Detection of CFTR mutations using temporal temperature gradient gel electrophoresis

Cystic fibrosis (CF), caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, is one of the most common autosomal recessive diseases with variable incidences and mutation spectra among different ethnic groups. Current commercially available mutation panels designed for the analysis of known recurrent mutations have a detection rate between 38 to 95%, depending upon the ethnic background of the patient. We describe the application of a novel mutation detection method, temporal temperature gradient gel electrophoresis (TTGE), to the study of the molecular genetics of Hispanic CF patients. TTGE effectively identified numerous rare and novel mutations and polymorphisms. One interesting observation is that the majority of the novel mutations are splice site, frame shift, or nonsense mutations that cause severe clinical phenotypes. Our data demonstrate that screening of the 27 exons and intron/exon junctions of the CFTR gene by TTGE greatly improves the molecular diagnosis of Hispanic CF patients.     

Band-broadening in capillary zone electrophoresis with axial temperature gradients

It is widely accepted that Joule heating effects yield radial temperature gradients in capillary zone electrophoresis (CZE). The resultant parabolic profile of electrophoretic velocity of analyte molecules is believed to increase the band-broadening via Taylor-Aris dispersion. This typically insignificant contribution, however, cannot explain the decrease in separation efficiency at high electric fields. We show that the additional band-broadening due to axial temperature gradients may provide the answer. These axial temperature variations result from the change of heat transfer condition along the capillary, which is often present in CZE with thermostating. In this case, the electric field becomes nonuniform due to the temperature dependence of fluid conductivity, and hence the induced pressure gradient is brought about to meet the mass continuity. This modification of the electroosmotic flow pattern can cause significant band-broadening. An analytical model is developed to predict the band-broadening in CZE with axial temperature gradients in terms of the theoretical plate height. We find that the resultant thermal plate height can be very high and even comparable to that due to molecular diffusion. This thermal plate height is much higher than that due to radial temperature gradients alone. The analytical model explains successfully the phenomena observed in previous experiments.     

Detection of mitochondrial DNA mutations using temporal temperature gradient gel electrophoresis

Mitochondrial disorders are a group of clinically and genetically heterogeneous diseases. Common recurrent mitochondrial DNA (mtDNA) point mutations account for the molecular defects of a small proportion of patients. In order to identify mtDNA mutations, comprehensive mutational analysis of the entire mitochondrial genome is necessary. We developed the temporal temperature gradient gel electrophoresis (TTGE) method to screen for mutations in mtDNA. The entire mitochondrial genome was amplified using 32 pairs of overlapping primers followed by TTGE analysis of the DNA fragments. TTGE method was first validated on 200 DNA fragments containing known mutations or polymorphisms. On TTGE, homoplasmic nucleotide substitutions show a single band shift and heteroplasmic mutations show multiple banding patterns. The known mutations or polymorphisms were correctly identified. TTGE was then used to screen for unknown mutations in the mitochondrial genome. DNA banding patterns, deviated from wild-type, suggestive of either homoplasmic or heteroplasmic mutations, were followed by direct DNA sequencing to identify the mutations. Numerous mutations and polymorphisms were detected. The results demonstrated that TTGE detects and distinguishes heteroplasmic mutations from homoplasmic polymorphisms. It also detects heteroplasmic changes in the background of a homoplasmic polymorphism. Overall, TTGE was proven to be a simple, rapid, sensitive, and effective mutation detection method.     

Detection of K-ras exon 1 mutations by constant denaturant capillary electrophoresis

Among various mutation detection methods, constant denaturant capillary electrophoresis (CDCE) is one of the most common techniques for rapid identification of known or unknown mutations. In this report, a CDCE analysis method with homemade linear polyacrylamide (LPA) kit was developed on ABI 310 genetic analyzer, the effect and relationship of various denaturing factors in CDCE analysis were investigated and K-ras gene mutations of 31 coloerctal cancer patients were detected. Results indicate that, with the increase of chemical danaturant concentration, the optimum temperature was lowered, and when the concentration of urea (formamide) was higher than 7 M (40%), the homoduplex and heteroduplex of mutant samples were separated with difficulty. Detection results of K-ras gene in colorectal samples indicated that mutations were present in eight (26%) of 31 patients; most mutations were localized in codon 12, which is thought to be a critical step and plays an important role in human colorectal carcinogenesisas.     

