High resolution DNA separations using microchip electrophoresis

Planar microfluidic devices have emerged as effective tools for the electrophoretic separation of a variety of different DNA inputs. The advancement of this miniaturized platform was inspired initially by demands placed on electrophoretic performance metrics by the human genome project and has provided a viable alternative to slab gel and even capillary formats due to its ability to offer high resolution separations of nucleic acid materials in a fraction of the time associated with its predecessors, consumption of substantially less sample and reagents while maintaining the ability to perform many separations in parallel for realizing ultra-high throughputs. Another compelling advantage of this separation platform is that it offers the potential for integrating front-end sample preprocessing steps onto the separation device eliminating the need for manual sample handling. This review aims to compile a recent survey of various electrophoretic separations using either glass or polymer-based microchips in the areas of genotyping and DNA sequencing as well as those involving the growing field of DNA-based forensics.     

Multiplexed DNA sizing by capillary electrophoresis using entangled polymer solutions and diode array detection

We developed a method for the analysis of multiplexed double-stranded DNA (dsDNA) samples complexed to various intercalating dyes using entangled polymer solution. A commercial single-column capillary electrophoresis (CE) instrument with diode array detection was used for multiplexed detection of DNA samples by addition of intercalating fluorescent molecules. A Phi X174HinfI and a pGEM DNA ladder (1 mg/mL) were used for the electrophoretic separation of dsDNA fragments ranging in size from 24 to 726 and 36 to 2645 bp, respectively. The results suggested that simultaneous electrophoretic separation of different DNA ladders multiplexed with different dyes could be performed in the same capillary yielding fast DNA sizing separations. CE analysis, which is often overpowered by slab gel in sample throughput, could now overcome this disadvantage by allowing multiplexed sample analysis in a fraction of the time needed for slab gel analysis. The separation efficiency of stained DNA molecules with both dyes were dramatically improved with buffers containing a large cation such as tetrapentylammonium ion (Npe(4) (+)) as the only cation in the buffer.     

Flow-through sampling for electrophoresis-based microfluidic chips using hydrodynamic pumping

This work presents a novel electrophoretic microchip design which is capable of directly coupling with flow-through analyzers for uninterrupted sampling. In this device, a 3 mm wide sampling channel (SC) was etched on quartz substrate to create the sample inlet and outlet and the 75 microm wide electrophoretic channels were also fabricated on the same substrate. Pressure was used to drive the sample flow through the external tube into the SC and the flow was then split into outlet and electrophoretic channels. A gating voltage was applied to the electrophoretic channel to control the sample loading for subsequent separations and inhibit the sample leakage. The minimum gating voltage required to inhibit the sample leakage depended on the solution buffer and increased with the hydrodynamic flow-rate. A fluorescent dye mixture containing Rhodamine B and Cy3 was introduced into the sample stream at either a continuous or discrete mode via an on-line injection valve and then separated and detected on the microchip using laser-induced fluorescence. For both modes, the relative standard deviation of migration time and peak intensity for consecutive injections was determined to be below 0.6 and 8%, respectively. Because the SC was kept floating, the external sampling equipment requires no electric connection. Therefore, such an electrophoresis-based microchip can be directly coupled with any pressure-driven flow analyzers without hardware modifications. To our best knowledge, this is something currently impossible for reported electrophoretic microchip designs.     

Impact of the sample matrix composition on the signal enhancement in the capillary electrophoretic separation of poliovirus samples

The development of capillary electrophoretic applications aiming to provide reliable stability assessment of viral suspensions, to detect subviral particles from cell extracts or to study the interactions between virus particles and various biomolecules, cannot be done without a thorough understanding of the sample matrix contribution to the observed electrophoretic behaviour. The present study thoroughly investigates the effect of the sample matrix on the electrophoretic behaviour of poliovirus injected as sample plugs of 1%, 5% and 12% effective capillary length. The effect of the sample matrix for three different poliovirus batches was evaluated. Additionally, simulated samples, obtained from concentrated poliovirus suspensions of high purity and diluted with commonly used lab buffers in order to obtain samples with either high or low conductivities, were also investigated. The goal of the study was to obtain a better understanding of the effect of the sample matrix on the signal enhancement, in order to define a general approach allowing a repeatable capillary electrophoretic (CE) separation of poliovirus from complex samples. This study clearly demonstrates that the sample matrix has an important influence on the sensitivity of the CE poliovirus separations. Translation of these observations into routine practice involves several compromises and a set of rules in order to reduce day-to-day variation and to maximize sensitivity.     

