

Stacking and separation of fluorescent derivatives of amino acids by micellar electrokinetic chromatography in the presence of poly(ethylene oxide)

A new approach for the analysis of large-volume naphthalene-2,3-dicarboxaldehyde (NDA) derivatives of amino acids by micellar electrokinetic chromatography (MEKC) in conjunction with a purple light-emitting diode-induced fluorescence detection is described. In order to optimize resolution, speed, and stacking efficiency, a discontinuous condition is essential for the analysis of NDA-amino acid derivatives. The optimum conditions use 2.0M TB (pH 10.0) buffer containing 40mM sodium dodecyl sulfate (SDS) to fill the capillary, deionized water to dilute samples, and 200mM TB (pH 9.0) containing 10mM SDS to prepare 0.6% poly(ethylene oxide) (PEO). Once high voltage is applied, PEO solution enters the capillary via electroosmotic flow and SDS micelles interact and thus sweep the NDA-amino acid derivatives having smaller electrophoretic mobilities than that of SDS micelles in the sample zone. When the aggregates between SDS micelles and NDA amino acid derivatives enter PEO zone, they are stacked due to decrease in electric field and increases in viscosity. Under the optimum conditions, the concentration and separation of 0.53-microL 13 NDA-amino acid derivatives that are negatively charged has been demonstrated by using a 60-cm capillary, with the efficiencies 0.3-9.0x10(5) theoretical plates and the LODs at signal-to-noise ratio 3 ranging from 0.30 to 2.76nM. When compared to standard injection (30-cm height for 10s), the approach allows the sensitivity enhancements over the range of 50-800 folds for the derivatives. The new approach has been applied to the analysis of a red wine sample, with great linearity of fluorescent intensity against concentrations (R(2)>0.98) and the RSD (three repetitive runs in one day) values of the migration times for the ten identified amino acids less than 2.8%.

Novel elution strategy for monitoring DNA counter-migration in the presence of electroosmotic flow

The migration behavior of native (i.e., unlabelled) DNA in the presence of electroosmotic flow (EOF) was investigated in bare fused-silica capillaries. Employing a novel elution strategy, the influence of EOF on the net mobility of DNA was assessed by collecting the DNA that migrated anodically (i.e., against EOF) and out of the capillary inlet. Various conditions of pH and buffer-zone continuity were employed to characterize this phenomenon. Tris acid (TA, pH 5.14) and Tris base (TB, pH 9.36) were used as buffers in continuous systems, in which the capillary and the inlet reservoir contain the same buffer, and discontinuous systems, in which the capillary contains either TA or TB, and the inlet reservoir contains water. DNA that was ejected into the inlet vial was subsequently analyzed by capillary electrophoresis-laser-induced fluorescence. Both phiX174/HaeIII DNA and the beta-actin product of single-cell reverse transcriptase-polymerase chain reaction were used as DNA samples in this study. The mechanism of elution was found to depend on bulk flow, in the case of continuous solutions. However, with the discontinuous system, a localized decrease in EOF generated in the capillary tip appeared to impact elution. These findings serve to introduce an alternative approach for characterizing the mobility of highly charged species.

Laser-induced fluorescence technique for DNA and proteins separated by capillary electrophoresis

Recent developments in capillary electrophoresis (CE) in conjunction with laser-induced fluorescence (LIF) using long-wavelength (maximum excitation wavelength>500 nm) dyes are reviewed. These dyes are particularly of interest when conducting the analyses of biopolymers by CE-LIF using He-Ne lasers. These systems are benefited from low background, low costs, easy maintenance, and compactness. Derivatizations of DNA and proteins with fluorescent or nonfluorescent chemicals can be carried out prior to, during, or after separations. With the advantages of sensitivity, rapidity, and high efficiency, the applications of CE-LIF to the analysis of polymerase chain reaction products, DNA sequencing, trace analysis of proteins, and single cell analysis have been presented.

Comparison of the separation of large DNA fragments in the presence and absence of electroosmotic flow at high pH

This paper describes the analysis of large DNA fragments at pH > 10.0 by capillary electrophoresis (CE) in the presence of electroosmotic flow (EOF) using hydroxyethylcellulose (HEC) solution. HEC solution in the anodic reservoir enters the capillaries filled with high-pH buffer by EOF after sample injection. With respect to resolution, sensitivity, and speed, separation conducted under discontinuous conditions (different pH values of HEC solutions and buffer filling the capillary) is appropriate. Using HEC solution at concentrations higher than its entanglement threshold ensures a good separation of large DNA fragments in the presence of EOF at high pH. In addition to pH and HEC, the electrolyte species, dimethylamine, methylamine, and piperidine, play different roles in determining the resolution. The separation of DNA fragments ranging in size from 5 to 40 kilo base pairs was completed in 6 min using 1.5% HEC prepared in 20 mM methylamine-borate, pH 12.0, and the capillary filled with 40 mM dimethylamine-borate, pH 10.0. In comparison, this method allows faster separations of large DNA fragments compared with that conducted in the absence of EOF using dilute HEC solutions.

