Principles of DNA separation with capillary electrophoresis

Food profiling goes green: Sustainable analysis strategies for food authentication

Omics technologies, such as genomics, proteomics, metabolomics, isotopolomics, and metallomics, are important tools for analytical verification of food authenticity. However, in many cases, their application requires the use of high-resolution technological platforms as well as careful consideration of sample collection, storage, preparation and, in particular, extraction. In this overview, the individual steps and disciplines are explained against the background of the term "Green Chemistry," and the various instrumental procedures for the respective omics disciplines are discussed. Furthermore, new approaches and developments are presented on how such analyses can be made sustainable in the future.

Assessment of the structural change of DNA by binding with a small molecule based on capillary sieving electrophoresis

In this study, capillary sieving electrophoresis (CSE) using polymer solutions was used to evaluate the structural changes in nucleic acids upon complexation with small molecules. As the model target and nucleic acids, L-tyrosinamide (Tyr-Am) and its aptamer, which is a type of DNA specifically binding to Tyr-Am, were selected. CSE was conducted using a capillary filled with background solution (BGS) containing hydroxypropyl cellulose (HPC) as a sieving matrix. When Tyr-Am or tyrosine was added to the BGS in CSE, the ratio of mobility differences of the Tyr-Am-aptamer complex increased compared to that of the free aptamer without the addition of Tyr-Am. In contrast, when other amino acids or their analogs were added, results showed no apparent change or decreases in electrophoretic mobility. These results indicate that the proposed method can be applied to assess structural changes in nucleic acids that target small molecules.

Analysis of DNA Origami Nanostructures Using Capillary Electrophoresis

DNA origami nanostructures are engineered nanomaterials (ENMs) that possess significant customizability, biocompatibility, and tunable structural and functional properties, making them potentially useful materials in fields, such as medicine, biocomputing, biomedical engineering, and measurement science. Despite the potential of DNA origami as a functional nanomaterial, a major barrier to its applicability is the difficulty associated with obtaining pure, well-folded structures. Therefore, rapid methods of analysis to ensure purity are needed to support the rapid development of this class of nanomaterials. Here, we present the development of capillary electrophoresis (CE) as an analytical tool for DNA origami. CE was investigated under both capillary zone electrophoresis (CZE) and capillary transient isotachophoresis (ctITP) modes. Optimization of both systems yielded baseline resolved separations of folded DNA origami nanostructures from excess staple strands. The ctITP separation mode demonstrated superior performance in terms of peak resolution (Rs = 2.05 ± 0.3), peak efficiency (N = 12,200 ± 230), and peak symmetry (As = 1.29 ± 0.032). The SYBR family dyes (Gold, Green I, and Green II) were investigated as highly efficient, noncovalent fluorophores for on-column labeling of DNA origami and detection using laser-induced fluorescence. Finally, ctITP analysis conditions were also applied to DNA origami nanostructures with different shapes and for the differentiation of DNA origami aggregates.

A microfluidic electrophoretic dual dynamic staining method for the identification and relative quantitation of dsRNA contaminants in mRNA vaccines

mRNA vaccines (i.e., COVID-19 vaccine) offer various advantages over traditional vaccines in preventing and reducing disease and shortening the time between pathogen discovery and vaccine creation. Production of mRNA vaccines results in several nucleic acid and enzymatic by-products, most of which can be detected and removed; however, double-stranded RNA (dsRNA) contaminants pose a particular challenge. Current purification and detection platforms for dsRNA vary in effectiveness, with problems in scalability for mass mRNA vaccine production. Effectively detecting dsRNA is crucial in ensuring the safety and efficacy of the vaccines, as these strands can cause autoimmune reactions with length-symptom dependency and enhance mRNA degradation. We present a new microfluidics method to rapidly identify and quantify dsRNA fragments in mRNA samples. Our innovation exploits the differences in the dynamic staining behavior between mRNA and dsRNA molecules to detect dsRNA contaminants in a high throughput approach. The limit of detection of the system for dsRNA was estimated to be between 17.7-76.6 pg μL-1 with a maximum loading capacity of mRNA of 12.99 ng μL-1. Based on these estimated values, our method allows for the detection of dsRNA contaminants present in percentages as low as 0.14-0.59% compared to the total mRNA concentration. Here, we discuss the molecular mechanism of the dynamic staining behavior of dsRNA and mRNA for two different stains. We believe our method will accelerate the mRNA vaccine development from initial development to quality control workflows.

