Band broadening of DNA fragments isolated by polyacrylamide gel electrophoresis in capillary electrophoresis

Polyacrylamide gel electrophoresis (PAGE) is used frequently for isolation and purification of DNA fragments. In the present study, DNA fragments extracted from polyacrylamide gels showed significant band broadening in capillary electrophoresis (CE). A pHY300PLK (a shuttle vector functioning in Escherichia coli and Bacillus subtilis) marker, which contained nine fragments ranging from 80 to 4870 bp, was separated by PAGE, and each fragment was isolated by phenol/chloroform extraction and ethanol precipitation. After extraction from the polyacrylamide gel, the peaks of the isolated DNA fragments exhibited band broadening in CE, where a linear poly(ethylene oxide) was used as a sieving matrix. The theoretical plate numbers of the DNA fragments contained in the pHY300PLK marker were >10⁶ for all the fragments before extraction. However, the DNA fragments extracted from the polyacrylamide gel showed decreased theoretical plate numbers (5–20 times smaller). The degradation of the theoretical plate number was significant for middle sizes of the DNA fragments ranging from 489 to 1360 bp, whereas the largest and smallest fragments (80 and 4870 bp) had no obvious influence. The band broadening was attributed to contamination of the DNA fragments by polyacrylamide fibers during the separation and extraction process.     

Characterization of single-stranded DNA separation by capillary gel electrophoresis

We have investigated the effect of polymer gel reconditioning, the shape of the capillary, the applied electric field, and the capillary length for single-stranded DNA. The polyethylene oxide gel had deformed under the high electric field causing the degradation of the separation power. By the reintroduction of the fresh polyethylene oxide gel for the next run, one-base resolution was recovered. It turned out that the tip of the capillary at the injection side needed to be clean and symmetric for much improved resolution. Changing DNA motion by the pulsed electric field resulted in the separation of DNA far more than 500 bases.     

Modification of the immobilized metal affinity electrophoresis using sodium dodecyl sulfate polyacrylamide gel electrophoresis

Modification to the original immobilized metal affinity electrophoresis (IMAEP) technique is presented. SDS-PAGE is used instead of native PAGE for improved extraction of phosphoproteins from a mixture of proteins. Protein samples treated with 2% w/v SDS instead of native sample buffer ensure that proteins are negatively charged. These negative charges on the proteins assure that the proteins migrate electrophoretically towards the anode regardless of their pI values and hence pass through the region embedded with the metal ions. Another benefit of treating proteins with SDS is that it unfolds the phosphoproteins exposing the phosphate groups to facilitate the metal-phosphate interactions. Phosphorylated ovalbumin can only be extracted after SDS sample buffer treatment. Data show that there is no detrimental effect upon SDS treatment on the extraction of phosphoproteins from a mixture of proteins. Electrophoretic migration of phosphoproteins ceases upon encounter with metal ions like Al+3, Ti+3, Fe+3, Fe+2, and Mn+2 whereas non-phosphorylated proteins migrate freely.     

Production of polyacrylamide gel filled capillaries for capillary gel electrophoresis (CGE): Influence of capillary surface pretreatment on performance and stability

Polyacrylamide gel filled capillaries for electrophoresis can be improved in performance and stability by a specially optimized and reproducible production procedure. After surface pretreatment as described in this contribution, gels polymerized in capillaries are stable for long series of routine separations. Bubbles formation during gel polymerization can be avoided. The procedure is compared with those described by other authors. Separations of different oligonucleotide samples illustrate the quality of the gel capillaries obtained. The peak symmetry achieved proved to be better than that obtained without surface pretreatment.     

Characterization of antithrombin III from human plasma by two-dimensional gel electrophoresis and capillary electrophoretic methods