Separation of anions by ion chromatography-capillary electrophoresis

Capillary electrophoresis (CE) with a water-soluble ion-exchange polymer in the background electrolyte is very efficient for the separation of organic and inorganic anions because the ion-exchange selectivity, as well as differences in electrophoretic mobility, can be used for separating sample ions. Poly(diallyldimethylammonium chloride) (PDDAC) was employed for this purpose. A very stable electroosmotic flow was obtained between pH 2.3 and 8.5 due to the strong adsorption of PDDAC onto the capillary wall. The effect of ion exchange on the migration of sample anions and their separation was controlled by varying the concentration of PDDAC, the concentration and the type of salt used in the CE background electrolyte. Addition of organic solvent (e.g., acetonitrile) could also modify the sample migration and the separation. Baseline separations were obtained for anions with very similar mobilities, such as bromide and iodide, naphthalenesulfonates, and bi- and tricarboxylic acids. Typical separation efficiencies were between 195,000 and 429,000 theoretical plates per meter. Ten replicate separations gave an average RSD of 1.0% for migration times of the sample anions studied. Excellent separations were obtained for a variety of samples, including a separation of 17 inorganic and organic anions in less than 6 min.     

A miniaturized electrode configuration for isoelectric focusing

An electrode configuration is described which allows fast isoelectric focusing (IEF) with conventional IEF systems. The equipment, which can be fixed on the cooling plate of a conventional IEF system, consists of a base plate on which flappable electrode holders are fastened. The handling is simple and needs only little time. Graphite rods are used as electrodes, thus avoiding the use of buffer strips. Samples are applied with special applicator strips--permitting the analysis of up to 19 samples on a 50 x 40 mm polyacrylamide gel and up to 44 samples on a 100 x 70 mm gel. Only 30 min are needed for one IEF run.     

Gas chromatographic separations on packed microcolumns using various 10 μm support particles

Packed columns using 10 μm HPLC-packing materials as supports for various liquid phases have been studied. The glass columns used were 80 mm long (o.d. 3 mm and i.d. 1.5 mm), the amount of solid support in the column being approximately 0.15 g. A. wide variety of separation characteristics were obtained by combining support material of various surface areas, chemically bonded surfaces, applied liquid phases, and various liquid phase loadings. This type of column is also characterized by a very short gas hold-up time, leading to possibilities for relatively fast separations. Other advantages are high sample loading, high sample capacity, and low operating cost.     

GESA--a two-dimensional processing system using knowledge base techniques

The successful analysis of two-dimensional (2-D) polyacrylamide electrophoresis gels demands considerable experience and understanding of the protein system under investigation as well as knowledge of the separation technique itself. The present work concerns the development of a computer system for analysing 2-D electrophoretic separations which incorporates concepts derived from artificial intelligence research such that non-experts can use the technique as a diagnostic or identification tool. Automatic analysis of 2-D gel separations has proved to be extremely difficult using statistical methods. Non-reproducibility of gel separations is also difficult to overcome using automatic systems. However, the human eye is extremely good at recognising patterns in images, and human intervention in semi-automatic computer systems can reduce the computational complexities of fully automatic systems. Moreover, the expertise and understanding of an "expert" is invaluable in reducing system complexity if it can be encapsulated satisfactorily in an expert system. The combination of user-intervention in the computer system together with the encapsulation of expert knowledge characterises the present system. The domain within which the system has been developed is that of wheat grain storage proteins (gliadins) which exhibit polymorphism to such an extent that cultivars can be uniquely identified by their gliadin patterns. The system can be adapted to other domains where a range of polymorpic protein sub-units exist. In its generalised form, the system can also be used for comparing more complex 2-D gel electrophoretic separations.     