The Effect of Molecular Mass of Hydroxyethyl Cellulose on the Performance of Capillary Electrophoretic Separation of Proteins

Capillary electrophoresis (CE) is a versatile analytical separation method in the field of biochemistry. Although it has been proved that the relative molecular mass (Mr) of the polymers determines the threshold concentration of the entangled polymer solution, which will affect the separation performance of DNA molecules, there is still no report on the effect of Mr on the separation performance of proteins. Herein, we have thoroughly performed the CE of proteins ranged from 14.3 kDa to 116 kDa in a mixed hydroxyethyl cellulose (HEC) solution. The mixed solution was obtained with various Mr including 90,000, 250,000, 720,000, and 1,300,000. Then, we found that the mixed polymer provided a high resolution for small protein molecules while increasing the efficiency of large ones. Results demonstrated that the migration time decreased if HEC (1,300,000) was mixed with the lower Mr one, and the mixed solution (1,300,000/250,000) offered the highest resolution. The resolution was negatively correlated with the electric field strength. Finally, we have employed the optimal electrophoretic conditions to separate proteins in human tears, and it showed that lysozyme, lipocalin, and lactoferrin from human tears were successfully resolved in the mixed HEC. Such work indicates that CE has the potential to be developed as a tool for the diagnosis of xerophthalmia, meibomian gland dysfunction, or other eye diseases.

Analysis of therapeutic nucleic acids by capillary electrophoresis

Nucleic acids are getting increased attention to fulfill unmet medical needs. The past five years have seen more than ten FDA approvals of nucleic acid based therapeutics. New analytical challenges have been posed in discovery, characterization, quality control and bioanalysis of therapeutic nucleic acids. Capillary electrophoresis (CE) has proven to be an efficient separation technique and has been widely used for analyzing oligonucleotides and nucleic acids. This review discusses the recent technical advances of CE in nucleic acid analysis such as polymeric matrices, separation conditions and detection methods, and the applications of CE to various therapeutic nucleic acids including antisense oligonucleotide (ASO), small interfering ribonucleic acid (siRNA), messenger RNA (mRNA), gene editing tools such as clustered regularly interspaced short palindromic repeats (CRISPR)-based gene and cell therapy, and other nucleic acid related therapeutics.

Fractionation of Single-stranded DNAs with/without Stable Preorganized Structures Using Capillary Sieving Electrophoresis for Aptamer Selection

Aptamers, single-stranded DNAs/RNAs with a strong and specific interaction towards a target molecule, have wide applications in the fields of medicine and biosensors. In conventional aptamer selection methods, it is difficult to obtain "preorganized" and/or "induced-fit" type of aptamers selectively. In this study, separation and fractionation of single-stranded DNAs with/without stable preorganized structures were carried out using capillary sieving electrophoresis. The fractionated DNAs showed different mobilities and thermodynamic stabilities of their secondary structures; this outcome is deemed to be necessary for the synthesis of novel aptasensors with a desirable sensing mechanism.

Nanofluidic charged-coupled devices for controlled DNA transport and separation

Controlled molecular transport and separation is of significant importance in various applications. In this work, we presented a novel concept of nanofluidic molecular charge-coupled device (CCD) for controlled DNA transport and separation. By leveraging the unique field-effect coupling in nanofluidic systems, the nanofluidic molecular CCD aims to store charged biomolecules such as DNAs in discrete regions in nanochannels and transfer and separate these biomolecules as a charge packet in a bucket brigade fashion. We developed a quantitative model to capture the impact of nanochannel surface charge, gating voltage and frequency, molecule diffusivity, and gating electrode geometry on the transport and separation efficiency. We studied the synergistic effects of these factors to guide the device design and optimize the DNA transport and separation in a nanofluidic CCD. The findings in this study provided insight into the rational design and implementation of the nanofluidic molecular CCD.