Detection of paracetamol by capillary electrophoresis with chemiluminescence detection

Indirect detection of paracetamol was accomplished using a capillary electrophoresis-chemiluminescence (CE-CL) detection system, which was based on its inhibitory effect on a luminol-potassium hexacyanoferrate(III) (K₃[Fe(CN)₆]) CL reaction. Paracetamol migrated in the separation capillary, where it mixed with luminol included in the running buffer. The separation capillary outlet was inserted into the reaction capillary to reach the detection window. A four-way plexiglass joint held the separation capillary and the reaction capillary in place. K₃[Fe(CN)₆] solution was siphoned into a tee and flowed down to the detection window. CL was observed at the tip of the separation capillary outlet. The CL reaction of K₃[Fe(CN)₆] oxidized luminol was employed to provide the high and constant background. Since paracetamol inhibits the CL reaction, an inverted paracetamol peak can be detected, and the degree of CL suppression is proportional to the paracetamol concentration. Maximum CL signal was observed with an electrophoretic buffer of 30 mM sodium borate (pH 9.4) containing 0.5 mM luminol and an oxidizer solution of 0.8 mM K₃[Fe(CN)₆] in 100 mM NaOH solution. Under the optimal conditions, a linear range from 6.6 × 10⁻¹⁰ to 6.6 × 10⁻⁸ M (r = 0.9999), and a detection limit of 5.6 × 10⁻¹⁰ M (signal-to-noise ratio = 3) for paracetamol were achieved. The relative standard deviation (R.S.D.) of the peak area for 5.0 × 10⁻⁹ M of paracetamol (n = 11) was 2.9%. The applicability of the method for the analysis of pharmaceutical and biological samples was examined.     

Detection in capillary electrophoresis

A review of the four major, on-line, capillary electrophoresis (CE) detection modalities is presented. It is shown that each detection method, fluorescence, absorbance (conventional and nonconventional), electrochemical and refractive index, have distinct advantages and limitations when applied to analysis in a CE format. Various aspects of CE detection are considered and a perspective regarding the applicability of the technique is provided. It is shown that because of widely varying detection limits (ranging from single molecule to 10(-5) M) and detection scheme complexity, the particular application should dictate the selection of detection methodology in CE.     

Flavonoid separation by capillary electrophoresis. Effect of temperature and pH

Summary The use of capillary electrophoresis for the analysis of selected flavonols present in fruit juices and wines (kaempferol-3-rutinoside, rutin, avicularin, quercitrin, isoquercitrin, isorhamnetin, kaempferol and quercetin) was explored, and the effect of pH and temperature on the separation studied. The method had good reproducibility and analyses were carried out in less than 10 minutes.     

Flavonoid separation by capillary electrophoresis. Effect of temperature and pH

Summary The use of capillary electrophoresis for the analysis of selected flavonols present in fruit juices and wines (kaempferol-3- rutinoside, rutin, avicularin, quercitrin, isoquercitrin, isorhamnetin, kaempferol and quercetin) was explored, and the effect of pH and temperature on the separation studied. The method had good reproducibility and analyses were carried out in less than 10 minutes.     

Detection of abnormal haemoglobin by capillary electrophoresis and structural identification.

