Highly reproducible capillary gel electrophoresis (CGE) of DNA fragments using uncoated columns. Detection of genetically modified maize by PCR-cGE

CGE-laser induced fluorescence of double-stranded DNA fragments using GelGreen dye

Nowadays, new solutions focused on the replacement of reagents hazardous to human health are highly demanded in laboratories and Green Chemistry. In the present work, GelGreen, a new nonhazardous DNA staining reagent, has been assayed for the first time to analyze double-stranded DNA by CGE with LIF detection. The effect of GelGreen concentration on S/N ratio and migration time of a wide concentration range of standard DNA mixtures was evaluated. Under optimum GelGreen concentration in the sieving buffer efficient and sensitive separations of DNA fragments with sizes from 100-500 base pairs (bp) were obtained. A comparison in terms of resolution, time of analysis, LOD, LOQ, reproducibility, sizing performance, and cost of analysis was established between two optimized CGE-LIF protocols for DNA analysis, one based on the dye YOPRO-1 (typically used for CGE-LIF of DNA fragments) and another one using the new GelGreen. Analyses using YOPRO-1 were faster than those using GelGreen (ca. 31 min versus 34 min for the analysis of 100-500 bp DNA fragments). On the other side, sensitivity using GelGreen was twofold higher than that using YOPRO-1. The cost of analysis was significantly cheaper (ninefold) using GelGreen than with YOPRO-1. The resolution values and sizing performance were not significantly different between the two dyes (e.g. both dyes allowed the separation of fragments differing in only 2 bp in the 100-200 bp range). The usefulness of the separation method using GelGreen is demonstrated by the characterization of different amplicons obtained by PCR.

Thirty years of capillary electrophoresis in food analysis laboratories: potential applications

CE has generated considerable interest in the research community since instruments were introduced by different trading companies in the 1990s. Nowadays, CE is popular due to its simplicity, speed, highly efficient separations and minimal solvent and reagent consumption; it can also be included as a useful technique in the nanotechnology field and it covers a wide range of specific applications in different fields (chemical, pharmaceutical, genetic, clinical, food and environmental). CE has been very well evaluated in research laboratories for several years, and different new approaches to improve sensitivity (one of the main drawbacks of CE) and robustness have been proposed. However, this technique is still not well accepted in routine laboratories for food analysis. Researching in data bases, it is easy to find several electrophoretic methods to determine different groups of analytes and sometimes they are compared in terms of sensitivity, selectivity, precision and applicability with other separation techniques. Although these papers frequently prove the potential of this methodology in spiked samples, it is not common to find a discussion of the well-known complexity of the matrices to extract analytes from the sample and/or to study the interferences in the target analytes. Summarizing, the majority of CE scientific papers focus primarily on the effects upon the separation of the analytes while ignoring their behavior if these analytes are presented in real samples.

Simultaneous detection of genetically modified organisms by multiplex ligation-dependent genome amplification and capillary gel electrophoresis with laser-induced fluorescence

In this work, an innovative method useful to simultaneously analyze multiple genetically modified organisms is described. The developed method consists in the combination of multiplex ligation-dependent genome dependent amplification (MLGA) with CGE and LIF detection using bare-fused silica capillaries. The MLGA process is based on oligonucleotide constructs, formed by a universal sequence (vector) and long specific oligonucleotides (selectors) that facilitate the circularization of specific DNA target regions. Subsequently, the circularized target sequences are simultaneously amplified with the same couple of primers and analyzed by CGE-LIF using a bare-fused silica capillary and a run electrolyte containing 2-hydroxyethyl cellulose acting as both sieving matrix and dynamic capillary coating. CGE-LIF is shown to be very useful and informative for optimizing MLGA parameters such as annealing temperature, number of ligation cycles, and selector probes concentration. We demonstrate the specificity of the method in detecting the presence of transgenic DNA in certified reference and raw commercial samples. The method developed is sensitive and allows the simultaneous detection in a single run of percentages of transgenic maize as low as 1% of GA21, 1% of MON863, and 1% of MON810 in maize samples with signal-to-noise ratios for the corresponding DNA peaks of 15, 12, and 26, respectively. These results demonstrate, to our knowledge for the first time, the great possibilities of MLGA techniques for genetically modified organisms analysis.