Atomic force microscopy of coated glasses

Atomic force microscopy has been used to investigate the topology of alkoxide gel dip coatings on different substrates. Results of SiO(2) - TiO(2) - ZrO(2) (STZ) coatings are presented on float glass, on polished fused silica, on commercially coated insulating flat glass, and on PtRh. Consolidated STZ coatings display the so-called glass pattern with ripples equal or less than 2 nm high. The same pattern is seen on partially dense STZ coatings, as soon as the surface is stiff enough for scanning, and also on the bottom of a 50 nm deep sputtering crater in the consolidated coating. The vitreous STZ coating on the fire side of the float glass is as flat as the float glass itself. It has the same tendency to contamination. 100 nm wide and 50 nm deep polishing grooves on fused silica have been filled up with the 80 nm thick coating, only dips of a few nm remain. The trenches between the SnO(2) crystallites on the insulating flat glass were filled up and the roughness of the substrate was partially reduced. PtRh sheet remained rough even after the coating. On the partially densified STZ coating, sputtering generates a grained surface.     

DNA separations in microfabricated devices with automated capillary sample introduction

A novel method is presented for automated injection of DNA samples into microfabricated separation devices via capillary electrophoresis. A single capillary is used to electrokinetically inject discrete plugs of DNA into an array of separation lanes on a glass chip. A computer-controlled micromanipulator is used to automate this injection process and to repeat injections into five parallel lanes several times over the course of the experiment. After separation, labeled DNA samples are detected by laser-induced fluorescence. Five serial separations of 6-carboxyfluorescein (FAM)-labeled oligonucleotides in five parallel lanes are shown, resulting in the analysis of 25 samples in 25 min. It is estimated that approximately 550 separations of these same oligonucleotides could be performed in one hour by increasing the number of lanes to 37 and optimizing the rate of the manipulator movement. Capillary sample introduction into chips allows parallel separations to be continuously performed in serial, yielding high throughput and minimal need for operator intervention.     

Fast electrophoretic analysis of individual mitochondria using microchip capillary electrophoresis with laser induced fluorescence detection

The analysis of mitochondria by capillary electrophoresis usually takes longer than 20 min per replicate which may compromise the quality of the mitochondria due to degradation. In addition, low sample consumption may be beneficial in the analysis of rare or difficult samples. In this report, we demonstrate the ability to analyze individual mitochondrial events in picoliter-volume samples (approximately 80 pL) taken from a bovine liver preparation using microchip capillary electrophoresis with laser-induced fluorescence detection (micro-chip CE-LIF). Using a commercial "double-T" glass microchip, the sample was electrokinetically loaded in the "double-T" intersection and then subjected to electrophoretic separation along the main separation channel. In order to decrease interactions of mitochondria with channel walls during the analysis, poly(vinyl alcohol) was used as a dynamic coating. This procedure eliminates the need for complicated covalent surface modifications within the channels that were previously used in capillary electrophoresis methods. For analysis, mitochondria, isolated from bovine liver tissue, were selectively labelled using 10-nonyl acridine orange (NAO). The results consist of electropherograms where each mitochondrial event is a narrow spike (240 +/- 44 ms). While the spike intensity is representative of its NAO content, its migration time is used to calculate and describe its electrophoretic mobility, which is a property still largely unexplored for intracellular organelles. The five-fold decrease in separation time (4 min for microchip versus 20 min for capillary electrophoresis) makes microchip electrophoretic separations of organelles a faster, sensitive, low-sample volume alternative for the characterization of individual organelle properties and for investigations of subcellular heterogeneity.     

Peak compression and resolution for electrophoretic separations in diverging microchannels

We report the results of experiments and simulations on electrokinetic flow in diverging microchannels (with cross-sectional area that increases with distance along the channel). Because of conservation of mass and charge, the velocity of an analyte in the channel decreases as the channel cross-section increases. Consequently, the leading edge of a band of sample moves more slowly than the trailing edge and the sample band is compressed. Sample peak widths, rather than increasing diffusively with time, can then be controlled by the geometry of the channel and can even be made to decrease with time. We consider the possibility of using this peak compression effect to improve the resolution of electrophoretic separations. Our results indicate that for typical separations that are dispersion limited, this peak compression effect is more than offset by the decreased distance between peaks, and the separation resolution in diverging channels is worse than that found for straight channels at the same applied voltage. For separations in very short channels or at very high field strengths, however, when the separation efficiency is injection limited, the peak compression effect is dominant and diverging channels can then be used to achieve improved separation resolution.     