Haemoglobin obtained from a male adult Ghanian with retinopathy, which was probably caused by haemoglobinopathy was analysed by capillary electrophoresis (CE) for clinical diagnosis. Two major peaks, which were in the ratio of nearly one, were detected. The elution times of these peaks (HbXI and HbXII) were faster than that of normal haemoglobin (HbA). The existence of two different abnormal types of haemoglobin was clear in the patient blood. The following sequence analysis revealed that the first peak (HbXI) was HbC and the second (HbXII) was HbS on the electropherogram, and that the patient was a heterozygote of HbS and HbC (HbSC disease). One of the diagnostic processes in a haemoglobin disease was shown by the combined use of CE, HPLC and a protein sequencer.     

Detection of apolipoprotein E genotypes by capillary electrophoresis

The apolipoprotein E (apo-E) genotype of an individual is of significant relevance in the associated risk of developing cardiovascular disease and late-onset Alzheimer's disease. Detection of the six common apo-E genotypes is based on the restriction fragment length polymorphisms (RFLPs) arising from the abolition or creation of HhaI restriction sites within an amplified target DNA sequence of the apo-E gene. Genomic DNA was extracted from leukocytes, a 230 bp target sequence within the apo-E gene was amplified by polymerase chain reaction (PCR) and digested with HhaI, and the restricted DNA fragments separated by capillary electrophoresis (CE). This was performed on the BioFocustrade mark 3000 automated CE system equipped with an experimental laser-induced fluorescence (LIF) detector (Bio-Rad Laboratories, Hercules, CA), using capillaries (27 cm length, 75 mum i.d.) coated internally with polyaminoacryloylethoxyethanol. The analysis buffer (2xTris borate-EDTA, pH 8.3) was supplemented with a proprietary sieving polymer and 0.05 muM thiazole orange six. Samples were injected electrophoretically. Separations were carried out at 40 degrees C under constant voltage, and the emitted fluorescence detected at 515 nm. Restriction fragment lengths of the cleaved PCR products were estimated from the migration times, with a 20/100 bp ladder (Bio-Rad Laboratories 20/100 bp molecular ruler) serving as reference. Six different reproducible patterns were obtained for the six common apo-E genotypes, with good resolution of the component restriction fragments. The calculated sizes of the separated peaks closely corresponded with the predicted restricted fragment lengths for each specific genotype. We believe this is the first published report demonstrating the feasibility of automating the post-PCR detection of the apo-E RFLPs(2). This methodology overcomes the most labour-intensive step in apo-E genotyping, thus making it amenable to routine clinical application.     

High-throughput screening of genetic mutations/polymorphisms by capillary electrophoresis

Genetic mutations/polymorphisms analyses play a great role in genetic and medical research, and clinical diagnosis. Most conventional methods for genetic assay are based on slab gel electrophoresis that is both labor-intensive and time-consuming. Recently, capillary electrophoresis (CE) has been used for genetic analysis instead of conventional slab gel electrophoresis. This technique can be automated and is characterized by short analysis time, small sample and reagents requirements, and high separation efficiency. CE has been successfully applied for mutation detection involving human tumor suppressor genes, oncogenes and disease-causing genes, and has shown a great potential for genetic mutation/polymorphism screening of large numbers of clinical samples. In this article, an overview of the fundamental aspects of mutation/polymorphism assay methods in combination with CE is given and some key applications are summarized.     

Fluorescence-based single-strand conformation polymorphism analysis of mutations by capillary electrophoresis

Capillary electrophoresis in combination with fluorescence-based single-strand conformation polymorphism (SSCP) analysis was used to screen for known mutations as well as for unknown mutations. The mutations causing hemochromatosis and thrombogenetic diseases (factor V Leiden mutation and prothrombin mutation) are well defined. Familial hypercholesterolemia is caused by mutations in the low density lipoprotein (LDL) receptor gene. Because the mutations are heterogeneously localized in all 18 exons of the LDL receptor gene, effective screening procedures are necessary. The three well known mutations and 59 of 61 previously characterized mutations in the LDL receptor gene were detected by a distinct abnormal fragment pattern in capillary electrophoresis. The remaining two mutations in the LDL receptor gene showed only slight abnormalities under standard electrophoresis conditions (13 kV, 30 degrees C, 30 min). However, the abnormal pattern could be amplified by increasing the electrophoresis temperature. In all cases, heterozygous and homozygous mutations could clearly be differentiated from wild-type alleles. Because of the high efficiency of mutation detection, capillary electrophoresis in combination with fluorescence-based SSCP analysis would be attractive for the detection of well-defined mutations as well as for the screening of unknown mutations. The accuracy and the degree of automation make this technique well suited for routine genetic diagnosis.     

