Electrophoresis today and tomorrow: Helping biologists' dreams come true

Electrophoretic Determination of Trimethylamine (TMA) in Biological Samples as a Novel Potential Biomarker of Cardiovascular Diseases Methodological Approach

In competitive athletes, the differential diagnosis between nonpathological changes in cardiac morphology associated with training (commonly referred to as “athlete’s heart”) and certain cardiac diseases with the potential for sudden death is an important and not uncommon clinical problem. The use of noninvasive, fast, and cheap analytical techniques can help in making diagnostic differentiation and planning subsequent clinical strategies. Recent studies have demonstrated the role of gut microbiota and their metabolites in the onset and the development of cardiovascular diseases. Trimethylamine (TMA), a gut bacteria metabolite consisting of carnitine and choline, has recently emerged as a potentially toxic molecule to the circulatory system. The present work aims to develop a simple and cost-effective capillary electrophoresis-based method for the determination of TMA in biological samples. Analytical characteristics of the proposed method were evaluated through the study of its linearity (R² > 0.9950) and the limit of detection and quantification (LOD = 1.2 µg/mL; LOQ = 3.6 µg/mL). The method shows great potential in high-throughput screening applications for TMA analysis in biological samples as a novel potential biomarker of cardiovascular diseases. The proposed electrophoretic method for the determination of TMA in biological samples from patients with cardiac disease is now in progress.

Gel-on-a-chip: continuous, velocity-dependent DNA separation using nanoscale lateral displacement

We studied the trajectories of polymers being advected while diffusing in a pressure driven flow along a periodic pillar nanostructure known as nanoscale deterministic lateral displacement (nanoDLD) array. We found that polymers follow different trajectories depending on their length, flow velocity and pillar array geometry, demonstrating that nanoDLD devices can be used as a continuous polymer fractionation tool. As a model system, we used double-stranded DNA (dsDNA) with various contour lengths and demonstrated that dsDNA in the range of 100-10 000 base pairs (bp) can be separated with a size-selective resolution of 200 bp. In contrast to spherical colloids, a polymer elongates by shear flow and the angle of polymer trajectories with respect to the mean flow direction decreases as the mean flow velocity increases. We developed a phenomenological model that explains the qualitative dependence of the polymer trajectories on the gap size and on the flow velocity. Using this model, we found the optimal separation conditions for dsDNA of different sizes and demonstrated the separation and extraction of dsDNA fragments with over 75% recovery and 3-fold concentration. Importantly, this velocity dependence provides a means of fine-tuning the separation efficiency and resolution, independent of the nanoDLD pillar geometry.

A microfluidic design for desalination and selective removal and addition of components in biosamples

We present the development of a microfluidic device that is able to selectively and nondisturbingly remove or add components to liquid samples, which allows control and conditioning of the samples for biomedical tests. The device consists of a series of chambers for sample retention and a through channel. Because smaller particles diffuse faster, small particles in the sample such as salt ions rapidly escape the chamber by diffusion and are subsequently removed by a carrier flow in the channel, leaving macromolecules of interest in the "desalted" solution. Conversely, components lacking in the sample can be diffused in by reversing the concentration gradient between the flow and the sample chamber. The ability to control the ionic strength of a sample offers many advantages in biological sample preparation as most biofluids contain high salt contents, making them unsuitable for downstream molecular analyses without additional sample treatments which could cause sample loss, contamination, and cost increase. Making use of the nature of laminar flow in a microfluidic device and mass transport by diffusion, we have developed an analytical model to calculate concentration profiles for different particles. Excellent agreements were found between the theory and the experiment, making the results highly reliable and predictable. Since the device and the principle is applicable to a wide range of biological samples, it can be incorporated into the workflow of various applications for research and in vitro diagnosis such as ion exchange, DNA sequencing, immuno assay, vesicle, cell secretion analysis, etc.