Column properties and flow profiles of a flat, wide column for high-pressure liquid chromatography

The design and the construction of a pressurized, flat, wide column for high-performance liquid chromatography (HPLC) are described. This apparatus, which is derived from instruments that implement over-pressured thin layer chromatography, can carry out only uni-dimensional chromatographic separations. However, it is intended to be the first step in the development of more powerful instruments that will be able to carry out two-dimensional chromatographic separations, in which case, the first separation would be a space-based separation, LC(x), taking place along one side of the bed and the second separation would be a time-based separation, LC(t), as in classical HPLC but proceeding along the flat column, not along a tube. The apparatus described consists of a pressurization chamber made of a Plexiglas block and a column chamber made of stainless steel. These two chambers are separated by a thin Mylar membrane. The column chamber is a cavity which is filled with a thick layer (ca. 1mm) of the stationary phase. Suitable solvent inlet and outlet ports are located on two opposite sides of the sorbent layer. The design allows the preparation of a homogenous sorbent layer suitable to be used as a chromatographic column, the achievement of effective seals of the stationary phase layer against the chamber edges, and the homogenous flow of the mobile phase along the chamber. The entire width of the sorbent layer area can be used to develop separations or elute samples. The reproducible performance of the apparatus is demonstrated by the chromatographic separations of different dyes. This instrument is essentially designed for testing detector arrays to be used in a two-dimensional LC(x) x LC(t) instrument. The further development of two-dimension separation chromatographs based on the apparatus described is sketched.     

Packing and performance of microbore columns for adsorption and partition chromatography

Summary Microbore columns of 1 mm i.d. have turned out to be very suitable for the achievement of efficient columns.The packing procedure for stainless steel 1 mm i.d. columns from 5 to 100 cm in length was studied. Stationary phases used were: pure silica gel, octyl, octadecyl and amino bonded silicas. The main parameters (slurry composition, packing system, choice of materials) are discussed.Short columns packed with 3 or 5m particles allow high speed separations. A separation in 18 seconds is described.Very high plate numbers can be obtained with long columns. With 7–8m particles, a 1 m column can produce 50,000 plates (h=3). Columns can be joined without loss of efficiency. 270 000 theoretical plates were obtained on a 6 m adsorption column with a test mixture. In reversed-phase chromatography, bile acid sodium salts can be separated on a 1 m column. In adsorption chromatography, details are given of the separation of a polystyrene oligomer sample, as well as a light and a heavy petroleum distillate samples on a 2 m column with refractive index detection in the last-case.     

Elektrophoretische Ionenfokussierung Anorganischer Ionen auf Kieselgeldünnschichten

Analyzing environmental samples it is often necessary to determine traces in a matrix or to separate elements easily activated. In this case the detection limit depends on the amount of sample which can be separated. Frequently group separations are sufficient. In this paper we describe the relationship between amount, focussing area and concentration of the electrolytes in electrophoretic focussing. The load capacity and the possibility of group separations are evaluated. It is shown that within 4–5 min up to mg amounts can be separated into at least five groups on a 2 cm broad strip and that the ions are concentrated into small zones with a concentration of up to 1 mg·cm⁻².      

High-speed separation of proteins by microchip electrophoresis using a polyethylene glycol-coated plastic chip with a sodium dodecyl sulfate-linear polyacrylamide solution

In this paper, we describe a method for size-based electrophoretic separation of sodium dodecyl sulfate (SDS)-protein complexes on a polymethyl methacrylate (PMMA) microchip, using a separation buffer solution containing SDS and linear polyacrylamide as a sieving matrix. We developed optimum conditions under which protein separations can be performed, using polyethylene glycol (PEG)-coated polymer microchips and electrokinetic sample injection. We studied the performance of protein separations on the PEG-coated PMMA microchip. The electrophoretic separation of proteins (21.5-116.0 kDa) was completed with separation lengths of 3 mm, achieved within 8 s on the PEG-coated microchip. This high-speed method may be applied to protein separations over a large range of molecular weight, making the PEG-coated microchip approach applicable to high-speed proteome analysis systems.     