Nitrogen-doped carbon dots aid in the separation of ssDNA molecules of different length by capillary transient isotachophoresis (ctITP) with laser-induced fluorescence (LIF) detection

This study demonstrates a novel application of nitrogen-doped carbon dots (NCDs) to enable the separation of different lengths of single-stranded DNA (ssDNA) by eletrokinetic means. Carbon dots have recently found widespread application in the fields of sensing, diagnostics, and healthcare due to their biocompatibility and low toxicity. In light of growing interest in the use of ssDNA aptamers over antibodies in the fields of biosensor development and drug delivery, it is important to establish a simple and effective method for aptamer separation. In this study, we employed NCDs as buffer additives in a capillary electrophoresis (CE)-based method, giving rise to the separation of FAM-labeled ssDNA samples ranging from 32 to 100 bases in length, with resolutions ranging from 1.30 - 1.77. In particular, we adopted a capillary transient isotachophoresis (ctITP) system with laser-induced fluorescence (LIF) detection, with both the separation and sample buffers modified by the addition of 30 μg/mL NCDs. These nanomaterials were prepared by a simple hydrothermal method from a mixture of citric acid and ethylenediamine. The NCDs themselves are highly fluorescent and photostable. As components in the background electrolyte, they did not interfere with the fluorescence emission of the FAM-labeled DNA samples. Under the conditions employed, no separation could be achieved in the absence of the NCDs nor with undoped CDs. The results show that NCDs function as buffer additives capable of enhancing electrokinetic-based separations of ssDNA, and hence, provide a new application for these carbon nanomaterials.

Dynamics of a driven confined polyelectrolyte solution

The transport of polyelectrolytes confined by oppositely charged surfaces and driven by a constant electric field is of interest in studies of DNA separation according to size. Using molecular dynamics simulations that include the surface polarization effect, we find that the mobilities of the polyelectrolytes and their counterions change non-monotonically with the confinement surface charge density. For an optimum value of the confinement charge density, efficient separation of polyelectrolytes can be achieved over a wide range of polyelectrolyte charge due to the differential friction imparted by oppositely charged confinement on the polyelectrolyte chains. Furthermore, by altering the placement of the charged confinement counterions, enhanced polyelectrolyte separation can be achieved by utilizing the surface polarization effect due to dielectric mismatch between the media inside and outside the confinement.

Characterization and minimization of band broadening in DNA electrohydrodynamic migration for enhanced size separation

The combination of hydrodynamic actuation with an opposing electrophoretic force in viscoelastic liquids enables the separation, concentration, and purification of DNA. Obtaining good analytical performances despite the use of hydrodynamic flow fields, which dramatically enhance band broadening due to Taylor dispersion, constitutes a paradox that remains to be clarified. Here, we study the mechanism of band broadening in electrohydrodynamic migration with an automated microfluidic platform that allows us to track the migration of a 600 bp band in the pressure-electric field parameter space. We demonstrate that diffusion in the electrohydrodynamic regime is controlled predominantly by the electric field and marginally by the hydrodynamic flow velocity. We explain this response with an analytical model of diffusion based on Taylor dispersion arguments. Furthermore, we demonstrate that the electric field can be modulated over time to monitor and minimize the breadth of a DNA band, and suggest guidelines to enhance the resolution of DNA separation experiments. Altogether, our report is a leap towards to the development of high-performance analytical technologies based on electrohydrodynamic actuation.

Study of the peak broadening due to detection in the electrophoretic separation of DNA by CE and microchip CE and the application of image sensor for ultra-small detection cell length

Narrow peaks are important to high-resolution and high-speed separation of DNA fragments by capillary electrophoresis and microchip capillary electrophoresis. Detection cell length is one of the broadening factors, which is often ignored in experiments. However, is it always safe to neglect detection cell length under any condition? To answer this question, we investigated the influence of detection cell length by simulation and experiments. A parameter named as detection cell length ratio was proposed to directly compare the detection cell length and the spatial length of sample band. Electrophoretic peaks generated by various detection cell length ratios were analyzed. A simple rule to evaluate the peak broadening due to detection cell length was obtained. The current states of the detection cell length of detection system and their reliabilities in capillary electrophoresis and microchip capillary electrophoresis were analyzed. Microchip capillary electrophoresis detection with an ultra-small detection cell length of 0.36 μm was easily achieved by using an image sensor.

