Rapid microwell polymerase chain reaction with subsequent ultrathin-layer gel electrophoresis of DNA

Large-scale genotyping, mapping and expression profiling require affordable, fully automated high-throughput devices enabling rapid, high-performance analysis using minute quantities of reagents. In this paper, we describe a new combination of microwell polymerase chain reaction (PCR) based DNA amplification technique with automated ultrathin-layer gel electrophoresis analysis of the resulting products. This technique decreases the reagent consumption (total reaction volume 0.75-1 microL), the time requirement of the PCR (15-20 min) and subsequent ultrathin-layer gel electrophoresis based fragment analysis (5 min) by automating the current manual procedure and reducing the human intervention using sample loading robots and computerized real time data analysis. Small aliquots (0.2 microL) of the submicroliter size PCR reaction were transferred onto loading membranes and analyzed by ultrathin-layer gel electrophoresis which is a novel, high-performance and automated microseparation technique. This system employs integrated scanning laser-induced fluorescence-avalanche photodiode detection and combines the advantages of conventional slab and capillary gel electrophoresis. Visualization of the DNA fragments was accomplished by "in migratio" complexation with ethidium bromide during the electrophoresis process also enabling real time imaging and data analysis.     

Ultrathin-layer gel electrophoresis of biopolymers

Emerging need for large-scale, high-resolution analysis of biopolymers, such as DNA sequencing polymerase chain reaction, (PCR) product sizing, single nucleotide polymorphism (SNP) hunting and analysis of protein molecules necessitated the development of automated and high-throughput gel electrophoresis based methods enabling rapid, high-performance separations in a wide molecular weight range. Scaling down electric field mediated separation processes supports higher throughput due to the applicability of higher voltages, thus speeding up analysis time. Indeed, efforts in miniaturization resulted in faster, easier, less costly and more convenient analyses, fulfilling the needs of the emerging biotechnology industry for microscale and massively parallel assays. The two primary approaches in miniaturizing electrophoresis dimensions are the capillary and microslab formats. This latter one evolved towards ultrathin-layer gel electrophoresis which is, except from the thickness of the separation platform, slightly in the upper side of the scale, resulting in considerably easier handling. Ultrathin-layer gel electrophoresis combines the advantages of conventional slab-gel electrophoresis (multilane format) and capillary gel electrophoresis (rapid, high-efficiency separations). It is readily automated, automatic versions of it have been extensively used for large-scale DNA sequencing in the Human Genome Project and more recently became popular in high throughput DNA fragment analysis. Ultrathin-layer techniques are the first step towards the wider use of electrophoresis microchips in perfecting a user-friendly interface between the user and the microdevice.     

Comparative study of capillary zone electrophoresis and high-performance liquid chromatography in the analysis of oligonucleotides and DNA.

Capillary zone electrophoresis and high-performance liquid chromatography were compared with regard to the separation of oligonucleotides and double-stranded DNA. Both anion-exchange and reversed-phase high-performance liquid chromatography on non-porous particles are considered to be superior to capillary electrophoresis in terms of speed and selectivity in the analysis of oligonucleotides up to 30 bases in length. Moreover, reversed-phase chromatography allows the simultaneous purification of detritylated oligonucleotides with recoveries > 90%. Compared with anion-exchange chromatography, there is no need for a subsequent desaltation step because the volatile buffer system can be readily evaporated. With regard to dsDNA, however, the resolving power of capillary electrophoresis cannot be matched by anion-exchange chromatography at present. Moreover, the combined use of hydroxyethylcellulose and ethidium bromide not only yielded a separation efficiency equal to that achieved by means of gel-filled capillaries but also avoids some of their limitations such as the destruction of the gel matrix at high current densities and the bias involved in electrokinetic injection.     

High-throughput genotyping of factor V Leiden mutation by ultrathin-layer agarose gel electrophoresis.

