RiboCAT: a new capillary electrophoresis data analysis tool for nucleic acid probing.

Chemical and enzymatic probing of RNA secondary structure and RNA/protein interactions provides the basis for understanding the functions of structured RNAs. However, the ability to rapidly perform such experiments using capillary electrophoresis has been hampered by relatively labor-intensive data analysis software. While these computationally robust programs have been shown to calculate residue-specific reactivities to a high degree of accuracy, they often require time-consuming manual intervention and lack the ability to be easily modified by users. To alleviate these issues, RiboCAT (Ribonucleic acid capillary-electrophoresis analysis tool) was developed as a user-friendly, Microsoft Excel-based tool that reduces the need for manual intervention, thereby significantly shortening the time required for data analysis. Features of this tool include (i) the use of an Excel platform, (ii) a method of intercapillary signal alignment using internal size standards, (iii) a peak-sharpening algorithm to more accurately identify peaks, and (iv) an open architecture allowing for simple user intervention. Furthermore, a complementary tool, RiboDOG (RiboCAT data output generator) was designed to facilitate the comparison of multiple data sets, highlighting potential inconsistencies and inaccuracies that may have occurred during analysis. Using these new tools, the secondary structure of the HIV-1 5' untranslated region (5'UTR) was determined using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE), matching the results of previous work.

Experimental design and measurement uncertainty in ligand binding studies by affinity capillary electrophoresis.

In all life sciences ligand binding assays (LBAs) play a crucial role. Unfortunately these are very error prone. One part of this uncertainty results from the unavoidable random measurement uncertainty, another part can be attributed to the experimental design. To investigate the latter, uncertainty propagation was evaluated as a function of the given experimental design. A design space including the normalized maximum response range (nMRR), the data point position (DPP), the data point range (DPR) and the number of data points (NoDP) was defined. Based on ten measured ms ACE source data sets 20 specific parameter sets were selected by Design of Experiments. Monte Carlo simulations using 100 000 repeats for every parameter set were employed. The resulting measurement uncertainty propagation factors (measurement uncertainty multiplier: MUM) were used to describe the whole design space by polynomial regression. The resulting 5-dimensional response surface was investigated to evaluate the design parameter's influence and to find the minimal uncertainty propagation. It could be shown, that the nMRR is of highest importance, followed by DPP and DPR. Interestingly, the NoDP is less relevant. However, the interactions of the four parameters need to be carefully considered during design optimization. Using at least five data points which cover over 40% of the upper part of the binding hyperbola (DPP > 0.57) the MUM will be minimized (MUM approximately 1.5) when the nMRR is appropriate. It is possible to reduce the measurement uncertainty propagation more than one order of magnitude.

Concordance of Capillary Electrophoresis and Conventional Gel Electrophoresis in Two Different Groups of Patients with.

BACKGROUND: Serum and urinary protein electrophoresis play an important role in the identification of monoclonal gammopathy. Recently, capillary electrophoresis (CE) has been adapted in many clinical laboratories because of several advantages such as short turnaround time, automation, and high reproducibility. However, there have been unsolved concerns for the concordance between conventional gel and automated capillary electrophoresis methods for protein separation in clinical specimens. In this study, we investigated the diagnostic performance of both methods for detecting monoclonal (M) protein. METHODS: From February 2012 to August 2015, a total of 3,013 CE tests were performed in our hospital. Among these cases, we reconfirmed results of CE (Capillary 2, Sebia, Lysse, France) with those of conventional agarose gel electrophoresis (GE) (Hydragel 4IF, Sebia, Lisses, France) in 28 specimens from 24 patients with newly diagnosed monoclonal gammopathy (group 1). In addition, 22 cases from 15 patients with previously diagnosed monoclonal gammopathy presenting indeterminate or suspicious results on CE (group 2) were also reconfirmed with GE. RESULTS: We compared the results between the two electrophoresis methods in two different groups of patients with newly diagnosed discrete monoclonal peaks vs. pre-existing monoclonal gammopathy with obscure results in follow-up courses. In group 1, agreement rate was 100% (28/28) and there was no discrepant result between these two electrophoresis methods. In contrast, group 2 showed 86.4% (19/22) agreement rate and 0.67 Cohen's kappa value (95% confidence interval, 0.51 - 1.02). CONCLUSIONS: According to our results, both electrophoresis methods can be used with the same level of assurance at the time of initial diagnosis for monoclonal gammopathy. However, in patients with previously diagnosed monoclonal gammopathy in follow-up course after appropriate treatments, discordant results can be observed due to the reduced amount of M proteins. Therefore, we suggest that some ambiguous cases with very small amounts of M components require a combination of both CE and GE methods for accurate interpretation to confirm the presence of M proteins.