Effects of metal ions on concentration of DNA in high-conductivity media by capillary electrophoresis

On-line concentration and separation of DNA prepared in low- or high-conductivity media has been demonstrated using poly(ethylene oxide) (PEO) solution in the presence of electroosmotic flow. DNA fragments migrating against EOF stacked at the boundary between the sample zone and PEO solutions, mainly because of sieving and increases in the viscosity. Unlike conventional methods, the large DNA fragments were detected earlier toward the cathode end in this study. The limit of detection (LOD) at a signal-to-noise ratio=3 for phiX174 RF DNA-Hae III digest prepared in 50 mM Tris-borate, pH 10.0, was down to 0.171 ng/ml, with an 860-fold improvement (compared to that obtained by 10-s injection at 25 V/cm) in the sensitivity, when injecting about 2.58 microl. By applying a short plug (2.3 cm) of 0.5 mM AgNO3 prepared in 1.5% PEO solution after sample injection, the analysis of up to 0.75 microl DNA prepared in phosphate-buffered saline (PBS) has been carried out without any tedious desalting processes. This results in an LOD of 6.86 ng/ml for the DNA sample and a 155-fold improvement in the sensitivity. Moreover, this method has allowed the analysis of 0.75 micro] of polymerase chain reaction products amplified after 18 cycles with good reproducibility.

DNA analysis on microfabricated electrophoretic devices with bubble cells

Microfluidic devices with bubble cells have been fabricated on poly(methyl methacrylate) (PMMA) plates and have been employed for the analysis of DNA using polyethylene oxide (PEO) solutions. First, the separation channel was fabricated using a wire-imprinting method. Then, wires with greater sizes or a razor blade glued in a polycarbonate plate was used to fabricate bubble cells, with sizes of 190-650 microm. The improvements in resolution and sensitivity have been achieved for large DNA (> 603 base pair, bp) using such devices, which depend on the geometry of the bubble cell. The main contributor for optimal resolution is mainly due to DNA migration at lower electric field strengths inside the bubble cell. On the other hand, slight losses of resolution for small DNA fragments have been found mainly due to diffusion, supported by the loss of resolution when separating two small solutes. With a bubble cell of 75 microm (width) x 500 microm (depth), the sensitivity improvement up to 17-fold has been achieved for the 271 bp fragment in the separation of PhiX-174/HaeIII DNA restriction fragments. We have also found that a microfluidic device with a bubble cell of 360 microm x 360 microm is appropriate for DNA analysis. Such a device has been used for separating DNA ranging from 8 to 2176 bp and polymerase chain reaction (PCR) products amplified after 30 cycles, with rapidity and improvements in the sensitivity as well as resolution.

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.

Maximization of injection volumes for DNA analysis in capillary electrophoresis

We report concentration and separation of DNA in the presence of electroosmotic flow (EOF) using poly(ethylene oxide) (PEO) solution. DNA fragments migrating against EOF stacked between the sample zone and PEO solution. To maximize the injection volume, several factors, such as concentrations of Tris-borate (TB) buffer and PEO solution, capillary size, and matrix, were carefully evaluated. The use of 25 mM TB buffers, pH 10.0, containing suitable amounts (less than 10 mM) of salts, such as sodium chloride, sodium phosphate, and sodium acetate, to prepare DNA is essential for the concentration of large-volume samples. In the presence of salts, the peaks also became sharper and the fluorescence intensity of DNA complexes increased. Using 2.5% PEO and a 150 microm capillary filled with 400 mM TB buffer, pH 10.0, up to 5 microL DNA samples (phiX 174 RF DNA-HaeIII digest or the mixture of pBR 322/HaeIII, pBR 328/Bg/I, and pBR 328/HinfI digests) have been analyzed, resulting in more than 400-fold improvements in the sensitivity compared to that by conventional injections (ca. 36 nL). Moreover, this method allows the analysis of 3.5 microL PCR products amplified after 17 cycles without any sample pretreatment.

Identifying the orientation of DNA fragment in recombinant plasmid by capillary electrophoresis with a non-gel sieving solution

It was demonstrated that a capillary electrophoresis (CE) method with a non-gel sieving solution has been developed to identify the orientation of DNA fragments in recombinant plasmids in molecular biology. The influences of the concentration of sieving polymer HEC, the applied electric field strength and sampling on CE separation were analyzed concerning the optimization of separation. YO-PRO-1 was used as a DNA intercalating reagent to facilitate fluorescence detection. Under the chosen conditions (buffer, 1 x TBE containing 1 microM YO-PRO-1 and 1.2% HEC; applied electric field strength, 200 V/cm; electrokinetic sampling: time, 5 s; voltage, -6 kV), three DNA markers (phi 174/HaeIII, pBR322/HaeIII and lambda DNA/HindIII) were tested for further evaluating the relationship between the DNA size and the mobility. The established CE method conjugated with the enzymatic approach was successfully applied to identifying the DNA orientation of recombinant plasmid in transgene operations of a newly cloned gene from Arabidopsis Thaliana.