Ultrathin-layer agarose gel electrophoresis is a novel combination of the established methodologies of slab gel electrophoresis and capillary gel electrophoresis. This new format provides a multilane separation platform with rapid analysis time and excellent sensitivity by using laser-induced fluorescence scanning detection system. Sample injection onto the ultrathin-layer separation platform is easily accomplished by membrane mediated loading technology. In this paper, we demonstrate the sensitivity and high-throughput fashion of this novel separation and detection system for rapid genotyping of the coagulation factor V Leiden mutation by polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) analysis. The PCR amplified fragment from exon 10 of the factor V gene was digested by the Mnl I restriction enzyme, followed by automated ultrathin-layer agarose gel electrophoresis analysis with "in migratio" fluorescent labeling during the separation process. Due to its speed and automation, this method should be considered for large scale screening of factor V Leiden mutation.     

Gel and polymer-solution mediated separation of biopolymers by capillary electrophoresis

In the age of genomics and proteomics, high-resolution separation techniques are routinely utilized in an integrated and automated fashion to solve formidable separation problems and provide the means for large-scale analysis of biological samples with excellent resolution. By automating the current manual procedures, capillary gel (CGE) and polymer-solution mediated electrophoresis greatly enhance the productivity of biopolymer analysis while also reducing both analysis time and the human intervention necessary from sample loading to data processing. The advent of this novel and high-performance bioseparation technique has made it possible to sequence the human genome and revealed global changes in the genome and proteome level, bringing about a revolutionary transition in our views of living systems on the molecular basis. CGE and polymer-solution mediated electrophoresis and related microseparation methods (e.g., electrophoresis microchips) are quickly becoming important separation and characterization tools in analytical biochemistry and molecular biology. This review gives an overview of the key application areas of DNA, protein, and complex carbohydrate analysis, and summarizes the latest developments on CGE column technology, including capillary coatings and sieving polymer matrices. Micropreparative aspects and related microseparation techniques are also discussed.     

Isolation of Xis Gen Fragment of λ Phage from Agarose Gel Using Magnetic Particles for Subsequent Enzymatic DNA Sequencing

Gel electrophoresis is one of the most important methods used in biochemistry and molecular biology. The recovery of analytes from the gel required for subsequent analysis including amplification by polymerase chain reaction (PCR) or DNA sequencing is an issue due to the gel contamination. Among the other methods used for sample recovery, the application of nanomaterials is also being investigated. In this study, the applicability of magnetic particles (1 μm) for isolation of DNA fragment from agarose gel with subsequent DNA sequencing was investigated. Electrochemical analysis and DNA sequencing was used to investigate the recovery yield. The influence of dilution of the gel prior to the purification was investigated and the linear dependence with regression coefficient R ² = 0.9972 was obtained using square wave voltammetry. Moreover, bioinformatic analysis was used for comparison of obtained sequences, and simple and easy identification of non-systematic errors caused by both fluorescence labeling reaction and electrophoretic separation. It was found that magnetic nanoparticles based isolation markedly lowered the errors occurring during sequencing of the isolated DNA fragment from 7 to 1 %.     

High resolution-separation of DNA bands by electrophoresis with a long gel in a fluorescence-detection DNA sequencer.

A high-resolution separation of DNA bands is achieved by electrophoresis with a long gel in DNA base sequencing using fluorescence detection. We separate 760 and 761 base DNA fragments using the 93 cm migration electrophoresis optimized for the separation of DNA bands. A T7 DNA polymerase and an Mn++ buffer are used in sequencing reactions to obtain fluorescence peaks of uniform strength, and the peak areas in the spectrum are used for recognizing the peak number in a cluster of successive peaks. This method is successfully applied to the DNA fragment spectrum obtained by 93 cm migration electrophoresis, which results in a single-band differentiation of bands of 1040 base DNA.     