Construction of a genetic linkage map in Pyropia yezoensis (Bangiales, Rhodophyta) and QTL analysis of several economic traits of blades

Pyropia yezoensis is an economically important seaweed but its molecular genetics is poorly understood. In the present study, we used a doubled haploid (DH) population that was established in our previous work to construct a genetic linkage map of P. yezoensis and analyze the quantitative trait loci (QTLs) of blades. The DH population was genotyped with fluorescent sequence-related amplified polymorphism (SRAP) markers. A chi-square test identified 301 loci with normal segregation (P ≥ 0.01) and 96 loci (24.18%) with low-level skewed segregation (0.001 ≤ P < 0.01). The genetic map was constructed after a total of 92 loci were assembled into three linkage groups (LGs). The map spanned 557.36 cM covering 93.71% of the estimated genome, with a mean interlocus space of 6.23 cM. Kolmogorov-Smirnov test (α = 5%) showed a uniform distribution of the markers along each LG. On the genetic map, 10 QTLs associated with five economic traits of blades were detected. One QTL was for length, one for width, two for fresh weight, two for specific growth rate of length and four for specific growth rate of fresh weight. These QTLs could explain 2.29–7.87% of the trait variations, indicating that their effects were all minor. The results may serve as a framework for future marker-assisted breeding in P. yezoensis.

Simple, sensitive and robust chicken specific sexing assays, compliant with large scale analysis

Chicken meat and eggs are important sources of food for the world population. The significant increase in food demand has pushed the food industry toward a rapid non-expensive production which in turn raises ethical issues. How chicken are cultivated and processed in food industry is no longer acceptable. Ethical and economical concerns emerging from chicken culling need to be solved in the near future. Indeed, in egg production industry, male chicken are killed at the age of 1-day post-hatching since they are not egg producers. A number of laboratory all over the world are looking for innovative non-invasive sexing methods to determine the sex of chicken in the early stages of the development before hatching. It will allow males' chicken elimination before the pain-feeling stages. In order to evaluate the efficiency of these methods, the scientific community need a reliable, easy to use and cost-effective in-ovo invasive sexing method. In this report, we developed two new invasive assays based on PCR and Q-PCR techniques respectively, which fulfil the above mentioned requirements. In the same line with other groups, we exploited the differences betweed males (ZZ) and females (ZW) chicken sexual chromosomes. We identified two genes, SWIM and Xho-I, on chromosome W and DMRT gene on chromosome Z allowing a clear discrimination between the two sexes using PCR and qPCR respectively. These two new genomic markers and their corresponding methods not only increase the accuracy but also reduce time and cost of the test compared to previously developed sexing methods. Depending on the technology available in the lab, one can choose between the two techniques requiring different machines and expertise.

Modeling of DNA transport in viscoelastic electro-hydrodynamic flows for enhanced size separation

DNA separation and analysis have advanced over recent years, benefiting from microfluidic systems that reduce sample volumes and analysis costs, essential for sequencing and disease identification in body fluids. We recently developed the μLAS technology that enables the separation, concentration, and analysis of nucleic acids with high sensitivity. The technology combines a hydrodynamic flow actuation and an opposite electrophoretic force in viscoelastic polymer solutions. Combining hydrodynamics first principles and statistical mechanics, we provide, in this paper, a quantitative model of DNA transport capable of predicting device performance with the exclusive use of one adjustable parameter associated with the amplitude of transverse viscoelastic forces. The model proves to be in remarkable agreement with DNA separation experiments, and allows us to define optimal conditions that result in a maximal resolution length of 7 bp. We finally discuss the usefulness of our model for separation technologies involving viscoelastic liquids.

Generation and validation of homozygous fluorescent knock-in cells using CRISPR-Cas9 genome editing

Gene tagging with fluorescent proteins is essential for investigations of the dynamic properties of cellular proteins. CRISPR-Cas9 technology is a powerful tool for inserting fluorescent markers into all alleles of the gene of interest (GOI) and allows functionality and physiological expression of the fusion protein. It is essential to evaluate such genome-edited cell lines carefully in order to preclude off-target effects caused by (i) incorrect insertion of the fluorescent protein, (ii) perturbation of the fusion protein by the fluorescent proteins or (iii) nonspecific genomic DNA damage by CRISPR-Cas9. In this protocol, we provide a step-by-step description of our systematic pipeline to generate and validate homozygous fluorescent knock-in cell lines.We have used the paired Cas9D10A nickase approach to efficiently insert tags into specific genomic loci via homology-directed repair (HDR) with minimal off-target effects. It is time-consuming and costly to perform whole-genome sequencing of each cell clone to check for spontaneous genetic variations occurring in mammalian cell lines. Therefore, we have developed an efficient validation pipeline of the generated cell lines consisting of junction PCR, Southern blotting analysis, Sanger sequencing, microscopy, western blotting analysis and live-cell imaging for cell-cycle dynamics. This protocol takes between 6 and 9 weeks. With this protocol, up to 70% of the targeted genes can be tagged homozygously with fluorescent proteins, thus resulting in physiological levels and phenotypically functional expression of the fusion proteins.