Chiral separation by capillary electrophoresis with oligosaccharides.

Maltodextrins, i.e., mixtures of linear alpha-(1-4)-linked D-glucose polymers, were found to be effective as chiral electrolyte modifiers to perform direct, rapid separations by capillary electrophoresis of racemic mixtures of 2-arylpropionic acid non-steroidal anti-inflammatory compounds and coumarinic anticoagulant drugs, and also diastereomeric cephalosporin antibiotics. Enantioselectivity seemed to be dependent on an as yet unidentified combination of variables.     

Detection of carbohydrates in capillary electrophoresis

This review focuses on recent developments in sensitive detection modes for carbohydrates after separation by capillary electrophoretic methods. To bring detection sensitivity for carbohydrates analysis in line with current methods in protein sequencing, concentration detection limits of 10⁻⁶ molar or better are requires. A discussion of mass detection limits and concentration detection limits is followed by an overview of detection modes for natural and labeled carbohydrates. Amperometric detection and UV and laser-induced fluorescence detection after reductive amination, in particular with 8-aminonaphthalene-1,3,6-trisulfonic acid (ANTS), are discussed in more detail. Finally, the paper outlines developments to be expected in the near future, focusing on the needs in glycobiology such as improved sensitivity and selectivity.     

Infrared-based temperature measurements in capillary electrophoresis

In capillary electrophoresis (CE), the temperature inside the capillary is one of the most important parameters. In a concept for Analytical Instrument Qualification (AIQ) of CE systems, the temperature accuracy and stability have to be included. This fact requires an accurate look at the measurement of temperature which is generated by the applied electrical power. The generation of Joule heating is measured on the outside of the capillary using an infrared (IR) thermometer. The thermometer linearity is demonstrated over a wide range of various electrical field strength, buffer systems, and different capillary inner diameters. A slope of 6.3 °C m/W was found for the optimal thermometer capillary distance of 8 mm. Furthermore, the temperature measurements are highly precise, depending almost solely on the current variability. The proposed method is compared with three methods calculating the temperature from the conductance, the electroosmotic velocity, or the current. These indirect methods estimate slopes ranging from 7 to 10 °C m/W. In addition, the maximal suitable electrical power per unit length is estimated. Joule heating can often be tolerated up to 4 W/m. However, sensitive analytes can already be affected by using more than 1 W/m. In conclusion, the consideration of the temperature is essential for not only Analytical Instrument Qualification, but also certainly useful for method optimisation and method transfer.     

pH programming in capillary electrophoresis by means of temperature programming

When using a background electrolyte with a buffer having strong temperature dependence of pK, different operating temperatures result in different operating pH values, using the same background electrolyte (BGE). It has been shown that this can be used to fine-tune selectivities of sample mixtures of weak analytes. Capillary electrophoresis (CE) equipment is designed to operate under isothermal conditions, but by proper programming, a very reproducible temperature and thus BGE pH program during the analysis can be realized. This was experimentally verified and illustrated by computer simulations. Equipment characteristics have been determined, and possibilities and restrictions to make use of this feature are presented.     

