Sequence‐based separation of single‐stranded DNA at high salt concentrations in capillary zone electrophoresis

DNA separation by fragment length can be readily achieved using sieving gels in electrophoresis. Separation by sequence has not been as simple, generally requiring adequate differences in native or induced conformation between single or hybridized strands or differences in thermal or chemical stability of hybridized strands. Previously, it was shown that four single‐stranded DNA (ssDNA) 76‐mers that differ by only a few A‐G substitutions could be separated based solely on sequence by adding guanosine‐5’‐monophosphate to the running buffer in capillary zone electrophoresis (CZE). The separation was attributed to interactions of the ssDNA with self‐assembled guanine‐tetrad structures; however, subsequent studies of an expanded set of ten 76‐mers showed that the separation was a more general phenomenon that occurred at high salt concentrations. With the long‐term goal of using experimental and computational methods to provide insight into the basis of the separation, a set of ssDNA 15‐mers was designed including a poly(dT) 15‐mer and nine variants. Separations were performed using fluorescent‐labeled ssDNA in CZE with laser‐induced fluorescence detection. Results show that separation improves with increasing buffer concentration and decreasing temperature, due at least in part to longer separation times. Migration times increase with increasing purine content, with A having a much larger effect that G. Circular dichroism spectra of the mixtures of the strands suggest that the separation is not due to changes in conformation of the ssDNA at high salt concentrations.     

Influence of electric field intensity, ionic strength, and migration distance on the mobility and diffusion in DNA surface electrophoresis

In order to increase the separation rate of surface electrophoresis while preserving the resolution for large DNA chains, e.g., genomic DNA, the mobility and diffusion of Lambda DNA chains adsorbed on flat silicon substrate under an applied electric field, as a function of migration distance, ionic strength, and field intensity, were studied using laser fluorescence microscope. The mobility was found to follow a power law with the field intensity beyond a certain threshold. The detected DNA peak width was shown to be constant with migration distance, slightly smaller with stronger field intensity, but significantly decreased with higher ionic strength. The molecular dynamics simulation demonstrated that the peak width was strongly related with the conformation of DNA chains adsorbed onto surface. The results also implied that there was no diffusion of DNA during migration on surface. Therefore, the Nernst-Einstein relation is not valid in the surface electrophoresis and the separation rate could be improved without losing resolution by decreasing separation distance, increasing buffer concentration, and field intensity. The results indicate the fast separation of genomic DNA chains by surface electrophoresis is possible.     

Investigation of the effect of ionic strength of Tris-acetate background electrolyte on electrophoretic mobilities of mono-, di-, and trivalent organic anions by capillary electrophoresis

The effect of ionic strength of the background electrolyte (BGE) composed of tris(hydroxymethyl)aminomethane (Tris) and acetic acid on the electrophoretic mobility of mono-, di- and trivalent anions of aliphatic and aromatic carboxylic and sulfonic acids was investigated by capillary zone electrophoresis (CZE). Actual ionic mobilities of the above anions were determined from their CZE separations in Tris-acetate BGEs of pH 8.1 to 8.2 in the 3 to 100 mM ionic strength interval at constant temperature (25 degrees C). It was found that the ionic strength dependence of experimentally determined actual ionic mobilities does not follow the course supposed by the classical Onsager theory. A steeper decrease of actual ionic mobilities with the increasing ionic strength of BGE and a higher estimated limiting mobility of the anions than that found in the literature could be attributed to the specific behavior of the Tris-acetate BGEs. Presumably, not only a single type of interaction of anionic analytes with BGE constituents but rather the combination of effects, such as ion association or complexation equilibria, seems to be responsible for the observed deviation of the concentration dependence of the actual ionic mobilities from the Onsager theory. Additionally, several methods for the determination of limiting ionic mobilities from CZE measured actual ionic mobilities were evaluated. It turned out that the determined limiting ionic mobilities significantly depend on the calculation procedure used.     

DNA fragment separations by on‐line combination of capillary isotachophoresis–capillary zone electrophoresis with UV detection

A high‐speed DNA fragment separation system based on an on‐line combination of capillary ITP with CZE (CITP‐CZE) and using UV detection at 260 nm was developed. A novel CITP‐CZE buffer system of pH 6.1 was designed for the separation of ten DNA fragments with sizes ranging from 100 to 1000 bp. An effect of underivatized α‐, β‐ and γ‐cyclodextrins on the resolution of DNA fragments in the CZE step of the CITP‐CZE combination was systematically investigated. Methylhydroxyethylcellulose present in the BGE was used to eliminate the EOF. DNA ladder fragments were separated within 10 min with LODs in the range of 1–5 ng/μL (S/N = 3). The RSDs of the migration time and peak area of individual DNA fragments were in the range of 1–3 and 3–9%, respectively. The developed CITP‐CZE system was further applied to the analysis of digest plasmid DNA samples.     