Real-time Tracking of DNA Fragment Separation by Smartphone

Slab gel electrophoresis (SGE) is the most common method for the separation of DNA fragments; thus, it is broadly applied to the field of biology and others. However, the traditional SGE protocol is quite tedious, and the experiment takes a long time. Moreover, the chemical consumption in SGE experiments is very high. This work proposes a simple method for the separation of DNA fragments based on an SGE chip. The chip is made by an engraving machine. Two plastic sheets are used for the excitation and emission wavelengths of the optical signal. The fluorescence signal of the DNA bands is collected by smartphone. To validate this method, 50, 100, and 1,000 bp DNA ladders were separated. The results demonstrate that a DNA ladder smaller than 5,000 bp can be resolved within 12 min and with high resolution when using this method, indicating that it is an ideal substitute for the traditional SGE method.

Effective length calibration method for processing the fluorescence signal detected by charge-coupled device in capillary electrophoresis

A novel method named effective length calibration method has been developed to process the fluorescence signal detected by charge-coupled device during capillary electrophoresis. The new method treated each pixel as an individual point detector, and effectively binned a large number of pixels into a final electropherogram without losing the narrow detection window defined by a single pixel. Capillary electrophoresis separations of DNA were carried out and detected by charge-coupled device and conventional detector (photomultiplier tube). Detection properties including signal-to-noise ratio, peak width, detection frequency, and tilt of detector were investigated. It was found that the new method achieved much higher signal-to-noise ratio and smaller peak width than the conventional detector did. A Detection width of 0.5 μm was easily achieved.

New design of hydrogels with tuned electro-osmosis: a potential model system to understand electro-kinetic transport in biological tissues

A series of charged polymer gels with precisely controlled magnitude and direction of electro-osmotic flow was prepared and opens up the possibility for understanding the contribution of electro-osmosis to transport phenomenon in native biological tissues.

Validation of alternative capillary electrophoresis detection of STRs using POP-6 polymer and a 22cm array on a 3130xl genetic analyzer

The goal of this project was to reduce capillary electrophoresis detection time on a 3130xl Genetic Analyzer for amplification product obtained from 4-dye and 5-dye STR amplification kits while still generating high quality STR profiles. This was accomplished by utilizing a more viscous polymer (POP-6™) and a shorter array (22 cm) than that which are typically used (POP-4(®) polymer and a 36 cm array) for human identification purposes. Spatial calibration and detection run modules were modified in response to the use of this polymer/array combination and to reduce detection time. Alternative detection resulted in 24-28 min run times, as compared to ∼45 min using traditional POP-4(®)/36 cm detection methods. POP-6™/22 cm detection run modules were validated for use with 4-dye Promega STR kits (e.g., PowerPlex(®) 16 and PowerPlex(®) 16HS) and 5-dye Life Technologies kits (e.g., Identifiler(®) and Identifiler(®) Plus). Three hundred ninety-five samples, controls and allelic ladders were used for the validation studies, which consisted of a comparison of alternative POP-6™/22 cm detection to traditional POP-4(®)/36 cm (including reproducibility/concordance of allele calls, resolution, ILS sizing quality, peak height and pass rates), a sizing study (precision and accuracy) and a sensitivity study to obtain a usable range of injection times. Compared to traditional POP-4(®)/36 cm detection, alternative detection resulted in 100% reproducible and concordant alleles, the ability to achieve one base resolution, slightly reduced ILS sizing quality, slightly reduced peak height and statistically similar pass rates (α=0.05). It should be noted that alternative detection offered improved resolution over that of traditional for amplicons less than ∼200 b, but had reduced resolution for products greater than ∼200 b. Additionally, alternative detection yielded acceptable precision and accuracy of sizing using Life Technologies criteria (<0.15 standard deviation of allele sizing and ±0.5b sizing differences for the same allele) and usable injection parameters of 2 kV 4-15s (compared to 3 kV 10s for traditional). The run modules developed and validated for 4-dye and 5-dye STR kits using POP-6™ polymer on a 22 cm array offer a tremendous reduction in detection time (∼40%) while still generating high quality STR profiles.