A tetrad apparatus for protein gel casting, electrophoresis, staining, and scanning techniques with dual sensors for automatic detection of gel polymerization and protein migration

Recent advancements in biochemical sciences have facilitated researchers to explore the structure and function of macro molecules in a cell. PAGE is one of the most favored and adapted laboratory techniques. Due to its simple and economical procedures, several variants or new modifications are routinely observed in the basic electrophoresis technique that comprises gel casting, electrophoresis, staining, and imaging process which consequently necessitates additional apparatuses/components in the laboratory. Operation of these additional apparatuses/components lengthens the pre- and postelectrophoresis procedures involving many intermittent tedious and time-consuming steps. A universal apparatus that can facilitate all such associated techniques is lacking and is of utmost importance for fast and effective results. An apparatus that can perform synchronized action of slab gel casting (16 × 16 cm), electrophoresis (SDS-PAGE), dye staining (Coomassie), and imaging (scanning) techniques with real-time monitoring through sensor technology is described in this article. The estimated cost (∼$150) of fabrication of the apparatus is very economical and simple assembly procedure of the main apparatus can be completed within ∼30 min after fabrication.

Direct sample injection from a syringe needle into a separation capillary

An automatic micro-injector was developed for electrophoretic analysis of a microlitre amount of clinical samples, enabling injection of the sample from a Hamilton syringe. The outlet of the syringe needle is located directly opposite the inlet of the separation capillary at a defined distance of the order of hundreds of μm in the injection space. During the injection, the background electrolyte is forced out by air from this space and a drop of the sample is forced out of the syringe by a micro-pump so that it is caught at the entrance to the capillary. From the drop the sample is injected into the capillary by applying a negative pressure pulse or simply by spontaneous injection. The injection space is then filled with background electrolyte, which washes away excess sample and separation is commenced. The injector was tested in electrophoretic separation of a model sample with equimolar concentrations of 100 μM NH₄⁺, K⁺, Na⁺, Mg²⁺ and Li⁺ in a short capillary with total/effective length of 16.5/11.5 cm. The repeatability of the migration time and peak area expressed as the RSD value is 2% and 4%, respectively. The practical applicability of the injector was verified on the determination of the antiparasitic pentamidine in 10 μL of rat plasma. Electrophoretic separation of pentamidine was performed in 100 mM of acetic acid/NaOH at pH 4.55, the sample consumption per analysis is 125 nL, the separation time is 45 s and the attained LOQ using contactless conductivity detection is 8 μM.

Capillary electrophoresis based on nucleic acid detection for diagnosing human infectious disease

Rapid transmission, high morbidity, and mortality are the features of human infectious diseases caused by microorganisms, such as bacteria, fungi, and viruses. These diseases may lead within a short period of time to great personal and property losses, especially in regions where sanitation is poor. Thus, rapid diagnoses are vital for the prevention and therapeutic intervention of human infectious diseases. Several conventional methods are often used to diagnose infectious diseases, e.g. methods based on cultures or morphology, or biochemical tests based on metabonomics. Although traditional methods are considered gold standards and are used most frequently, they are laborious, time consuming, and tedious and cannot meet the demand for rapid diagnoses. Disease diagnosis using capillary electrophoresis methods has the advantages of high efficiency, high throughput, and high speed, and coupled with the different nucleic acid detection strategies overcomes the drawbacks of traditional identification methods, precluding many types of false positive and negative results. Therefore, this review focuses on the application of capillary electrophoresis based on nucleic detection to the diagnosis of human infectious diseases, and offers an introduction to the limitations, advantages, and future developments of this approach.