Prediction of the separation of phenols by capillary zone electrophoresis

The effect of pH and ionic strength on the migration of neutral acids in capillary zone electrophoresis (CZE) has been studied for several phenols. The mobilities of the phenols and the efficiency of the capillary have been related to the studied factors. The mobility can be related to the pH of the running buffer through the mobility of the phenolate ion, and the conditional acidity pK value of the phenol at the working ionic strength. This allows prediction of the migration of the phenol, solely from its pK_a^′ value (literature pK_a corrected for the ionic strength of the solution) and mobility of the anion, which can be easily calculated from the mobility at a basic pH value and the pK_a^′ value. Combination of the predicted mobility with the efficiency allows estimation of the resolution of the consecutive peaks obtained for a mixture of phenols. This method has been tested for two groups of phenols of environmental interest.     

Electrophoresis versus electrochromatography

In separation techniques, such as Liquid Chromatography and Capillary Zone Electrophoresis, separation is performed on the basis of differences in velocity of the various separands, making use of differences in k′ and/or effective mobility. While in chromatography the flow of the eluent is elementary, in electrophoretic techniques the electroosmotic flow is generally suppressed in order to avoid disturbing of the sample zone boundaries, which migrate with a maximal velocity of 10^?3 m s^?1. This holds especially for isotachophoretic separations, where separands migrate in consecutive zones with minimal detectable lengths of about 0.1 mm. If electroosmotic flow is applied as a transport mechanism, using capillaries as small as about 50 μm, linear velocities of the liquid flow can reach about 2 × 10^?3 m s^?1. Especially for ionic species with a low effective mobility, this velocity can be a multiple of the electrophoretic migration velocity in the separation compartment. Therefore, anionic, non-ionic, and cationic separands can migrate in the same direction. Depending on whether repulsive or attractive forces are operative, the electrophoretic separation power can be counteracted or favored. The separation mechanisms making use of (quasi)stationary phases are studied. Plotting the chromatographic behavior versus the electrophoretic shows transition areas to exist between the “purely” electrophoretic techniques and the “purely” chromatographic techniques. It must be stated that most of the recent publications in CZE, especially those with very narrow bore capillaries, can be allocated to the transition areas, sometimes with a strong chromatographic retention component.     

Use of 1-alkyl-3-methylimidazolium-based ionic liquids as background electrolytes in capillary electrophoresis for the analysis of inorganic anions

Separation of inorganic anions in CE is often a challenging task because the electrophoretic mobilities of inorganic anions are comparable to or even greater than the EOF mobility. In this study, we present the use of ionic liquids (ILs) as background electrolytes (BGEs) in CE of inorganic anions. The 1-alkyl-3-methylimidazolium-based ILs as BGEs dynamically coated the capillary wall and induced a reversed EOF. This allowed the anions to comigrate with the EOF and yielded a rapid separation. Increasing the alkyl chain length of the ILs and BGE concentration can significantly improve the separation resolution. With 40 mM 1-butyl-3-methylimidazolium tetrafluoroborate as BGE, good separations of five model anions (Br-, I-, NO2(-), NO3(-), and SCN-) were achieved in a range of buffer pH values. The separation efficiency was as high as 34 600-155 000, and the RSDs of the migration times were less than 0.8% (n = 5).     

Capillary zone electrophoresis of sub-microm-sized particles in electrolyte solutions of various ionic strengths: size-dependent electrophoretic migration and separation efficiency

To gain insight into the mechanisms of size-dependent separation of microparticles in capillary zone electrophoresis (CZE), sulfated polystyrene latex microspheres of 139, 189, 268, and 381 nm radius were subjected to CZE in Tris-borate buffers of various ionic strengths ranging from 0.0003 to 0.005, at electric field strengths of 100-500 V cm(-1). Size-dependent electrophoretic migration of polystyrene particles in CZE was shown to be an explicit function of kappaR, where kappa(-1) and rare the thickness of electric double layer (which can be derived from the ionic strength of the buffer) and particle radius, respectively. Particle mobility depends on kappaR in a manner consistent with that expected from the Overbeek-Booth electrokinetic theory, though a charged hairy layer on the surface of polystyrene latex particles complicates the quantitative prediction and optimization of size-dependent separation of such particles in CZE. However, the Overbeek-Booth theory remains a useful general guide for size-dependent separation of microparticles in CZE. In accordance with it, it could be shown that, for a given pair of polystyrene particles of different sizes, there exists an ionic strength which provides the optimal separation selectivity. Peak spreading was promoted by both an increasing electric field strength and a decreasing ionic strength. When the capillary is efficiently thermostated, the electrophoretic heterogeneity of polystyrene microspheres appears to be the major contributor to peak spreading. Yet, at both elevated electric field strengths (500 V/cm) and the highest ionic strength used (0.005), thermal effects in a capillary appear to contribute significantly to peak spreading or can even dominate it.     