Analysis of large-volume DNA markers and polymerase chain reaction products by capillary electrophoresis in the presence of electroosmotic flow

We have demonstrated on-line concentration and separation of DNA in the presence of electroosmotic flow (EOF) using poly(ethylene oxide) (PEO) solutions. After injecting large-volumes DNA samples, PEO solutions entered a capillary filled with 400 mM Tris-borate (TB) buffers by EOF and acted as sieving matrices. DNA fragments stacked between the sample zone and PEO solutions. Because sample matrixes affected PEO adsorption on the capillary wall, leading to changes in EOF, migration time, concentration, and resolving power varied with the injection length. When injecting phiX174 RF DNA-HaeIII digest prepared in 5 mM Tris-HCl buffer, pH 7.0, at 250 V/cm, peak height increased linearly as a function of injection volume up to 0.9 microl (injection time 150 s). The sensitivity improvement was 100-fold compare to that injected at 25 V/cm for 10 s (0.006 microl). When injecting 1.54 microl of GeneScan 1000 ROX, the sensitivity improvement was 265-fold. The sensitivity improvement was 40-fold when injecting 0.17 microl DNA sample containing pBR 322/HaeIII, pBR 328/BglI, and pBR 328/HinfI digests prepared in phosphate-buffered saline. This method allows the analysis of polymerase chain reaction (PCR) products amplified after 17 cycles when injecting 0.32 microl (at 30 cm height for 300 s). The total analysis time was shorter (91.6 min) than that (119.6 min) obtained from injecting PCR products after 32 cycles for 10 s.

Regulation of electroosmotic flow and electrophoretic mobility of proteins for concentration without desalting

Proteins were concentrated and separated in 0.6% poly(ethylene oxide) (PEO) solution using a capillary filled with Tris-borate (TB) buffer prior to analysis and detected by laser-induced native fluorescence using a pulsed Nd:YAG laser. During the concentration and separation, PEO solution entered the capillary by electroosmotic flow. When proteins dissolved in high salts (phosphate-buffered saline) were separated using 0.6% PEO solution prepared in 200 mM TB buffer, pH 9.0, the limits of detection (LODs) at signal-to noise ratios=3 for carbonic anhydrase (CA) and alpha-lactalbumin (alpha-lac) were on the levels of sub microM and microM, respectively. The LOD values compared to those obtained in 38 mM TB buffer were relatively high, which is likely due to salt quenching, Joule heating and poor stacking. To improve sensitivity for analysis of proteins in high-conductivity media, two on-line concentration approaches without desalting were developed. When using a capillary filled with 1.5 M TB buffer, pH 10.0, and PEO solution prepared in 800 mM TB buffer, pH 9.0, the LOD values for CA and alpha-lac were 13.8 nM and 126.0 nM, respectively, which were about 4.7 and 11.2-fold sensitivity enhancements compared to those obtained by a conventional hydrodynamic injection (30 cm height for 10 s), respectively. The sensitivity was further improved by injecting a short plug of low pH buffer after protein injection using a capillary filled with 1.5 M TB buffer, pH 10.0, and PEO solution prepared in 400 mM TB buffer, pH 9.0. A linear relationship between the peak height and the injection volume up to 0.81 microl was obtained and the LOD values for CA and alpha-lac were down to 4.7 and 37.8 nM.

Separation of dsDNA in the presence of electroosmotic flow under discontinuous conditions

Separations of phiX-174/HaeIII DNA restriction fragments have been performed in the presence of electroosmotic flow (EOF) using five different polymer solutions, including linear polyacrylamide (LPA), poly(ethylene oxide) (PEO), hydroxypropylcellulose (HPC), hydroxyethylcellulose (HEC), and agarose. During the separation, polymer solutions entered the capillary by EOF. When using LPA solutions, bulk EOF is small due to adsorption on the capillary wall. On the other hand, separation is faster and better for the large DNA fragments (> 872 base pairs, bp) using derivative celluloses and PEO solutions. Several approaches to optimum resolution and speed by controlling EOF and/or altering electrophoretic mobility of DNA have been developed, including (i) stepwise changes of ethidium bromide (0.5-5 microg/mL), (ii) voltage programming (125-375 V/cm), (iii) use of mixed polymer solutions, and (iv) use of high concentrations of Tris-borate (TB) buffers. The DNA fragments ranging from 434 to 653 bp that were not separated using 2% PEO (8,000,000) under isocratic conditions have been completely resolved by either stepwise changes of ethidium bromide or voltage programming. Compared to PEO solutions, mixed polymer solutions prepared from PEO and HEC provide higher resolving power. Using a capillary filled with 600 mM TB buffers, pH 10.0, high-speed (< 15 min) separation of DNA (pBR 322/HaeIII digest, pBR 328/ Bg/l digest and pBR 328/Hinfl digest) has been achieved in 1.5% PEO.