Parallel single-cell analysis of active caspase-3/7 in apoptotic and non-apoptotic cells

Analysing the chemical content of individual cells has already been proven to reveal unique information on various biological processes. Single-cell analysis provides more accurate and reliable results for biology and medicine than analyses of extracts from cell populations, where a natural heterogeneity is averaged. To meet the requirements in the research of important biologically active molecules, such as caspases, we have developed a miniaturized device for simultaneous analyses of individual cells. A stainless steel body with a carousel holder enables high-sensitivity parallel detections in eight microvials. The holder is mounted in front of a photomultiplier tube with cooled photocathode working in photon counting mode. The detection of active caspase-3/7, central effector caspases in apoptosis, in single cells is based on the bioluminescence chemistry commercially available as Caspase-Glo^® 3/7 reagent developed by Promega. Individual cells were captured from a culture medium under microscope and transferred by micromanipulator into detection microvial filled with the reagent. As a result of testing, the limits of detection and quantification were determined to be 0.27/0.86 of active caspase-3/7 content in an average apoptotic cell and 0.46/2.92 for non-apoptotic cells. Application potential of this technology in laboratory diagnostics and related medical research is discussed. Graphical abstract Miniaturized device for simultaneous analyses of individual cells.

Analysis of quantum dots and their conjugates by capillary electrophoresis with detection of laser-induced luminescence

In many bioanalytical applications, important molecules such as DNA, proteins, and antibodies are routinely conjugated with fluorescent tags to reach an extraordinary sensitivity of analyses. Semiconductor nanoparticles, quantum dots, have already proved to be suitable components of highly luminescent tags, probes, and sensors with a broad applicability in analytical chemistry. Quantum dots provide high extinction coefficients together with a wide range of excitation wavelengths, size- and composition-tunable emissions, narrow and symmetric emission spectra, good quantum yields, relatively long size-dependent luminescence lifetime, and practically no photobleaching. Most of these properties are superior when compared with conventional organic fluorescent dyes. In this chapter, optimized procedures for the preparation of water-dispersed cadmium telluride (CdTe) quantum dots, conjugating reactions with antibodies, DNA, and macrocycles as well as their analyses by capillary electrophoresis are described. The potential of capillary electrophoresis for fast analyses of nanoparticles, their conjugates with antibodies, and immunocomplexes with targeted antigens is demonstrated on examples.

Recent advances in the development of single cell analysis--a review

Development of techniques for the analysis of the content of individual cells represents an important direction in modern bioanalytical chemistry. While the analysis of chromosomes, organelles, or location of selected proteins has been traditionally the domain of microscopic techniques, the advances in miniaturized analytical systems bring new possibilities for separations and detections of molecules inside the individual cells including smaller molecules such as hormones or metabolites. It should be stressed that the field of single cell analysis is very broad, covering advanced optical, electrochemical and mass spectrometry instrumentation, sensor technology and separation techniques. The number of papers published on single cell analysis has reached several hundred in recent years. Thus a complete literature coverage is beyond the limits of a journal article. The following text provides a critical overview of some of the latest developments with the main focus on mass spectrometry, microseparation methods, electrophoresis in capillaries and microfluidic devices and respective detection techniques for performing single cell analyses.

Non-uniform velocity of homogeneous DNA in a uniform electric field: consequence of electric-field-induced slow dissociation of highly stable DNA-counterion complexes

Identical molecules move with identical velocities when placed in a uniform electric field within a uniform electrolyte. Here we report that homogeneous DNA does not obey this fundamental rule. While most DNA moves with similar velocities, a fraction of DNA moves with velocities that vary within a multiple-fold range. The size of this irregular fraction increases several orders of magnitude when exogenous counterions are added to DNA. The irregular fraction decreases several orders of magnitude when DNA counterions are removed by dialysis against deionized water in the presence of a strong electric field (0.6 kV/cm). Dialysis without the field is ineffective in decreasing the size of irregular fraction. These results suggest that (i) DNA can form very stable complexes with counterions, (ii) these complexes can be dissociated by an electric field, and (iii) the observed non-uniform velocity of DNA is caused by electric-field-induced slow dissociation of these stable complexes. Our findings help to better understand a fundamental property of DNA: its interaction with counterions. In addition, these findings suggest a practical way of making electromigration of DNA more uniform: removal of strongly bound DNA counterions by electro-dialysis against deionized water.