The isoforms distribution of the glycoprotein antithrombin III (ATIII) derived from human plasma was investigated by means of isoelectric focusing (IEF) in polyacrylamide gels with immobilized pH gradients (IPG) and two-dimensional gel electrophoresis (2-DE) as well as capillary electrophoretic methods. It turned out that the presence of high concentrations of chaotropics (urea, thiourea) and zwitterionic detergents (3-[(3-cholamidepropyl)dimethylammonio]-1-propanesulfonate (CHAPS)) was decisive for attaining good resolution of the protein isoforms. Resolution by IPG-IEF was obtained with excellent reproducibility and pI differences down to 0.01 pH units could be distinguished. ATIII-alpha and ATIII-beta-fractions preseparated by heparin affinity chromatography showed an analogous but shifted spot pattern consisting each of one major and three minor isoforms. The main isoforms of ATIII-alpha and ATIII-beta exhibit pI values of 5.18 and 5.32, respectively, both values determined in the presence of high concentrations of urea. The pI difference of 0.14 pH units correspond to the effect of two sialic acids absent in ATIII-beta. The formation and occurrence of ATIII dimers and trimers turned out to be dependent on the sample preparation. The results obtained by 2-DE were compared with those of capillary zone electrophoresis (CZE) and capillary IEF (CIEF). Quantitative analysis regarding the CZE separated isoforms of plasma derived ATIII yielded a content of about 70% ATIII-alpha main isoform and about 6.6% of ATIII-beta. The pI values of ATIII determined by CIEF with internal calibration were in fair agreement with the pI values of the main isoforms achieved with 2-DE.     

High-sensitive analysis of DNA fragments by capillary gel electrophoresis using transient isotachophoresis preconcentration and fluorescence detection

In this report aimed on further development of a high-sensitivity capillary gel electrophoresis (CGE) method for analysis of DNA fragments, we firstly explored online transient isotachophoresis (tITP) preconcentration combined with fluorescence detection (FD). The fluorescence signal (excitation: 488 nm; emission: 590 nm) was generated using the intercalating dye of ethidium bromide (EB). It was found when the leading electrolyte (LE) was injected behind the sample zone, such a special tITP mode has significant advantages to solve the bubble formation issue and to improve the analytical performance stability. Two standard DNA samples, a 50 bp DNA step ladder and the φX174/HaeIII digest, were used to evaluate the qualitative and quantitative abilities of the tITP-FD approach. A highly diluted sample (10,000-fold in the water, e.g. the φX174/HaeIII digest diluted from 500 μg/ml to the 50 ng/ml level) was enriched and detected; the LOD was down to 0.09 ng/ml for the 72 bp fragment, apparently improved more than 1000-fold in comparison with UV detection. Although the RSD of peak areas (n = 3) was around 15.5% for the sample was electrokinetically injected, good linearity of peak area response showed that the proposed method is suitable for quantitative analysis.     

Preparation and evaluation of stable coating for capillary electrophoresis using coupled chitosan as coated modifier

A coated capillary modified with a coupled chitosan (COCH) was developed by using a simple and fast (60 min) process that could be easily automated in capillary electrophoresis instrument. The COCH coating was achieved by first attaching chitosan to the capillary inner wall, and then coupling with glutaraldehyde, and rinsing chitosan again to react with glutaraldehyde. The COCH coating was stable and showed amphoteric character over the pH range of 1.8-12.0. When the pH value was lower than 4.5, the capillary surface possessed positive charges, which caused a reversal in the direction of the electroosmotic flow (EOF). The normal EOF direction could be obtained when the pH value was higher than 4.5. The COCH coating showed strong stability against 0.1 mol/L HCl, 0.1 mol/L NaOH and other solvents compared with conventional chitosan coating. The relative standard deviation of the run-to-run, day-to-day and capillary-to-capillary coating was all below 2% for the determination of EOF. The COCH-modified capillary was applied to acidic and basic proteins analyses and high efficiency could be attained. The comparison between unmodified capillary, chitosan-modified and COCH-modified capillary for the separation of real sample, extract from Elaphglossum yoshinagae with water, was also studied. Better results could be obtained on COCH-modified capillary than the other two capillaries.     

Highly efficient size separation of CdTe quantum dots by capillary gel electrophoresis using polymer solution as sieving medium

In this paper, we present a new method for highly efficient size separation of water-soluble CdTe quantum dots (QDs) based on CGE using polymer solution as sieving medium. CdTe QDs were synthesized in aqueous phase by a chemical route with mercaptopropionic acid as a ligand. In the alkaline solution, CdTe QDs possess negative charges and migrate to the anode in the electric field. In linear polyacrylamide sieving medium, the migration time of CdTe QDs was increased with the size of CdTe QDs. The effects of some factors, such as types, concentrations, and pH of sieving media, on the separation of CdTe QDs were investigated systematically. Highly efficient separation of CdTe QDs was obtained in linear polyacrylamide sieving medium, and collection of fractions was automatically accomplished by CGE technique. Our preliminary results show that CGE technique is an efficient tool for characterization and size-dependent separation of water-soluble nanoparticles. In addition, the fraction collection in CGE may be useful in certain special applications such as fabrication of nanodevices in the future.     