Selective Trapping of DNA Using Glass Microcapillaries.

We show experimentally that an inexpensive glass microcapillary can accumulate λ-phage DNA at its tip and deliver the DNA into the capillary using a combination of electro-osmotic flow, pressure-driven flow, and electrophoresis. We develop an efficient simulation model based on the electrokinetic equations and the finite-element method to explain this phenomenon. As a proof of concept for the generality of this trapping mechanism we use our numerical model to explore the effect of the salt concentration, the capillary surface charge, the applied voltage, the pressure difference, and the mobility of the analyte molecules. Our results indicate that the simple microcapillary system has the potential to capture a wide range of analyte molecules based on their electrophoretic mobility that extends well beyond our experimental example of λ-phage DNA. Our method for separation and preconcentration of analytes therefore has implications for the development of low-cost lab-on-a-chip devices.

Extracting kinetics from affinity capillary electrophoresis (ACE) data: a new blade for the old tool.

We describe a mathematical approach that enables extraction of kinetic rate constants from thousands of studies conducted over the past two decades with affinity capillary electrophoresis (ACE). Previously, ACE has been used almost exclusively for obtaining equilibrium constants of intermolecular interactions. In this article, we prove that there exists an analytical solution of partial differential equations describing mass transfer in ACE. By using an in silico study, we demonstrate that the solution is applicable to experimental conditions that are typically used in ACE and found in most historical ACE experiments. The solution was validated by extracting rate constants from previously published ACE data and closely matching independently obtained results. Lastly, it was used to obtain previously unknown rate constants from historical ACE data. The new mathematical approach expands the applicability of ACE to a wider range of biomolecular interactions and enables both prospective and retrospective data analysis. The obtained kinetic information will be of significant practical value to the fields of pharmacology and molecular biology.

Classification of quinoa varieties based on protein fingerprinting by capillary electrophoresis with ultraviolet absorption diode array detection and advanced chemometrics.

Quinoa (Chenopodium quinoa Willd.) is an andean grain with exceptional nutritional properties that has been progressively introduced in western countries as a protein-rich super food with a broad amino acid spectrum. Quinoa is consumed as whole grain, but it is also milled to produce high-value flour, which is susceptible to adulteration. Therefore, there is a growing interest in developing novel analytical methods to get further information about quinoa at the chemical level. In this study, we developed a rapid and simple capillary electrophoresis-ultraviolet absorption diode array detection (CE-UV-DAD) method to obtain characteristic multiwavelength electrophoretic profiles of soluble protein extracts from different quinoa grain varieties. Then, advanced chemometric methods (i.e. multivariate curve resolution alternating least squares, MCR-ALS, followed by principal component analysis, PCA, and partial least squares discriminant analysis, PLS-DA) were applied to deconvolute the components present in the electropherograms and classify the quinoa varieties according to their differential protein composition.

Orthogonal Comparison of Analytical Methods by Theoretical Reconstruction from Bottom-up Assay Data.

In the never-ending endeavor to produce stable and efficacious protein therapeutics, biopharmaceutical companies often employ numerous analytical techniques to characterize and quantify a drug candidate's stability. Mass spectrometry, due to the information-rich data it produces, is commonly used in its numerous configurations to ascertain chemical and structural stability. At issue is the comparison of the various configurations utilized, that is, comparing bottom-up methods such as proteolytic digest followed by reversed phase LC-MS with intact LC-MS methods. Similar issues also arise when using capillary isoelectric focusing to see how charge variants change over time, that is, monitoring the progression of charge altering modifications like deamidation. To this end, site-specific degradations as quantified from bottom-up methods like peptide mapping can be used to build reconstructions of both theoretical intact mass spectra as well as theoretical electropherograms. The result can then be superimposed over the experimental data to qualitatively, and perhaps quantitatively, evaluate differences. In theory, if both experimental bottom-up data and intact data are accurate, the theoretical reconstruction produced from the bottom-up data should perfectly overlay with that of the experimental data. Valuable secondary information can also be ascertained from reconstructions, such as whether modifications are stochastic, as well as a detailed view of all possible combinations of modifications and their quantities used in the reconstruction. This comparison is also useful in determining unknown mass differences in deconvoluted intact protein spectra that may be a result of multiple modifications in combination. The comparison of data from alternate sources provides a holistic and more comprehensive view of the molecule under study.