Bleomycin DNA damage: Anomalous mobility of 3'-phosphoglycolate termini in an automated capillary DNA sequencer

An automated capillary DNA sequencer with laser-induced fluorescence detection can be utilised for DNA fragment analysis. The precise mobilities of DNA fragments with different chemical termini are especially important in the determination of the sequence specificity of DNA damaging agents. The aim of this study was to examine the electrophoretic mobility profile of DNA fragments with different 3'-termini. The nature of the 3'-teminal residue was found to have a major effect on the electrophoretic mobility of the DNA fragment, especially for 3'-phosphoglycolate termini that migrated anomalously by 3-6 nucleotides. Using the automated capillary sequencer, the electrophoretic mobilities of DNA fragments with different 3'-termini including 3'-hydrogen, 3'-hydroxyl, 3'-phosphate, and 3'-phosphoglycolate were extensively quantified and compared relative to each other. The 3'-hydrogen termini were generated by dideoxy sequencing; 3'-hydroxyl ends by minus sequencing; 3'-phosphate by Maxam-Gilbert chemical sequencing; and 3'-phosphoglycolate by bleomycin cleavage. The mobilities of these DNA fragments with different 3'-termini were found to be: (slowest) 3'-hydroxyl<3'-hydrogen<3'-phosphate<3'-phosphoglycolate (fastest); with average relative mobilities of 0.00<0.12<0.63<4.42 nucleotides, respectively. The possible causes of the unusual electrophoretic mobility of the 3'-phosphoglycolate termini were discussed.

Optofluidics incorporating actively controlled micro- and nano-particles

The advent of optofluidic systems incorporating suspended particles has resulted in the emergence of novel applications. Such systems operate based on the fact that suspended particles can be manipulated using well-appointed active forces, and their motions, locations and local concentrations can be controlled. These forces can be exerted on both individual and clusters of particles. Having the capability to manipulate suspended particles gives users the ability for tuning the physical and, to some extent, the chemical properties of the suspension media, which addresses the needs of various advanced optofluidic systems. Additionally, the incorporation of particles results in the realization of novel optofluidic solutions used for creating optical components and sensing platforms. In this review, we present different types of active forces that are used for particle manipulations and the resulting optofluidic systems incorporating them. These systems include optical components, optofluidic detection and analysis platforms, plasmonics and Raman systems, thermal and energy related systems, and platforms specifically incorporating biological particles. We conclude the review with a discussion of future perspectives, which are expected to further advance this rapidly growing field.

The electrophoretic mobility of DNA fragments differing by a single 3'-terminal nucleotide in an automated capillary DNA sequencer

The electrophoretic mobility of DNA fragments that differ by a single 3'-terminal nucleotide was assessed by capillary electrophoresis. This was accomplished using dideoxy sequencing with a 5'-fluorescently labelled primer to generate DNA fragments with 3'-hydrogen ends. The resulting DNA fragments were electrophoresed on the ABI 3730 automated capillary sequencer, and the data were analysed with the GeneMapper software to determine the electrophoretic mobility differences on addition of a 3'-terminal nucleotide. It was found that the 3'-terminal nucleotide gave rise to different electrophoretic mobility profiles depending on the identity of the terminal nucleotide. The apparent electrophoretic mobility was (faster) -C > -A > -T > -G (slower). The C-terminated fragments were the fastest and the G-terminated fragments the slowest, relative to other nucleotides. It was proposed that the terminal nucleotide effect was due to changes in partial net charges on the nucleotides that resulted in alterations in the electrophoretic mobility of the DNA fragments in the automated capillary DNA sequencer. Other alternative explanations are also discussed.

Rapid identification of the copy number of α-globin genes by capillary electrophoresis analysis

OBJECTIVES

The current study aimed at the rapid identification of the copy number of α-globin genes for the diagnosis of α-thalassemia.

DESIGN AND METHODS

To identify the copy number of α-globin genes in α-thalassemia, we developed a novel method using a multiplex polymerase chain reaction (PCR) in combination with the CE analysis.