The next generation of capillary electrophoresis instruments: Performance of CE‐SDS protein analysis

Over the last decade, capillary electrophoresis gained tremendous importance, because it became an indispensible tool for the quality control of biologics, e.g. therapeutic antibodies. Consequently, there has been a continuous development within the CE market. Microchip techniques have been established in the last years. Further trends are complete solutions for specific applications by the usage of reagent kits. Step by step instructions and facilitated handling of the instruments are becoming more common. This work focuses on the sized‐based protein analysis with CE‐SDS. The instruments CE 7100 by Agilent Technologies, LabChip® GXII Touch HT by PerkinElmer, Maurice S. by Protein Simple and PrinCE NextI870 by Prince Technologies have been evaluated, mainly analyzing protein mixtures of different molecular weights in long series. Published data of the PA 800 plus by SCIEX are also included in the tabled results. Precision, reliability, flexibility, and speed have been identified as the most important performance parameters, others such as resolution, sensitivity, linearity, ease of use and sustainability have also been considered. All tested instruments have shown an excellent performance. Depending on application and necessities, each user can find the most appropriate one.     

A semipermanent coating for preventing protein adsorption at physiological pH in kinetic capillary electrophoresis

Protein adsorption to the inner capillary wall hinders the use of kinetic capillary electrophoresis (KCE) when studying noncovalent protein-ligand interactions. Permanent and dynamic capillary coatings have been previously reported to alleviate much of the problems associated with protein adsorption. The characteristic limitations associated with permanent and dynamic coatings motivated us to look at a third type of coating - semipermanent. Here, we demonstrate that a semipermanent capillary coating, designed by Lucy and co-workers, comprised of dioctadecyldimethylammonium bromide (DODAB) and polyoxyethylene (POE) stearate, greatly reduces protein adsorption at physiological pH - a necessary requirement for KCE. The coating (i) does not inhibit protein-DNA complex formation, (ii) prevents the adsorption of the analytes, and (iii) supports an electoosmotic flow required for many applications of KCE. The coating was tested in three physiological buffers using a well-known DNA aptamer and four proteins that severely bind to bare silica capillaries as standards. For every protein, a condition was found under which the semipermanent coating effectively suppresses protein adhesion. While no coating can completely prevent the adsorption of all proteins, our findings suggest that the DODAB/POE stearate coating can have a broad impact on CE at large, as it prevents the absorption of several well studied, highly adhesive proteins at physiological pH.     

Nonaqueous and aqueous capillary electrophoresis of synthetic polymers

In this work, the use of capillary electrophoresis (CE) to analyze synthetic polymers is reviewed including works published till February 2004. The revised works have been classified depending on the CE mode (e.g., free solution capillary electrophoresis, capillary gel electrophoresis, etc.) and type of buffer (i.e., nonaqueous, aqueous and hydro-organic background electrolytes) employed to separate synthetic macromolecules. Advantages and drawbacks of these different separation procedures for polymer analysis are discussed. Also, physicochemical studies of complex polymer systems by CE are reviewed, including drug release studies, synthetic polyampholytes, dendrimers, fullerenes, carbon nanotubes and associative copolymers.     

Quantitation in two-dimensional fluorescence difference gel electrophoresis: effect of protein fixation

Analyzing a large number of unfixed gels in a 2-D fluorescence difference gel electrophoresis (2-DIGE) experiment presents a challenge of avoiding variable protein diffusion within and across the comparison groups. The characteristics of protein detection and quantitation in a 2-D differential in gel fluorescence experiment were compared for gels with and without protein fixation. The current study tests and concludes that when dealing with a large sample size with variable protein diffusion across the 2-D gel over a period of 2-4 days, it is a preferred choice to fix the gel without affecting the protein quantitation.     