Capillary electrophoresis of DNA for molecular diagnostics

A number of applications of capillary zone electrophoresis (CZE) in sieving liquid polymers (notably linear polyacrylamides and cellulose) for the analysis of polymerase chain reaction (PCR) products of clinically relevant, diagnostic DNA, are reviewed. The fields covered are: human genetics, quantitative gene dosage, microbiology and virology, forensic medicine and therapeutic DNA (notably, antisense nucleotides). Some unique, novel developments are highlighted, such as: (i) nonisocratic CZE, i.e., temperature-programmed CZE for detection of DNA point mutations; (ii) the synthesis of novel N-substituted acrylamides, offering extreme resistance to alkaline hydrolysis coupled to high hydrophilicity. In the field of denaturing gradient gel electrophoresis (DGGE), as routinely performed in gel slabs, a novel methodology is described in CZE: double-gradient DGGE. In this technique, two gradients are simultaneously applied along the migration direction: a chemical (or thermal) denaturing gradient, for partially unwinding homo- and hetero-duplexes of DNA, and a porosity gradient, for recompacting diffuse bands melting over a broader range of denaturing conditions. It is thus demonstrated that chemical gradients, in addition to temperature gradients, can be easily implemented even in a capillary format.     

Analysis of aromatic acids by nonaqueous capillary electrophoresis with ionic‐liquid electrolytes

The separation of six kinds of aromatic acids by CZE with 1‐ethyl‐3‐methylimidazolium chloride (EMIMCl) and 1‐ethyl‐3‐methylimidazolium hydrogen sulfate (EMIMHSO₄)_, two kinds of ionic liquids (ILs) as background electrolytes, and acetonitrile as solvent were investigated. The six kinds of aromatic acids can be separated under positive voltage with low IL concentration with either of the two ILs and separation with EMIMHSO₄ is better in consideration of peak shapes and separation efficiency. But the migration order is different when the IL is different. Under negative voltage with high IL concentration, the six analytes can be separated with EMIMCl as background electrolytes and the migration order of the analytes is opposite to those with low concentration of EMIMCl as background electrolyte. The separations are based on the combination effects of heteroconjugation between the anions and cations in the ILs and the analytes, of which the heteroconjugation between the anions in the ILs and the analytes plays a dominant role. The heteroconjugation between the anions of the ILs and analytes is proton sensitive and only a very small amount of proticsolvents added into the electrolyte solution can harm the separation. When EMIMCl concentration is high, the heteroconjugation between the IL anions and the proton in the analytes make the effective mobility of the analytes much higher than the EOF and their migration direction reversed. Finally, the six aromatic acids in water samples were analyzed by nonaqueous CE with low concentration of EMIMHSO₄ as background electrolytes with satisfactory results.     

Peptide separation in hydrophilic interaction capillary electrochromatography

Separation of small peptides by hydrophilic interaction capillary electrochromatography (HI-CEC) has been investigated. The negative surface charge of a hydrophilic, strong-cation-exchange stationary phase (PolySULFOETHYL A) provided a substantial cathodic electroosmotic flow (EOF). The influence of acetonitrile content, ionic strength, mobile phase pH as well as applied voltage on the migration of the peptides was studied. Possible retention mechanisms of the peptides in HI-CEC were discussed. It was found that hydrophilic interaction between the solutes and the stationary phase played a major role in this system, especially when mobile phases with high acetonitrile content were used. However, an ion-exchange mechanism and electrophoretic mobility also affect the migration of the peptides in HI-CEC. Elution order and selectivity was proved to be different in HI-CEC and capillary zone electrophoresis (CZE), thus revealing the potential of HI-CEC as a complementary technique to CZE for the separation of peptides. Efficiency and selectivity of HI-CEC for the separation of peptides were demonstrated by baseline separating nine peptides in 6 min.     