Multiplex SSR-PCR approaches for semi-automated genotyping and characterization of loci linked to blast disease resistance genes in rice

In the present study, 63 polymorphic microsatellite markers related to rice blast resistance genes were fluorescently labelled at the 5'-end with either 6-FAM or HEX using the G5 dye set and incorporated into a multiplex SSR-PCR for the detection of fragments using an automated system. For rice F3 families obtained from crosses between Pongsu Seribu 2 (Malaysian blast resistant cultivar) and Mahsuri (a susceptible rice cultivar), the genotypes for 13 designated multiplex SSR panels were determined. The genotyping assays were performed using a capillary-based ABIPRISM 3100 genetic analyser. The sizes of the SSRs alleles observed in the range from 79 to 324 bp. The observed marker segregation data were analysed using the Chi(2) test. A genetic linkage map covering ten chromosomes and comprising 63 polymorphic SSR markers was constructed, and the distorted loci were localised to linkage groups. The results indicated that distorted loci are presented on eight chromosomes.

Theoretical investigation on the performance of DNA electrophoresis under programmed step electric field strength: Two-step condition

Programmed step electric field strength is a simple-to-use technique that has already been reported to be effective to enhance the efficiency or speed of DNA electrophoresis. However, a global understanding and the details of this technique are still vague. In this paper, we investigated the influence of programmed step electric field strength by theoretical calculation and concentrated on a basic format named as two-step electric field strength. Both subtypes of two-step electric field strength conditions were considered. The important parameters, such as peak spacing, peak width, resolution, and migration time, were calculated in theory to understand the performance of DNA electrophoresis under programmed step electric field strength. The influence of two-step electric field strength on DNA electrophoresis was clearly revealed on a diagram of resolution versus migration time. Both resolution and speed of DNA electrophoresis under two-step electric field strength conditions are simply expressed by the shape of curves in the diagram. The possible shapes of curve were explored by calculation and shown in this paper. The subtype II of two-step electric field strength brings drastic variation on the resolution. Its limitations of enhancement and deterioration of resolution were predicted in theory.

Polyethylene Oxide (PEO) and Polyethylene Glycol (PEG) Polymer Sieving Matrix for RNA Capillary Electrophoresis

The selection of sieving polymer for RNA fragments separation by capillary electrophoresis is imperative. We investigated the separation of RNA fragments ranged from 100 to 10,000 nt in polyethylene glycol (PEG) and polyethylene oxide (PEO) solutions with different molecular weight and different concentration. We found that the separation performance of the small RNA fragments (<1000 nt) was improved with the increase of polymer concentration, whereas the separation performance for the large ones (>4000 nt) deteriorated in PEG/PEO solutions when the concentration was above 1.0%/0.6%, respectively. By double logarithmic plot of mobility and RNA fragment size, we revealed three migration regimes for RNA in PEG (300-500k) and PEO (4,000k). Moreover, we calculated the smallest resolvable nucleotide length (N_min) from the resolution length analysis.

Analysis of small interfering RNA by capillary electrophoresis in hydroxyethylcellulose solutions

The analysis of small interfering RNA (siRNA) is important for gene function studies and drug developments. We employed CE to study the separation of siRNA ladder marker, which were ten double-stranded RNA (dsRNA) fragments ranged from 20 to 1000 bp, in solutions of hydroxyethylcellulose (HEC) polymer with different concentrations and molecular weights (Mws). Migration mechanism of dsRNA during CE was studied by the mobility and resolution length (RL) plots. We found that the RL depended on not only the concentration of HEC, but also the Mw of HEC. For instance, RL of small dsRNA fragment was more influenced by concentration of high Mw HEC than large dsRNA fragment and RL of large dsRNA fragment was more influenced by concentration of low Mw HEC than small dsRNA fragment. In addition, we found electrophoretic evidence that the structure of dsRNA was more compact than dsDNA with the same length. In practice, we succeeded to separate the glyceraldehyde 3-phosphate dehydrogenase siRNA in the mixture of the siRNA ladder marker within 4 min.