Rapid determination of globin chains in red blood cells by capillary electrophoresis using INSTCoated fused‐silica capillary

A laboratory‐made INSTCoated fused‐silica capillary has been newly used for CE separation of four mixtures of proteins in sodium phosphate BGEs at pH 3.0 and 2.5, respectively. The obtained separation efficiencies range from 145 000 theoretical plates per meter for myoglobin to 1 216 000 m^?1 for lysozyme. A total of 49–89% of the number of theoretical plates was obtained in a commercial polyvinyl alcohol coated capillary compared to the INSTCoated capillary under the same experimental conditions, 0–86% was obtained in a laboratory polyacrylamide‐coated capillary, and only 0–6% was obtained in an uncoated fused‐silica capillary. The RSD values for the intraday repeatability for an INSTCoated capillary were 0.1–1.0% (migration time) and 0.3–2.4% (peak area); RSD values for the interday repeatability in the same capillary are 0.6–1.4% (migration time) and 2.4–5.5% (peak area); RSD values for interday repeatability between different capillaries equaled 1.7–2.1% (migration time) and 2.8–10.9% (peak area). The INSTCoated capillary has been further used for rapid determination of globin chains isolated from red blood cells. A separation of α and β chains prepared from adult blood has been completed in 3 min with a peak resolution of 1.3, and the separation of α and ^Gγ chains prepared from newborn blood took 3 min with a peak resolution of 3.6.     

Telomerase activity measurement in magnetically captured epithelial cells: comparison of slab-gel and capillary electrophoresis

We have compared telomerase activity measurements by slab-gel and capillary electrophoresis in cultured cells (A549 and H125 human cancer cell lines) and in cells isolated from clinical peripheral blood specimens epithelial cells of patients with lung and esophageal cancer. Telomerase activity was determined using the telomerase repeat amplification protocol (TRAP) assay with phosphoimager scanning of slab-gels and by laser-induced fluorescence capillary electrophoresis (LIF-CE). Experiments using A549 and H125 cells were performed to determine the reproducibility of each method and to identify the contribution of each stage of the TRAP/polymerase chain reaction (PCR) assay to the variability. In these experiments, it was found that more than half of the overall variability (coefficient of variation, CV = 35%) of the slab-gel method and almost all of the overall variability (CV = 20%) of the CE method was due to the PCR stage of the TRAP assay. In the clinical samples, classification as positive or negative was by visual inspection of the slab-gel and CE electropherograms for the presence of the characteristic 6 base-pair TRAP ladder and by GeneScan analysis of the CE. We examined several criteria including the use of 3, 4, or 5 TRAP bands as the definition of a positive test. Using the slab-gel method, the 5-band criterion gave 40% sensitivity with 100% specificity (no false positives in inactive controls). The CE method yielded a comparable 38% sensitivity and 100% specificity using this criterion. These data indicate that detection of telomerase activity in epithelial cells isolated from peripheral blood has a useful level of sensitivity and specificity and may be useful in the detection and monitoring of aerodigestive cancers. However, analysis by slab-gel is cumbersome and the precision is poor (inter-replicate CV = 20%) compared to LIF-CE (CV = 5%). A high-throughput CE-LIF detection platform will be indispensable for validation studies of telomerase activity measurements.     

Quaternized celluloses as new dynamic coatings in capillary electrophoresis for basic protein separation

In this work, a series of quaternized celluloses (QCs), homogeneously synthesized in the NaOH/urea aqueous solutions, were studied as dynamic coatings for capillary electrophoresis. Capillaries coated with these cationic cellulose derivatives at the concentration as low as 3 μg/mL were able to generate a stable, reversed electroosmotic flow. The effects of QC molecular parameters, such as the degree of cationic substitution and molecular weight, and the effect of buffer pH on the EOF mobility as well as the separation of basic proteins were investigated in detail. It was shown that the use of QC coatings in CE could drastically reduce the analysis time and improve the separation performance within a broad pH range. Five basic proteins, that is, lysozyme, ribonuclease A, cytochrome C, bovine pancreatic trypsin inhibitor, and chymotrypsinogen were baselinely separated even at pH 8.0. The separation efficiency and analysis reproducibility demonstrated that the QC coatings were efficient in minimizing the adsorption of basic proteins on the fused silica capillary. The successful performance was further demonstrated for biosample analysis.     