A theoretical study of an empirical function for the mobility of DNA fragments in sieving matrices

The separation of DNA fragments by gel electrophoresis has been studied extensively over the last two decades. More recently, similar studies have been carried out to characterize the separation achieved by the current capillary array electrophoresis systems and their sieving polymer solutions. In all cases, at least three different mobility regimes have been shown to exist: the Ogston regime when the radius of gyration of the DNA fragment is smaller than the pore size, the reptation regime when the DNA is larger than the pore size but remains in a random coil conformation, and finally the reptation-with-orientation regime where the DNA orients in the field direction and essentially all resolution is lost. Unfortunately, although theory helps us understand the different regimes and how to properly exploit them, we still have no theory-based general equations that would apply to all regimes. Such equations would be especially useful to analyze data, optimize separation systems and interpolate mobilities to estimate unknown molecular sizes. Recently, van Winkle, Beheshti and Rill (Electrophoresis 2002, 23, 15-19) proposed an intriguing empirical formula that seems to adequately fit the mobility of dsDNA fragments across all three regimes. In this paper, I investigate the relation between this empirical formula and the known theories of gel electrophoresis, and I study the dependence of its fitting parameters upon the experimental conditions. Finally, I examine how this equation may need to be modified to capture the more subtle details predicted by fundamental theories of DNA gel electrophoresis.     

Fast separation of oligonucleotide and triplet repeat DNA on a microfabricated capillary electrophoresis device and capillary electrophoresis

A laser-induced fluorescence detection system coupled with a highly sensitive silicon-intensified target (SIT) camera is successfully applied to the imaging of a band for DNA fragment labeling by fluorescence dye in a microchannel, and to the visualizing of the separation process on a microfabricated chip. We demonstrated that an only 6 mm separation channel is sufficient for the separation of triplet repeat DNA fragment and DNA molecular marker within only 12 s. The separation using the microfabricated capillary electrophoresis device is confirmed to be at least 18 times faster than the same separation carried out by conventional capillary electrophoresis with 24.5 cm effective length. The use of a short capillary with 8.5 cm effective length is also efficient for fast separation of DNA; however, the microchip technology is even faster than capillary electrophoresis using a short capillary.     

Ultra-thin-layer agarose gel electrophoresis. I. Effect of the gel concentration and temperature on the separation of DNA fragments

A novel, rapid and efficient separation method is described for the analysis of double stranded (ds) DNA fragments in the form of horizontal ultra-thin-layer agarose gel electrophoresis. This separation technique combines the multilane, high-throughput separation format of agarose slab gel electrophoresis with the excellent performance of capillary electrophoresis. The electrophoretic separation of the fluorophore (Cy5)-labeled dsDNA molecules were imaged in real time by a scanning laser-induced fluorescence/avalanche photodiode detection system. Effects of the gel concentration (Ferguson plot) and separation temperature (Arrhenius plot) on the migration characteristics of the DNA fragments are discussed. An important genotyping application is also shown by characterizing the polymorphic region (2× or 4×48 base pair repeats) of the dopamine D₄ receptor gene (D₄DR, exon III region) for ten individuals, using PCR technology with Cy5-labeled primers and ultra-thin-layer agarose gel electrophoresis.     

High-throughput separation of DNA and proteins by three-dimensional geometry gel electrophoresis: feasibility studies

We report a novel separation method that is applicable to both DNA and protein samples, based on electrophoresis in a three-dimensional (3-D) geometry. In contrast to conventional electrophoresis, samples are applied in a two-dimensional, planar array to one of the surfaces of a 3-D geometry separation medium. Loading onto a plane results in a very high sample capacity. Sample migration and separation occur along the third spatial dimension, which is perpendicular to the loading plane. The key problem of electrophoresis in a 3-D geometry separation setup is that temperature gradients are caused by Joule's heat, affecting the electrical conductivity and viscosity of the separation medium. A means of achieving straight sample migration under these circumstances is to force heat flow through the separation medium parallel to the axis of sample migration. This can be done by dissipating the heat via the electrode sides of the gel and blocking any other heat transfer. The separation of DNA and proteins by this method has been tested using agarose gel electrophoresis, polyacrylamide gel electrophoresis, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Data were acquired off-line by conventional staining methods as well as on-line by detection of laser-induced fluorescence. We describe how to excise samples from the separation medium for preparative purposes. Possible unique applications of this 3-D geometry electrophoresis separation method are also discussed.     