Continuous microfluidic DNA and protein trapping and concentration by balancing transverse electrokinetic forces

Sample pre-concentration can be a critical element to improve sensitivity of integrated microchip assays. In this work a converging Y-inlet microfluidic channel with integrated coplanar electrodes was used to investigate transverse DNA and protein migration under uniform direct current (DC) electric fields to assess the ability to concentrate a sample prior to other enzymatic modifications or capillary electrophoretic separations. Employing a pressure-driven flow to perfuse the microchannel, negatively charged samples diluted in low and high ionic strength buffers were co-infused with a receiving buffer of the same ionic strength into a main daughter channel. Experimental results demonstrated that, depending of the buffer selection, different DNA migration and accumulation dynamics were seen. Charged analytes could traverse the channel width and accumulate at the positive bias electrode in a low electroosmotic mobility, high electrophoretic mobility, high ionic strength buffer or migrated towards an equilibrium position within the channel in a high electroosmotic mobility, high electrophoretic mobility, low ionic strength buffer. The various migration behaviours are the result of a balance between the electrophoretic force and a drag force induced by a recirculating electroosmotic flow generated across the channel width due to the bounding walls. Under continuous flow conditions, DNA samples were concentrated several-fold by balancing these transverse electrokinetic forces. The electrokinetic trapping technique presented here is a simple technique which could be expanded to concentrate or separate other analytes as a preconditioning step for downstream processes.     

Parallel analysis of biomolecules on a microfabricated capillary array chip

This paper focused on a self-developed microfluidic array system with microfabricated capillary array electrophoresis (mu-CAE) chip for parallel chip electrophoresis of biomolecules. The microfluidic array layout consists of two common reservoirs coupled to four separation channels connected to sample injection channel on the soda-lime glass substrate. The excitation scheme for distributing a 20 mW laser beam to separation channels in an array is achieved. Under the control of program, the sample injection and separation in multichannel can be achieved through six high-voltage modules' output. A CCD camera was used to monitor electrophoretic separations simultaneously in four channels with LIF detection, and the electropherograms can be plotted directly without reconstruction by additional software. Parallel multichannel electrophoresis of series biomolecules including amino acids, proteins, and nucleic acids was performed on this system and the results showed fine reproducibility.     

Electrophoretic methods for separation of nanoparticles

This article reviews progress in the application of electrophoretic techniques for the separation of nanoparticles. Numerous types of nanoparticles have recently been synthesised and integrated into different products and procedures. Consequently, analytical methods for the efficient characterisation of nanoparticles are now required. Several studies have revealed that gel electrophoresis can readily be used for separating nanoparticles according to their size or shape. However, many other studies focused on separation of nanoparticles by CE. In some cases nanoparticles could be separated by CZE, simply using pure buffer as the BGE. In other studies, buffer additives (most often SDS) were used, enabling fast separations of metallic nanoparticles by size. Other CE methods also allowed for separation of nanoparticle conjugates with biomolecules. Dielectrophoresis is yet another electrophoretic technique useful in separation and characterisation of nanoparticles; particularly nanotubes. Detection methods often used after electrophoretic separation include UV/Vis absorption and fluorescence spectroscopy. Examples of recent and relevant older reports are presented here. The authors conclude that electrophoretic methods for nanoanalysis can provide inexpensive and efficient tools for quality assurance and safety control; and as a consequence, they can augment transfer of nanotechnologies from research to industry.     

Isoelectric focusing in an ordered micropillar array

An original micropillar array dedicated to electrophoretic separations has been developed. It consists of a rectangular zone of PDMS micropillars protruding on a PDMS block. This area has been chosen to mimic a diluted gel structure and remains uncovered to keep the ability to perform an immunoblot after the protein separation for further applications in the field of allergy diagnosis. The micropillar array geometry has been optimized by evaluating the influence of pillar shape, pillar size and interpillar distance on evaporation and IEF separation. The separation conditions namely electrolyte composition, temperature and sample loading have been studied. Finally a protein mixture with pI ranging from 4.7 to 10.6 has been successfully separated within this microdevice by IEF without decreasing the resolving power obtained with conventional minigel. The micropillar array developed for electrophoretic separations leads to much shorter analysis times and can be reused several times while gels are disposable.