Quantification of global DNA methylation by capillary electrophoresis and mass spectrometry.

Two approaches for the evaluation of the relative degree of global DNA methylation through the quantification of 2' deoxynucleosides are described. Detection and quantification of 5-methyl 2'-deoxycytidine in genomic DNA is performed using both high-performance capillary electrophoresis (HPCE) with UV-Vis detection or liquid chromatography with electrospray ionization mass spectrometric detection (LC-ESI/MS). Treatment of genomic DNA with a ribonuclease and generation of nucleosides through enzymatic hydrolysis notably increases the specificity of both techniques. Both approaches have been demonstrated to be highly specific and sensitive, being useful for the rapid quantification of the degree of global DNA methylation and its exploitation for the analysis of poorly purified and/or concentrated DNA samples, such as tumor biopsies.

Sensitive profiling of biogenic amines in urine using CE with transient isotachophoretic preconcentration.

A transient ITP-CZE system is proposed for the determination of biogenic amines in urine. The complete separation and identification of dopamine, tyramine (TA), tryptamine (T), serotonin, epinephrine, norepinephrine, and normetanephrine have been achieved in a twofold diluted urine sample (in which the analytes were below the LODs by normal CZE). The tITP preconcentration conditions were created by introducing a 30 mM solution of NaOH, containing 0.1% hydroxypropylcellulose (pH 6.5 adjusted with MES), and 0.1 M HCl before and after the sample zone to work as leading and terminating electrolytes, respectively. This allowed the LODs of direct UV absorption detection to be decreased down to the 10(-8) M level that is comparable with the sensitivity thresholds of LIF detection or inline SPE-CE. The RSDs of migration time and peak area for real-biofluid analysis were in the range of 0.1-4.5% and 0.8-16% (n=3), respectively. Quantification of dopamine, TA, T, and serotonin was performed using internal calibration. To the best of our knowledge, this is the first report on probing urinal biogenic amines and their metabolites by tITP-CZE.

Determination of ammonia, creatinine and inorganic cations in urine using CE with contactless conductivity detection.

CE with capacitively coupled contactless conductivity detection (C(4)D) was used to determine waste products of the nitrogen metabolism (ammonia and creatinine) and of biogenic inorganic cations in samples of human urine. The CE separation was performed in two BGEs, consisting of 2 M acetic acid + 1.5 mM crown ether 18-crown-6 (BGE I) and 2 M acetic acid + 2% w/v PEG (BGE II). Only BGE II permitted complete separation of all the analytes in a model sample and in real urine samples. The LOD values for the optimized procedure ranged from 0.8 microM for Ca(2+) and Mg(2+) to 2.9 microM for NH(4)(+) (in terms of mass concentration units, from 7 microg/L for Li(+) to 102 microg/L for creatinine). These values are adequate for determination of NH(4)(+), creatinine, Na(+), K(+), Ca(2+) and Mg(2+) in real urine samples.

Competitive affinity capillary electrophoresis assay based on a "hybrid" pre-incubation/on-capillary mixing format using an enantioselective aptamer as affinity ligand.

In this paper, we describe an aptamer-based competitive affinity CE (ACE) assay involving (i) the pre-incubation of the target (D-arginine) and the specific ligand (anti-D-arginine-L-RNA aptamer) before (ii) the competition with the labeled target (dansylated D-arginine) through an on-capillary mixing strategy. The effects of some critical operating parameters such as the applied voltage and the sample-aptamer mixture plug length on the assay sensitivity were investigated. The ACE assay appeared particularly dependent on the plug length of the pre-incubated sample-aptamer solution. It was shown that this "hybrid" strategy significantly improved the assay sensitivity relative to that obtained with a "full" on-capillary mixing approach.