Determination of oversulfated chondroitin sulfate and dermatan sulfate impurities in heparin by capillary electrophoresis

Recently, oversulfated chondroitin sulfate (OSCS) present in certain lots of heparin was identified as the toxic contaminant responsible for severe side effects following intravenous heparin administration. The United States Pharmacopeia (USP) and European Pharmacopeia (Eur.Ph.) announced an immediate revision of their monographs for heparin sodium by adding two US Food and Drugs Administration-recommended tests for OSCS based on nuclear magnetic resonance and capillary electrophoresis (CE). However, the proposed CE method provides only partial separation of the OSCS contaminant from heparin, thereby hindering appropriate impurity profiling. Here we present an improved CE method that is especially useful for the reliable quantification of OSCS in heparin samples, but also allows determination of the common impurity dermatan sulfate (DS). Parameters such as type and concentration of background electrolyte, capillary temperature, sample concentration and injection volume were investigated and optimized. Enhancement of the OSCS–heparin separation was achieved by using high concentrations of Tris phosphate (pH 3.0) as background electrolyte. High currents and excessive Joule heating were prevented by employing fused-silica capillaries with an internal diameter of 25 μm. Good separations of OSCS, heparin and DS are obtained within 17 min. The method permits injection of relatively high heparin concentrations (up to 50 mg/ml) and large sample volumes (up to 5% of the capillary volume) allowing OSCS and DS determination in heparin down to the 0.05% and 0.5% (w/w) level, respectively. The CE method is shown to be repeatable and linear (R² > 0.99) for OSCS, heparin and DS. CE analyses of OSCS-contaminated heparin samples and different heparin standards further demonstrate the utility of the method.     

Use of quasi-isoelectric buffers to limit protein adsorption in capillary zone electrophoresis

The use of quasi-isoelectric buffers consisting of narrow pH cuts of carrier ampholytes (NC) has been investigated to limit protein adsorption on capillary walls during capillary zone electrophoresis experiments. To quantify protein adsorption on the silica surface, a method derived from that of Towns and Regnier has been developed. alpha-Lactalbumin (14 kDa, pI 4.8) and alpha-chymotrypsinogen A (25 kDa, pI 9.2) have been used as model proteins. Acidic narrow pH cuts of carrier ampholytes (NC, pH 3.0) obtained from fractionation of Serva 4-9 carrier ampholytes were used as BGE in bare-silica capillaries, and allowed to decrease significantly protein adsorption, as compared to experiments performed with classical formate buffer. The use of NC as BGE appeared to be as efficient as the use of polydimethylacrylamide coating to prevent protein adsorption. This increase of protein recovery when using NC was attributed to the interaction of carrier ampholytes with the silica surface, leading to a shielding of the capillary wall.     

Rapid detection of perchlorate in groundwater using capillary electrophoresis

Summary Perchlorate is a groundwater contaminant originating from facilities that manufacture and test solid rocket fuel. A new technology, capillary electrophoresis, has the potential to measure perchlorate rapidly and inexpensively in water samples. With its speed and simplicity, this method would complement existing methods. The perchlorate anion is routinely detected in water samples using high performance ion exchange chromatography, a very sensitive yet time consuming and expensive method. In this work, the parameters for detection of perchlorate are optimized to permit detection of 0.400 mgL⁻¹ perchlorate in a standard solution. The usefulness of this technology is demonstrated for measuring perchlorate in several ground-water samples from the Western United States. The results demonstrate that CE can be used to rapidly screen environmental samples for perchlorate at intermediate to high levels (greater than 0.400 mgL⁻¹). This technique allows faster, easier screening of potential contamination sites and could complement the use of ion exchange chromatography for groundwater testing.     

On-line microheterogeneity analysis and rapid phenotyping of haptoglobin by capillary electrophoresis using sodium dodecyl sulfate as additive

To improve the detection sensitivity and determine phenotypes of haptoglobin (Hp), a prefilling technique was developed and tested in capillary electrophoresis (CE) with UV–vis absorbance detection. Adding 0.01% sodium dodecyl sulfate (SDS) to the protein sample and 0.1% SDS to the prefilling buffer solution, on-line stacking and microheterogeneity separation of Hp were achieved. In addition, the influences of pH, buffer concentration, sample and prefilling buffer SDS concentration upon resolution were examined. Under optimized conditions, Hp-microheterogeneity was well resolved and two phenotypes of Hp (Hp 1-1 and Hp 2-2) were differentiated. This method was applied to the analysis of sera from normal individuals and β-Thalassemia patients. After the depletion of albumin (HSA) and immunoglobulin G (IgG), this method allowed to determine two phenotypes in different individuals and to detect the decrease of Hp in β-Thalassemia patients. Featuring high efficiency, speed and simplicity, the proposed method shows great potential for use in clinical diagnosis and proteome research.