Capillary electrophoresis for the direct determination of cephalosporins in clinical samples

Summary The possibility of determination of four cephalosporin antibiotics in clinical samples by capillary electrophoresis has been investigated. The separation conditions for capillary zone electrophoresis (CZE) were studied in detail. The precision of migration times measured by use of the optimized method was satisfactory (RSD<1%) and response was linearly dependent on concentration over the approximate range 2–150 mg L⁻¹ for all the compounds studied (cefuroxime, cefotaxime, ceftriaxone, and ceftazidime). Complete separation could be achieved within 5 min. The CZE method was found to be highly suitable for direct determination of the antibiotics in clinical samples such as wound drainage, cerebrospinal fluid, and urine; for serum, however, the use of micellar electrokinetic capillary chromatography (MECC) was more advantageous. Presented at Balaton Symposium '01 on High-Performance Separation Methods, Siófok, Hungary, September 2–4, 2001     

Sweeping of neutral analytes via complexation with borate in capillary zone electrophoresis

Summary The sweeping concept is extended to capillary zone electrophoresis (CZE) separation of neutral solutes involving complexation with borate. Analogous to the pseudostationary phase in electrokinetic chromatography (EKC), the complexing agent (borate) serves as carrier for sweeping and separation in CZE. Therefore, similar to the retention factor in EKC, the focusing effect in the present system is directly related to the association constant between the analyte and complexing agent. Theoretical and some preliminary experimental studies gerenally suggest that the electrophoretic mobility of the complex and the concentration of the complexing agent affect the resulting length of narrowed zones. Moreover, sweeping using borate is affected by pH since borate complexation is pH dependent. From around 10 to 40-fold improvement in peak heights has been observed experimentally for some neutral test analytes (monosaccharides, catechols, and nucleosides)     

Validation of CE modeling with a contactless conductivity array detector

Dynamic computer simulation data are compared for the first time with CE data obtained with a laboratory made system comprising an array of 8 contactless conductivity detectors (C⁴Ds). The experimental setup featured a 50 μm id linear polyacrylamide (LPA) coated fused‐silica capillary of 70 cm length and a purpose built sequential injection analysis manifold for fluid handling of continuous or discontinuous buffer configurations and sample injection. The LPA coated capillary exhibits a low EOF and the manifold allows the placement of the first detector at about 2.7 cm from the sample inlet. Agreement of simulated electropherograms with experimental data was obtained for the migration and separation of cationic and anionic analyte and system zones in CZE configurations in which EOF and other column properties are constant. For configurations with discontinuous buffer systems, including ITP, experimental data obtained with the array detector revealed that the EOF is not constant. Comparison of simulation and experimental data of ITP systems provided the insight that the EOF can be estimated with an ionic strength dependent model similar to that previously used to describe EOF in fused‐silica capillaries dynamically double coated with Polybrene and poly(vinylsulfonate). For the LPA coated capillaries, the electroosmotic mobility was determined to be 17‐fold smaller compared to the case with the charged double coating. Simulation and array detection provide means for quickly investigating electrophoretic transport and separation properties. Without realistic input parameters, modeling alone is not providing data that match CE results.     

Length-dependent DNA separations using multiple end-attached peptide nucleic acid amphiphiles in micellar electrokinetic chromatography

End-labeled free-solution electrophoresis (ELFSE) is an alternative approach to gel-based methods for size-based electrophoretic separation of DNA. In ELFSE, an electrically neutral "drag-tag" is appended to DNA to add significant hydrodynamic drag, thereby breaking its constant charge-to-friction ratio. Current drag-tag architecture relies on covalent attachment of polymers to each DNA molecule. We have recently proposed the use of micellar drag-tags in conjunction with sequence-specific hybridization of peptide nucleic acid amphiphiles (PNAAs). This work investigates the effect of multiple PNAA attachment on DNA resolution using MEKC. Simultaneous PNAA hybridization allows for the separation of long DNA targets, up to 1012 bases, using micellar drag-tags. Each PNAA handle independently interacts with the micellar phase, reducing the overall mobility of this complex relative to individual PNAA binding. The sequence- and size-based dependence of this separation technique is maintained with multiple PNAA binding over a range of DNA sizes. Results are accurately described by ELFSE theory, yielding alpha=54 for single-micelle tagging and alpha=142 for dual-micelle tagging. This method is the first example of a non-covalent drag-tag used to separate DNA of 1000 bases based on both size and sequence.     