RESULTS

The proposed method provides a rapid detection of the common α-globin gene deletions. Sixty-six patients with α-thalassemia and 46 normal controls were included in the present study. The obtained results showed good correlation with those obtained by gap PCR. Moreover, a low amount of maternal cell contamination in the fetus specimen for the prenatal diagnosis of hemoglobin Barts hydrops fetalis as well as the rare multiplicated α-globin genes can be identified using this method.

CONCLUSION

This method provides a convenient and efficient tool for the rapid identification of the copy number of α-globin genes in α-thalassemia and the individuals with α-globin gene multiplication.

Gel-based and gel-free quantitative proteomics approaches at a glance

Two-dimensional gel electrophoresis (2-DE) is widely applied and remains the method of choice in proteomics; however, pervasive 2-DE-related concerns undermine its prospects as a dominant separation technique in proteome research. Consequently, the state-of-the-art shotgun techniques are slowly taking over and utilising the rapid expansion and advancement of mass spectrometry (MS) to provide a new toolbox of gel-free quantitative techniques. When coupled to MS, the shotgun proteomic pipeline can fuel new routes in sensitive and high-throughput profiling of proteins, leading to a high accuracy in quantification. Although label-based approaches, either chemical or metabolic, gained popularity in quantitative proteomics because of the multiplexing capacity, these approaches are not without drawbacks. The burgeoning label-free methods are tag independent and suitable for all kinds of samples. The challenges in quantitative proteomics are more prominent in plants due to difficulties in protein extraction, some protein abundance in green tissue, and the absence of well-annotated and completed genome sequences. The goal of this perspective assay is to present the balance between the strengths and weaknesses of the available gel-based and -free methods and their application to plants. The latest trends in peptide fractionation amenable to MS analysis are as well discussed.

Simultaneous determination of deoxycytidine diphosphate and deoxycytidine triphosphate by capillary electrophoresis with transient isotachophoretic stacking: a sensitive monitoring method for ribonucleotide reductase activity

A simple and rapid capillary electrophoretic method was developed for simultaneous determination of sub-micromolar 2'-deoxycytidine 5'-diphosphate (dCDP) and 2'-deoxycytidine 5'-triphosphate (dCTP) levels in enzyme assays without using radioactively labeled substrates. The separation was performed at 25°C using MES in the BGE as the terminating ion, the chloride ions in the sample buffer as the leading ion, and PEG 4000 in the BGE as the EOF suppressor for sample stacking by transient isotachophoresis (tITP). Several parameters affecting the separation were investigated, including the pH of the BGE, the concentration of sodium chloride in the sample buffer, and the concentrations of MES and PEG 4000 in the running buffer. Good separation with high separation efficiency was achieved within 6 min under optimal conditions. In comparison with the simple CZE method, the present tITP-CZE method enabled a 150-fold increase in the injection time without any decrease in resolution and the sensitivity was enhanced up to two orders of magnitude with the new method. The linear range of the method was 0.1-10 μM for dCDP and dCTP. The limits of detection of dCDP and dCTP were 85 and 73 nM, respectively. The proposed method was successfully applied for the activity assay of ribonucleotide reductase from Hep G2 and Sf9 cells.

Synthesis and characterization of a hydrogel with controllable electroosmosis: a potential brain tissue surrogate for electrokinetic transport

Electroosmosis is the bulk fluid flow initiated by application of an electric field to an electrolyte solution in contact with immobile objects with a nonzero ζ-potential such as the surface of a porous medium. Electroosmosis may be used to assist analytical separations. Several gel-based systems with varying electroosmotic mobilities have been made in this context. A method was recently developed to determine the ζ-potential of organotypic hippocampal slice cultures (OHSC) as a representative model for normal brain tissue. The ζ-potential of the tissue is significant. However, determining the role of the ζ-potential in solute transport in tissue in an electric field is difficult because the tissue's ζ-potential cannot be altered. We hypothesized that mass transport properties, namely the ζ-potential and tortuosity, could be modulated by controlling the composition of a set of hydrogels. Thus, poly(acrylamide-co-acrylic acid) gels were prepared with three compositions (by monomer weight percent): acrylamide/acrylic acid 100/0, 90/10, and 75/25. The ζ-potentials of these gels at pH 7.4 are distinctly different, and in fact vary approximately linearly with the weight percent of acrylic acid. We discovered that the 25% acrylic acid gel is a respectable model for brain tissue, as its ζ-potential is comparable to the OHSC. This series of gels permits the experimental determination of the importance of electrokinetic properties in a particular experiment or protocol. Additionally, tortuosities were measured electrokinetically and by evaluating diffusion coefficients. Hydrogels with well-defined ζ-potential and tortuosity may find utility in biomaterials and analytical separations, and as a surrogate model for OHSC and living biological tissues.