Sensitive determination of norepinephrine, synephrine, and isoproterenol by capillary electrophoresis with indirect electrochemiluminescence detection.

A new and sensitive method for the determination of norepinephrine (NE), synephrine, and isoproterenol was developed by CE separation and indirect electrochemiluminescence detection (ECL) based on their quenching effects on the tris(2,2'-bipyridyl)-ruthenium(II)/tripropylamine (TPA) system. The conditions for CE separation and ECL detection were investigated in detail. Under the optimum conditions, the three analytes were well separated within 9 min. The LODs (S/N = 3) in standard solution are 2.6 x 10(-8) mol/L for NE, 6.6 x 10(-9) mol/L for synephrine and 8.4 x 10(-8) mol/L for isoproterenol, respectively. The precisions of intraday and interday are less than 4.4 and 6.1%, respectively. The LOQs (S/N = 10) in real human urine samples are 2.6 x 10(-7) mol/L for NE, 8.8 x 10(-8 ) mol/L for synephrine, and 8.8 x 10(-7) mol/L for isoproterenol, respectively. The applicability of the proposed method was illustrated in the determination of 20 human urine samples from diabetic patients and healthy persons. The results obtained indicated that the level of NE in patients (mean value 0.41 micromol/L) was higher than that in healthy persons (mean value 0.24 micromol/L).

Selective determination of catechin, epicatechin and ascorbic acid in human urine using chiral capillary electrophoresis.

Chiral CE was successfully applied to the separation and quantification of catechin, epicatechin and ascorbic acid in some commercial drinks and human urine. Analysis involved the separation of analytes in less than 5.0 min at 240 nm with an untreated fused-silica capillary under hydrodynamic injection mode. The running buffer consisted of 50 mM borate buffer with 3 mM beta-CD at pH 8.35. Detection limits for catechin, epicatechin and ascorbic acid were 0.028, 0.011 and 0.004 microg/mL, respectively. Linearity was investigated by selecting the ranges of calibration according to the amount of analytes in urine giving correlation coefficient percent (% r(2)) ranging between 99.4 and 99.6 at 99% confidence level. The maximum urinary excretion of catechin and epicatechin were noted at 2.0 and 4.0 h of the administrated dose. Unchanged catechin, epicatechin and ascorbic acid amounted to about 1.500, 8.696 and 0.003% of the administered dose in the 48.0 h urine collection. The proposed method achieved 99.2% completeness (n = 20) in urine media.

Capillary electrophoretic determination of main components of natural dyes with MS detection.

CE with UV-Vis and MS detections was investigated as a technique for detection of main components of selected natural dyes of plant and insect origin. The BGE giving the best separation of the investigated flavonoids and anthraquinoids, suitable for MS detection consisted of 40 mM ammonium acetate solution of pH 9.5 with 40% ACN. LODs obtained with MS detection were even one order of magnitude lower than the ones obtained with UV-Vis detection. Application of MS detection enabled determination of eleven dye compounds from three different chemical groups in 15 min. and proved to be more satisfactory than diode-array detection in the electrophoretic analysis of main classes of natural dyes both in terms of selectivity and sensitivity of analysis.

Development of a capillary electrophoresis method for the enantioselective estimation of primaquine in pharmaceutical formulations.

A capillary electrophoresis (CE) method has been developed that allows the separation and estimation of primaquine enantiomers using hydroxypropyl-gamma-cyclodextrin (HP-gamma -CD) as a chiral selector. The influence of chemical and instrumental parameters on the separation, such as type and concentration of CD, buffer concentration, buffer pH, applied voltage, capillary temperature, and injection time, were investigated. Good separation of the racemic mixture of primaquine was achieved using a fused-silica capillary (52.5 cm effective length x 50 microm id) and a background electrolyte composed of tris-phosphate buffer solution (50 mM, pH 2.5) containing 15 mM HP-gamma-CD as a chiral selector. The recommended applied voltage, capillary temperature, and injection time were 15 kV, 25 degrees C, and 6 s, respectively. Within-day and interday reproducibility of peak area and migration time gave relative standard deviation values ranging from 1.05-3.30%. Good recoveries (range of 96.8-104.9%) were obtained from the determination of placebos that were spiked with 0.25-1.00 mg/L primaquine. The proposed CE method was successfully applied to the assay of primaquine diphosphate in pharmaceutical formulations (tablets).