Recent advances in the application of capillary electromigration methods for food analysis and Foodomics

The use of capillary electromigration methods to analyze foods and food components is reviewed in this work. Papers that were published during the period April 2007 to March 2009 are included following the previous review by García-Cañas and Cifuentes (Electrophoresis, 2008, 29, 294-309). These works include the analysis of amino acids, biogenic amines, peptides, proteins, DNAs, carbohydrates, phenols, polyphenols, pigments, toxins, pesticides, vitamins, additives, small organic and inorganic ions and other compounds found in foods and beverages, as well as those applications of CE for monitoring food interactions and food processing. The use of microchips, CE-MS, chiral-CE as well as other foreseen trends in food analysis are also discussed including their possibilities in the very new field of Foodomics.

Maize authentication: quality control methods and multivariate analysis (chemometrics)

Maize is one of the most important cereals because of its numerous applications in processed foods where it is the major or minor component. Apart from maize authenticity issues related to cultivar and geographical origin (national and/or international level), there is another important issue related to genetically modified maize. Various objective parameters such as fatty acids, phenolic compounds, pigments, heavy metals were determined in conjunction with subjective (sensory analysis) in order to identify the maize authenticity. However, the implementation of multivariate analysis (principal component analysis, cluster analysis, discriminant analysis, canonical analysis) is of great importance toward reaching valid conclusions on authenticity issues. This review summarized the most important finding of both objective and subjective evaluations of maize in five comprehensive tables in conjunction with the discussion.

Ultrarapid quantitation of maize proteins by perfusion and monolithic reversed-phase high-performance liquid chromatography

The main objective of this study was to develop a new methodology alternative to the classical Kjeldahl analysis for determining maize proteins in maize products and seeds. For that purpose, two different chromatographic methodologies using perfusion and monolithic stationary phases, both enabling rapid separations of maize proteins, were investigated. Due to the difficulty to find suitable standards for this type of analysis, three different maize products were initially tested as proteins standards: zein F4000, corn gluten meal, and maize flour. Different figures of merit (i.e., linearity, correlation coefficient, precision, limits of detection and quantitation), as well as the presence of matrix inferences, were investigated. The results obtained for the different chromatographic stationary phases and protein standards were compared in order to select the most suitable analytical conditions. Despite both perfusion and monolithic methodologies resulting, in general, as appropriate for the quantitation of maize proteins, the highest reduction of analysis time and lowest detection and determination limits provided by perfusion methodology enabled to select this one as the method of choice for the quantitation of maize proteins. Regarding the different protein standards studied in this work, in general the best results were obtained using the zein standard. Compared to Kjeldahl methodology, perfusion chromatography yields total protein contents in shorter analysis time while enabling the separation of the different kinds of proteins. Due to the high diversity and complexity of industrial maize products, the proposed chromatographic method could be a very useful tool for their routine analysis.

Simultaneous confirmatory analysis of different transgenic maize (zea mays) lines using multiplex polymerase chain reaction-restriction analysis and capillary gel electrophoresis with laser induced fluorescence detection

A novel analytical procedure based on the combination of multiplex PCR, restriction analysis, and CGE-LIF to unambiguosly and simultaneously confirm the presence of multiple lines of genetically modified corn is proposed. This methodology is based on the amplification of event-specific DNA regions by multiplex PCR using 6-FAM-labeled primers. Subsequently, PCR products are digested by a mixture containing specific restriction endonucleases. Thus, restriction endonucleases selectively recognize DNA target sequences contained in the PCR products and cleave the double-stranded DNA at a given cleavage site. Next, the restriction digest is analyzed by CGE-LIF corroborating the length of the expected restriction fragments, confirming (or not) the existence of GMOs. For accurate size determination of the DNA fragments by CGE-LIF a special standard DNA mixture was produced in this laboratory for calibration. The suitability of this mixture for size determination of labeled DNA fragments is also demonstrated. The usefulness of the proposed methodology is demonstrated through the simultaneous detection and confirmatory analysis of samples containing 0.5% of GA21 and MON863 maize plus an endogenous gene of maize as control.