The use of denaturing gradient gel electrophoresis to screen for DNA sequence polymorphisms in the human factor VIII gene

We describe the use of denaturing gradient gel electrophoresis to screen for DNA sequence polymorphisms in the human factor VIII gene. DNA fragments that differ in sequence by only a single base pair can be separated on denaturing gradient gels due to changes in their melting behavior. Previous studies have demonstrated the use of denaturing gradient gels to detect sequence changes in human genomic DNA, including mutations in the beta globin gene and polymorphisms on chromosome 20. We have begun to use denaturing gradient gels to look for polymorphisms within the human factor VIII gene. The DNA sequences of seven cloned fragments from introns in the human factor VIII gene were determined and used to predict a melting map for each fragment. The melting behavior of each cloned fragment was evaluated by electrophoresis into denaturing gradient gels. Appropriate fragments were then used as radioactive probes for hybridization to human DNA samples that had been digested with restriction enzymes. Heteroduplexes formed between the probe and genomic DNA samples were electrophoresed into denaturing gradient gels. The final positions of heteroduplex bands were determined by autoradiography. We describe a general approach for using denaturing gradient gel electrophoresis to find DNA polymorphisms, with particular emphasis on the predictive value of DNA sequence data. We compare the efficiency of polymorphism detection by denaturing gradient gel electrophoresis with detection by restriction fragment length polymorphism (RFLP) analysis. The factor VIII gene appears to have a low level of DNA sequence polymorphism.(ABSTRACT TRUNCATED AT 250 WORDS)     

High-sensitivity capillary gel electrophoretic analysis of DNA fragments on an electrophoresis microchip using electrokinetic injection with transient isotachophoretic preconcentration

The research adopted a single-channel microchip as the probe, and focused electrokinetic injection combined with transient isotachophoresis preconcentration technique on capillary electrophoresis microchip to improve the analytical sensitivity of DNA fragments. The channel length, channel width and channel depth of the used microchip were 40.5 mm, and 110 and 50 μm, respectively. The separation was detected by CCD (charge-coupled device) (effective LENGTH=25 mm, 260 nm). A 1/100 diluted sample (0.2 mg/l of each DNA fragment) of commercially available stepladder DNA sample could be baseline separated in 120 s with S/N=2–5. Compared with conventional chip gel electrophoresis, the proposed method is ideally suited to improve the sensitivity of DNA analysis by chip electrophoresis.     

Star-shaped polymers for DNA sequencing by capillary electrophoresis

The separation and sequencing of DNA are the main objectives of the Human Genome Project, and this project has also been very useful for gene analysis and disease diagnosis. Capillary electrophoresis (CE) is one of the most common techniques for the separation and analysis of DNA. DNA separations are usually achieved using capillary gel electrophoresis (CGE) mode, in which polymer gel is packed into the capillary. Compared with a traditional CGE matrix, a hydrophilic polymer matrix, which can be adsorb by the capillary wall has numerous advantages, including stability, reproducibility and ease of automation. Various water-soluble additives, such as linear poly(acrylamide) (PAA) and poly(N,N-dimethylacrylamide) (PDMA), have been employed as media. In this study, different star-shaped PDMA polymers were designed and synthesized to achieve lower polymer solution viscosity. DNA separations with these polymers avoid the disadvantages of high viscosity and long separation time while maintaining high resolution (10 bp between 271 bp and 281 bp). The influences of the polymer concentration and structure on DNA separation were also determined in this study; higher polymer concentration yielded better separation performance, and star-like polymers were superior to linear polymers. This work indicates that modification of the polymer structure is a potential strategy for optimizing DNA separation.     

Capillary electrophoresis of peptides. Analysis of adrenocorticotropic hormone-related fragments.