Influence of buffer composition on the capillary electrophoretic separation of carbon nanoparticles

Carbon nanoparticles obtained from the flame of an oil lamp were examined by means of capillary electrophoresis. The influence of buffer composition on the separation of the mixture of negatively charged carbon nanoparticles was studied by varying buffer selection, pH, and concentration. The electrophoretic pattern was affected by both the co- and counter-ion in the buffer solution, influencing selectivity and peak shape. The capillary electrophoretic separations at different pH revealed species with large electrophoretic mobilities under a wide range of pH. The mobility of selected species in the mixture of nanoparticles showed a strong dependence upon the solution ionic strength. The mobility of these nanoparticles as a function of ionic strength was compared to classical electrokinetic theory, suggesting that under the experimental conditions utilized, the species are small, highly charged particles with appreciable zeta potentials, even at low pH.     

Contaminant-induced current decline in capillary array electrophoresis

High-throughput capillary array electrophoresis (CAE) instruments for DNA sequencing suffer to varying degrees from read length degradation associated with electrophoretic current decline and inhibition or delay in the arrival of fragments at the detector. This effect is known to be associated with residual amounts of large, slow-moving fragments of template or genomic DNA carried through from sample preparation and sequencing reactions. Here, we investigate the creation and expansion of an ionic depletion region induced by overloading the capillary with low-mobility DNA fragments, and the effect of growth of this region on electrophoresis run failure. Slow-moving fragments are analytically and experimentally shown to reduce the ionic concentration of the downstream electrolyte. With injection of large fragments beyond a threshold quantity, the anode-side boundary of the nascent depletion region begins to propagate toward the anode at a rate faster than the contaminant DNA migration. Under such conditions, the depletion region expands, the capillary current declines dramatically, and the electrophoresis run yields a short read length or fails completely.     

Guanosine gel for sequence-dependent separation of polymorphic ssDNA

The separation of fluorescent-labeled ssDNA fragments of equal length based on differences in sequence was achieved through the use of guanosine gels (G-gels) formed by guanosine-5'-monophosphate (GMP) in capillary gel electrokinetic chromatography (CGEKC) with LIF detection. Baseline resolution was achieved for homodimers and homopentamers of A, T, and C. G-gel CGEKC provided better resolution than CZE, MEKC, or a sieving gel in CGE. Resolution improved with increasing GMP, indicating that the interaction is linked to structural organization of the G-gel. Fluorescence intensity and anisotropy show that the order of interaction with G-gels is T>C>A. We then investigated four conformationally similar, polymorphic 76-mers with A/G substitutions that are utilized in forensic DNA typing. Resolution was achieved by CGEKC but not CZE or CGE. In CGEKC, the negatively charged G-gels and oligonucleotides electromigrate toward the positive inlet while being driven by EOF to the negative outlet. The net forward velocity is the greatest for oligonucleotides most closely associated with the slower, more cumbersome G-gel network. For the 76-mers, resolution increases with increasing difference in guanosine content between strands and, for a given difference, with increasing total guanosines in the strands.     

Detection of the major mutation M467T causing cystinuria by single-strand conformation polymorphism analysis using capillary electrophoresis

We present a fast detection of M467T, the major mutation causing cystinuria, by capillary electrophoresis version of single-strand conformation polymorphism (SSCP). The DNA fragment (317 bp) carrying the point mutation was amplified by polymerase chain reaction (PCR) on the exon 8 of the SLC3A1 gene, which encodes for the transmembrane glycoprotein rBAT, a part of the active cystine and dibasic amino acids transporter. The complementary strands of the fragment were labeled by fluorescein and TAMRA, respectively. Thus, the electromigration of both strands was recorded independently as a laser-induced fluorescence (LIF) signal, what enabled an effective optimization of separation conditions. The injected sample was denatured by immersing the inlet of the separation capillary into a vial with 0.1 M solution of NaOH prior to analysis. Under optimum conditions, the SSCP analysis in poly(vinyl alcohol) (PVA)-coated silica-fused capillary of an effective length of 15 cm, filled with 4% linear polyacrylamide (LPA) solution, was accomplished in approximately 6 min. The experimentally observed mobility shifts of single-stranded DNA (ssDNA) fragments were compared to the appearance of their calculated two-dimensional conformations using Version 3.0 of MFOLD software. The number of nucleotides involved in the duplex regions of theoretical structures correlates well with their real migration order in the sieving medium.     

Metal ion capillary zone electrophoresis with direct UV detection: Comparison of different migration modes for negatively charged chelates

Summary Several migration modes suitable for capillary zone electrophoretic (CZE) separation of metal ions in the form of 8-hydroxyquinoline-5-sulphonic acid complexes are described and compared. Superior analysis time, resolution, efficiency and detectability were achieved using reversed movement of anionic metal complexes (in the anode-to-cathode direction) under the action of the electroosmotic flow. This method allows the CZE analysis of multicomponent mixtures of transition metal ions as well as aluminium within about six minutes.