Two-dimensional gel electrophoresis of platelet polypeptides with immobilized pH gradients in capillary tubes

Two-dimensional electrophoresis (2-DE) with immobilized pH gradient (IPG) gels in capillary tubes was used in the first-dimensional isoelectric focusing (IEF) for the separation of human platelet polypeptides. Two types of IPG tube gels, pH ranges 4-8 and 7-10, containing 8 M urea, 1% Nonidet P-40 and 0.1% pH 3.5-10 Ampholine carrier ampholytes (CA) were prepared by a simple method not requiring special equipment. The addition of CA to both gel and sample solutions was essential in the tube gel IPG system. Proteins were visualized by a modification of Wray's silver-staining technique. The degree of resolution and the number of spots observed on an IPG 2-DE gel with pH 4-8 were comparable with those obtained with O'Farrell's high-resolution 2-DE. Approximately 200 basic polypeptides, which are difficult to separate by conventional CA-based IEF 2-DE or the non-equilibrium pH gradient system, were well resolved by 2-DE with a pH 7-10 IPG tube gel in the first-dimension. The gel patterns with either pH gradient 4-8 or 7-10 were highly reproducible among gels prepared and run simultaneously. These results demonstrated the potential and usefulness of the 2-DE system with IPG gels in capillary tubes.     

Influence of temperature control in capillary electrophoresis

We have investigated the influence of capillary temperature on migration time and peak area and have evaluated different cooling systems. It was found that for applied voltages below 15 kV (i.e. those most frequently used) temperature control effectively improves peak area reproducibility but has less effect on migration time.     

Separation principles of cycling temperature capillary electrophoresis

High throughput means to detect and quantify low-frequency mutations (<10(-2) ) in the DNA-coding sequences of human tissues and pathological lesions are required to discover the kinds, numbers, and rates of genetic mutations that (i) confer inherited risk for disease or (ii) arise in somatic tissues as events required for clonal diseases such as cancers and atherosclerotic plaque.While throughput of linear DNA sequencing methods has increased dramatically, such methods are limited by high error rates (>10(-3) ) rendering them unsuitable for the detection of low-frequency risk-conferring mutations among the many neutral mutations carried in the general population or formed in tissue growth and development. In contrast, constant denaturing capillary electrophoresis (CDCE), coupled with high-fidelity PCR, achieved a point mutation detection limit of <10(-5) in exon-sized sequences from human tissue or pooled blood samples. However, increasing CDCE throughput proved difficult due to the need for precise temperature control and the time-consuming optimization steps for each DNA sequence probed. Both of these problems have been solved by the method of cycling temperature capillary electrophoresis (CTCE). The data presented here provide a deeper understanding of the separation principles involved in CTCE and address several elements of a previously presented two-state transport model.     

BRAF mutation detection and identification by cycling temperature capillary electrophoresis

BRAF mutations are found in many human tumors, namely melanomas ( approximately 70%) and colon carcinomas ( approximately 15%). This paper presents a method for identification of exon 15 BRAF mutations by denaturant capillary electrophoresis (CE), an analysis method that is sensitive, cost-effective (involving only polymerase chain reaction (PCR) and electrophoresis) and capable of high-throughput screening. In total, we found 21 (70%) out of 30 melanoma cell lines with BRAF mutations in exon 15: two of which were the p.Val600Asp (c.1799-800TG>AT) mutation, one cell line contained the p.Val600Arg (c.1798-99GT>AG) mutation, and 18 cell lines contained the p.Val600Glu (c.1799T>A) mutation. Of the nine cell lines that did not contain a BRAF mutation, five contained an NRAS mutation at exon 2, and no mutations were detected in NRAS exon 1. There was no overlap of NRAS and BRAF mutations in the same cell line. In addition, we looked at 221 colon biopsy samples and identified one further BRAF mutation, the p.Asp594Gly (c.1781A>G) mutation, in seven samples. The p.Val600Glu mutation was identified in 11 of the colon biopsy samples. Using the four mutations of BRAF exon 15, we then constructed a denaturing CE standard capable of distinguishing between each of the mutations; therefore, sequencing does not need to be performed to confirm the mutation. In conclusion, this sensitive, cost-effective mutation assay for BRAF (and RAS) will provide the opportunity to detect and determine mutations without the need to purify samples for sequencing. Future large-scale studies will provide the clinical usefulness of such mutations.