Separation of proteins using supramolecular gel electrophoresis

An amphiphilic low-molecular-weight hydrogelator 1 was synthesized. A tris-glycine-SDS solution gel of 1 was applied for electrophoresis to separate proteins. Centrifugation of a mixture of protein and a hydrogel of 1 enabled the recovery of protein. Various combinations of proteins were applied for supramolecular gel electrophoresis (SUGE), and remarkably poor mobility for small proteins (<45 kDa) was found.

Recent developments in capillary and chip electrophoresis of bioparticles: Viruses, organelles, and cells

In appropriate aqueous buffer solutions, biological particles usually exhibit a particular electric surface charge due to exposed charged or chargeable functional groups (amino acid residues, acidic carbohydrate moieties, etc.). Consequently, these bioparticles can migrate in solution under the influence of an electric field allowing separation according to their electrophoretic mobilities or their pI values. Based on these properties, electromigration methods are of eminent interest for the characterization, separation, and detection of such particles. The present review discusses the research papers published between 2008 and 2010 dealing with isoelectric focusing and zone electrophoresis of viruses, organelles and microorganisms (bacteria and yeast cells) in the capillary and the chip format.

Microfluidics using spatially defined arrays of droplets in one, two, and three dimensions

Spatially defined arrays of droplets differ from bulk emulsions in that droplets in arrays can be indexed on the basis of one or more spatial variables to enable identification, monitoring, and addressability of individual droplets. Spatial indexing is critical in experiments with hundreds to millions of unique compartmentalized microscale processes--for example, in applications such as digital measurements of rare events in a large sample, high-throughput time-lapse studies of the contents of individual droplets, and controlled droplet-droplet interactions. This review describes approaches for spatially organizing and manipulating droplets in one-, two-, and three-dimensional structured arrays, including aspiration, laminar flow, droplet traps, the SlipChip, self-assembly, and optical or electrical fields. This review also presents techniques to analyze droplets in arrays and applications of spatially defined arrays, including time-lapse studies of chemical, enzymatic, and cellular processes, as well as further opportunities in chemical, biological, and engineering sciences, including perturbation/response experiments and personal and point-of-care diagnostics.

Single cell metabolomics

Recent discoveries suggest that cells of a clonal population often display multiple metabolic phenotypes at the same time. Motivated by the success of mass spectrometry (MS) in the investigation of population-level metabolomics, the analytical community has initiated efforts towards MS-based single cell metabolomics to investigate metabolic phenomena that are buried under the population average. Here, we review the current approaches and illustrate their advantages and disadvantages. Because of significant advances in the field, different technologies are now at the verge of generating data that are useful for exploring and investigating metabolic heterogeneity.

Proteomic strategies and challenges in tumor metastasis research

The rapidly evolving field of proteomics offers new approaches to understanding the pathogenesis of cancer and metastatic disease. Although numerous tumor markers have been identified with different genomic methods in the past, most are either not specific or sensitive enough to be used in routine clinical setting. The rationale for proteomic profiling is based on the fact that proteins represent the dynamic state of the cells, reflecting pathophysiological changes in the disease more accurately than genomic and epigenetic alterations. Emerging proteomic techniques allow simultaneous assessment of a large number of proteins at one time. The study of protein profiles in complex systems, such as plasma, serum or tissues of cancer patients is likely to become valuable for monitoring the response of patients during treatment or for detecting recurrence of the disease.