Capillary electrophoresis can be used successfully to analyse small peptides to give additional information to that obtained using high-performance liquid chromatography (HPLC). The separation of a modified adrenocorticotropic hormone (4-9) fragment (Org 2766) and several of its fragments was investigated using capillary zone electrophoresis. Prediction of migration in aqueous systems using pKa-related data and the migration behaviour using sodium dodecyl sulphate in the buffer are discussed, as is the choice of buffer systems. The electrophoretic patterns are compared with the HPLC separation.     

Pharmaceutical applications of micelles in chromatography and electrophoresis

This review surveys the use of micelles as separation media in chromatography and electrophoresis. Applications to pharmaceuticals whose molecular masses are relatively small are focused on in this review. In high-performance liquid chromatography (HPLC), chromatography using micelles and reversed-phase stationary phases such as octadecylsilylized silica gel (ODS) columns is known as micellar liquid chromatography (MLC). The main application of MLC to pharmaceutical analysis is the same as in ion-pair chromatography using alkylsulfonate or tetraalkylammonium. In most cases, selectivity is much improved compared with other short alkyl chain ion-pairing agents such as pentanesulfonate or octanesulfonate. Direct plasma/serum injection can be successful in MLC. Separation of small ions is also successful by using gel filtration columns and micellar solutions. In electrophoresis, especially capillary electrophoresis (CE), micelles are used as pseudo-stationary phases in capillary zone electrophoresis (CZE). This mode is called micellar electrokinetic chromatography (MEKC). Most of the drug analysis can be performed by using the MEKC mode because of its wide applicability. Enantiomer separation, separation of amino acids and closely related peptides, separation of very complex mixtures, determination of drugs in biological samples etc. as well as separation of electrically neutral drugs can be successfully achieved by MEKC. Microemulsion electrokinetic chromatography (MEEKC), in which surfactants are also used in forming the microemulsion, is successful for the separation of electrically neutral drugs as in MEKC. This review mainly describes the typical applications of MLC and MEKC for the analysis of pharmaceuticals.     

Separation performance of single-stranded DNA electrophoresis in photopolymerized cross-linked polyacrylamide gels

Considerable effort has been directed toward optimizing performance and maximizing throughput in ssDNA electrophoresis because it is a critical analytical step in a variety of genomic assays. Ultimately, it would be desirable to quantitatively determine the achievable level of separation resolution directly from measurements of fundamental physical properties associated with the gel matrix rather than by the trial and error process often employed. Unfortunately, this predictive capability is currently lacking, due in large part to the need for a more detailed understanding of the fundamental parameters governing separation performance (mobility, diffusion, and dispersion). We seek to address this issue by systematically characterizing electrophoretic mobility, diffusion, and dispersion behavior of ssDNA fragments in the 70-1,000 base range in a photopolymerized cross-linked polyacrylamide matrix using a slab gel DNA sequencer. Data are collected for gel concentrations of 6, 9, and 12%T at electric fields ranging from 15 to 40 V/cm, and resolution predictions are compared with corresponding experimentally measured values. The data exhibit a transition from behavior consistent with the Ogston model for small fragments to behavior in agreement with the biased reptation model at larger fragment sizes. Mobility data are also used to estimate the mean gel pore size and compare the predictions of several models.     

自由溶液和筛分介质条件下芯片DNA瞬间等速电泳预浓缩的比较

利用芯片电泳方法考察瞬间等速电泳-筛分电泳偶联分析的结果,比较了自由溶液和筛分介质中DNA瞬间等速电泳的预浓缩效果.结果显示,相比较于筛分介质条件,自由溶液瞬间等速电泳有利于改善预浓缩和后续筛分电泳分离效果.对此结果的解释是:自由溶液条件下DNA迁移速度的提高可以延长瞬间等速电泳持续时间,有利于提高预浓缩效率.此外,样品压缩区带在自由溶液-筛分介质界面的二次富集也是预浓缩效果得到改善的原因之一.