Universal probe amplification: multiplex screening technologies for genetic variations

In order to achieve multiplex screening of genetic variations, multiplex amplification of target genomic DNA is necessary. Universal amplification technology meets this requirement by simultaneously amplifying a number of different regions within the target genomic DNA using a single pair of universal primers and thus eliminating the limitations associated with the use of multiple pairs of primers. We comprehensively review universal probe amplification and its use with multiplex technologies for the identification of the most representative genetic variation, i. e. single nucleotide polymorphisms. The progress and key issues relating to universal probe amplification are discussed and the representative technologies are summarized with an emphasis on their application for the identification of susceptibility to human diseases.

A multiplex single nucleotide polymorphism genotyping method using ligase-based mismatch discrimination and CE-SSCP

Accuracy, simplicity, and cost-effectiveness are the most important criteria for a genotyping method for SNPs compatible with clinical use. One method developed for SNP genotyping, ligase-based discrimination, is considered the simplest for clinical diagnosis. However, multiplex assays using this method are limited by the detection method. Although CE has been introduced as an alternative to error prone microarray-based detection, the design process and multiplex assay procedure are complicated because of the DNA size-dependent separation principle. In this study, we developed a simple and accurate multiplex genotyping method using reaction condition-optimized ligation and high-resolution CE-based SSCP. With this high-resolution CE-SSCP system, we are able to use similar-sized probes, thereby eliminating the complex probe design step and simplifying the optimization process. We found that this method could accurately discriminate single-base mismatches in SNPs of the tp53 gene, used as targets for multiplex detection.

Electromigration behavior of nucleic acids in capillary electrophoresis under pulsed-field conditions

We have presented a study focused on the migration pattern of double-stranded DNA (dsDNA) and RNA under pulsed field conditions. By calculating the dependence of nucleic acid mobility on its molecular size in a double logarithm plot, we found that (I) dsDNA molecules proceeded by a sigmoidal migration regime which was probably related to Ogston sieving, transition regime, and reptation model. Furthermore, the transition regime disappeared if DNA was resolved in a higher molecular mass HEC. (II) The migration pattern of RNA was relevant to the denaturant used for separation. When RNA was denatured by acetic acid, its mobility parabolically declined with its molecular size. The mobility was linearly decreased with the molecular size if urea was employed as denaturant. (III) RNA may migrate by Ogston, reptation without orientation mechanism when denatured by urea, whereas these two models were not suitable for RNA if denatured by acetic acid. Even though the electrophoretic conditions of PFCE were varied, the sigmoidal, linear, parabolic migration patterns could still be observed. (IV) Under certain modulation depth, the migration time (Tm) of acetic acid decreased with the increase of average separation voltage (Va), and when RNA denatured in 4.0M urea, Tm showed a linear correlation with Va. (V) The mobility of nucleic acids increased with the growth of artificial temperature in the capillary volume due to the decrease in the viscosity of the polymer. This is the first systematic and comparative research of high molecular mass nucleic acids in PFCE, which provides us deep insight into RNA and DNA migration behavior under pulsed electric field conditions.

Ion concentration polarization-based continuous separation device using electrical repulsion in the depletion region

We proposed a novel separation method, which is the first report using ion concentration polarization (ICP) to separate particles continuously. We analyzed the electrical forces that cause the repulsion of particles in the depletion region formed by ICP. Using the electrical repulsion, micro- and nano-sized particles were separated based on their electrophoretic mobilities. Because the separation of particles was performed using a strong electric field in the depletion region without the use of internal electrodes, it offers the advantages of simple, low-cost device fabrication and bubble-free operation compared with conventional continuous electrophoretic separation methods, such as miniaturizing free-flow electrophoresis (μ-FFE). This separation device is expected to be a useful tool for separating various biochemical samples, including cells, proteins, DNAs and even ions.

Electrokinetics of non-Newtonian fluids: a review

This work presents a comprehensive review of electrokinetics pertaining to non-Newtonian fluids. The topic covers a broad range of non-Newtonian effects in electrokinetics, including electroosmosis of non-Newtonian fluids, electrophoresis of particles in non-Newtonian fluids, streaming potential effect of non-Newtonian fluids and other related non-Newtonian effects in electrokinetics. Generally, the coupling between non-Newtonian hydrodynamics and electrostatics not only complicates the electrokinetics but also causes the fluid/particle velocity to be nonlinearly dependent on the strength of external electric field and/or the zeta potential. Shear-thinning nature of liquids tends to enhance electrokinetic phenomena, while shear-thickening nature of liquids leads to the reduction of electrokinetic effects. In addition, directions for the future studies are suggested and several theoretical issues in non-Newtonian electrokinetics are highlighted.