Modeling the electrophoretic mobility of analytes in binary solvent electrolyte systems in capillary electrophoresis using an artificial neural network.

An artificial neural network (ANN) methodology was used to model the electrophoretic mobility of basic analytes in binary solvent electrolyte systems. The electrophoretic mobilities in pure solvent electrolytes, and the volume fractions of the solvents in mixtures were used as input. The electrophoretic mobilities in mixed solvent buffers were employed as the output of the network. The optimized topology of the network was 3-3-1. 32 experimental mobility data sets collected from the literature were employed to test the correlation ability and prediction capability of the proposed method. The mean percentage deviation (MPD) between the experimental and calculated values was used as an accuracy criterion. The MPDs obtained for different numerical analyses varied between 0.21% and 13.74%. The results were also compared with similar calculated mobilities which were derived from the best multiple linear model from the literature. From these results it was found that the ANN methodology is superior to the multiple linear model.

A genome wide scan for association with multiple sclerosis in a N. Irish case control population.

In order to screen the genome for linkage disequilibrium (LD) in multiple sclerosis (MS), we typed 2537 microsatellite markers in separately pooled DNA from 200 cases and 200 controls from N. Ireland. Twenty two markers showing significant evidence of association were identified including three from the HLA region on chromosome 6p21. Putative candidate genes mapping close to the 19 novel markers include the IL10RA and CD3E genes on 11q23 (which both lie close to the marker D11S1998). Individual typing of the marker D11S1998 confirmed its association.

Clinical applications of capillary electrophoresis. Status at the new millennium.

Capillary electrophoresis (CE) is an extremely sensitive technique, which has been used in the clinical laboratory for almost 10 yr. The components of CE instrumentation are described, as are injection modes, buffers, and effects of electroosmotic flow. The modes of separation used in CE, namely, capillary zone electrophoresis, capillary isoelectric focusing, capillary isotachophoresis, and micellar electrokinetic capillary chromatography, are explained. References for 26 different clinical applications of CE are included, among them assays that are used routinely as well as niche assays for specialized applications of CE. Verification of CE assays, current instrumentation, and future development of CE in the clinical laboratory are addressed.

Rapid analysis of amplified double-stranded DNA by capillary electrophoresis with laser-induced fluorescence detection.

DNA amplification technology has been applied to clinical diagnosis of infectious disease, genetic disorder, and cancer. After in vitro amplification of a particular DNA region, the methods of analysis for these amplified samples play a pivotal role in clinical diagnosis. Conventional gel electrophoresis has been routinely used in the lab for checking DNA. The whole procedure is time consuming and requires more than 1 ng of DNA for detection. To achieve greater performance in DNA diagnosis, we demonstrated capillary electrophoresis with laser induced fluorescence detection for analysis of amplified DNA. The analysis of DNA could be completed within 3 min and the data is directly entered into the computer. Considering the automatic and rapid process, we believe that this method could be routinely utilized for the clinical diagnosis of amplified DNA products.

Capillary electrophoretic analyses of drugs in body fluids: sample pretreatment and methods for direct injection of biofluids.

A variety of strategies for the analysis of biological samples by capillary electrophoresis (CE) are described, with particular emphasis on the determination of drugs and metabolites. Analytical methods involving extensive sample pretreatment before CE analysis are considered, as well as strategies for directly injecting untreated biofluids. The application in CE of techniques common in liquid chromatography is first described, e.g. protein precipitation, liquid-liquid extraction and solid-phase extraction. On-capillary methods of sample concentration are considered. Approaches to performing CE assays of urine and plasma, without prior sample treatment, are described. The use of both capillary zone electrophoresis and micellar electrokinetic chromatography for direct-injection assays is compared for both urine and plasma analyses, and capillary washing strategies are discussed. Finally, direct-injection microanalyses are mentioned.