Sieving polymer synthesis by reversible addition fragmentation chain transfer polymerization

Replaceable sieving polymers are the fundamental component for high resolution nucleic acids separation in CE. The choice of polymer and its physical properties play significant roles in influencing separation performance. Recently, reversible addition fragmentation chain transfer (RAFT) polymerization has been shown to be a versatile polymerization technique capable of yielding well defined polymers previously unattainable by conventional free radical polymerization. In this study, a high molecular weight PDMA at 765 000 gmol-1 with a PDI of 1.55 was successfully synthesized with the use of chain transfer agent - 2-propionic acidyl butyl trithiocarbonate (PABTC) in a multi-step sequential RAFT polymerization approach. This study represents the first demonstration of RAFT polymerization for synthesizing polymers with the molecular weight range suitable for high resolution DNA separation in sieving electrophoresis. Adjustment of pH in the reaction was found to be crucial for the successful RAFT polymerization of high molecular weight polymer as the buffered condition minimizes the effect of hydrolysis and aminolysis commonly associated with trithiocarbonate chain transfer agents. The separation efficiency of PABTC-PDMA was found to have marginally superior separation performance compared to a commercial PDMA formulation, POP™-CAP, of similar molecular weight range.

Automated method for analysis of tryptophan and tyrosine metabolites using capillary electrophoresis with native fluorescence detection

Capillary electrophoresis (CE) with laser-induced native fluorescence (LINF) detection offers the ability to characterize low levels of selected analyte classes, depending on the excitation and emission wavelengths used. Here a new automated CE-LINF system that provides deep ultraviolet (DUV) excitation (224 nm) and variable emission wavelength detection was evaluated for the analysis of small molecule tryptophan- and tyrosine-related metabolites. The optimized instrument design includes several features that increase throughput, lower instrument cost and maintenance, and decrease complexity when compared with earlier systems using DUV excitation. Sensitivity is enhanced by using an ellipsoid detection cell to increase the fluorescence collection efficiency. The limits of detection ranged from 4 to 30 nmol/L for serotonin and tyrosine, respectively. The system demonstrated excellent linearity over several orders of magnitude of concentration and intraday precision from 1-11 % relative standard deviation (RSD). The instrument's performance was validated via tryptophan and serotonin characterization using tissue extracts from the mammalian brain stem, with RSDs of less than 10 % for both metabolites. The flexibility and sensitivity offered by DUV laser excitation and tunable emission enables a broad range of small-volume measurements.

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.

Millimeter scale separation of DNA with a replaceable polymer matrix

Electrophoresis is a powerful method that has seen a wide range of applications, often in automated genetic diagnostic instruments that require the use of a replaceable sieving matrix. The power and simplicity of electrophoresis as an analysis technique would be ideal for highly integrated and low-cost analysis systems if the method could be implemented in microfluidics on the scale of several mm. We demonstrate the electrophoretic analysis of DNA with separation lengths as small as 2 mm and with a resolution adequate for the analysis of PCR products, i.e. resolutions of 10-20 base pairs. Such small-scale separations enable analysis systems consisting of microfluidics and microelectronics integrated into a single inexpensive package, thereby overcoming a key challenge facing the development of the lab on chip technologies.

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.

High-performance capillary electrophoretic separation of double-stranded oligonucleotides using a poly-(ethylpyrrolidine methacrylate-co-methylmethacrylate)-coated capillary

Here we describe a capillary electrophoretic method for the separation of double-stranded oligonucleotides (ds-ODNs) ranging from 16-20 bp with 2 bp resolution using a low concentration of poly(ethylpyrrolidine methacrylate-co-methyl methacrylate) (PEPyM-co-PMMA) copolymer physically adsorbed to a capillary surface. Contrary to traditional DNA separations, we show that the ds-ODN with the highest molecular size eluted first and propose that this phenomena is due to a screening effect by the PEPyM-co-PMMA coating on the smaller ds-ODNs negative charge during elution. Key to the performance of this separation was a sample preparation time of less than 1 h and analysis time of 40 min. Repeatability of intraday migration time for the mixtures was typically < 1% relative standard deviation (n = 3). In addition, we demonstrate that the coating has an acceptable capillary lifetime of over 70 injections.