Comparative metabolomic study of transgenic versus conventional soybean using capillary electrophoresis-time-of-flight mass spectrometry

In this work, capillary electrophoresis-time-of-flight mass spectrometry (CE-TOF-MS) is proposed to identify and quantify the main metabolites found in transgenic soybean and its corresponding non-transgenic parental line both grown under identical conditions. The procedure includes optimization of metabolites extraction, separation by CE, on-line electrospray-TOF-MS analysis and data evaluation. A large number of extraction procedures and background electrolytes are tested in order to obtain a highly reproducible and sensitive analytical methodology. Using this approach, a large number of metabolites were tentatively identified based on the high mass accuracy provided by TOF-MS analyzer, together with the isotopic pattern and expected electrophoretic mobility of these compounds. In general, the same metabolites and in similar amounts were found in the conventional and transgenic variety. However, significant differences were also observed in some specific cases when the conventional variety was compared with its corresponding transgenic line. The selection of these metabolites as possible biomarkers of transgenic soybean is discussed, although a larger number of samples need to be analyzed in order to validate this point. It is concluded that metabolomic procedures based on CE-MS can open new perspectives in the study of transgenic foods in order to corroborate (or not) the equivalence with their conventional counterparts.

Ultra-fast simultaneous analysis of genetically modified organisms in maize by microchip electrophoresis with LIF detector

This study examined the potential of microchip electrophoresis (ME) with a LIF detector using a programmed field strength gradient (PFSG) in a conventional glass double-T microchip for the ultra-fast detection and simultaneous analysis of genetically modified (GM) maize. The separation efficiency and sensitivity at various sieving gels (poly(ethylene oxide) (PEO, M(r) 8,000,000) and 2-hydroxyethylcellulose (HEC) (M(r) 250,000)) and fluorescent dye concentrations were investigated. The PCR products of both the GM and non-GM maize were analyzed within 30 s under the PFSG (470.6 V/cm for 20 s, 117.6 V/cm for 12 s, and 470.6 V/cm for 30 s) with a 2.5% HEC sieving matrix in the running buffer, 1 x Tris-borate EDTA (TBE) (pH 8.30) and 0.5 ppm ethidium bromide. The five transgenic maize varieties (Event176, MON810, Bt11, GA21, and T25) examined in this study were also clearly differentiated by ME-PFSG within 30 s in a single run without any loss of resolution. The ME-PFSG technique is a powerful tool for the ultra-fast detection and simultaneous analysis of GMOs in a variety of foods including maize.

Analysis of Chiral Amino Acids in Conventional and Transgenic Maize

In this work, a new chiral micellar electrokinetic chromatography with laser-induced fluorescence detection (chiral-MEKC-LIF) method is proposed to identify and quantify D- and L-amino acids in three lines of transgenic maize and their corresponding nontransgenic parental lines grown under identical conditions. The optimized procedure includes amino acids extraction, derivatization with FITC and chiral-MEKC-LIF separation in a background electrolyte composed of 100 mM sodium tetraborate, 80 mM SDS, and 20 mM beta-CD at pH 10.0. The D- and L-forms of Arg, Ser, Ala, Glu, and Asp, corresponding to the majority amino acids usually found in maize, are separated in less than 25 min with efficiencies up to 890,000 plates/m and high sensitivity (i.e., LODs as low as 160 nM were obtained for D-Arg for a signal-to-noise ratio of three), allowing the detection of 1% D-Arg in the presence of 99% of its opposite enantiomer. Using this method, different D-amino acids are detected in all investigated maize samples providing the reproducible quantification of the D-enantiomeric excess (% d-aa) for each amino acid calculated as % D-aa = 100D-aa/(D-aa + L-aa). Thus, significant differences were observed among the % d-aa values for the different conventional varieties (Aristis, Tietar, and PR33P66 maize) as could be expected from their natural variability. More interestingly, comparing each conventional maize with its corresponding transgenic line, very similar % D-aa values were obtained for one of the studied maize couples (Tietar vs Tietar-Bt) what could be presented as a new proof of their substantial equivalence. However, significant differences in the % d-aa values were observed for the other lines of maize studied. It is concluded that enantioselective procedures can open new perspectives in the study of transgenic organisms in order to corroborate (or not) the equivalence with their conventional counterparts.

A simple capillary gel electrophoresis approach for efficient and reproducible DNA separations. Analysis of genetically modified soy and maize

It is generally assumed that in order to achieve suitable separations of DNA fragments, capillary gel electrophoresis (CGE)-coated capillaries should be used. In this work, a new method is presented that allows to obtain reproducible CGE separations of DNA fragments using bare fused-silica capillaries without any previous coating step. The proposed method only requires: (i) a capillary washing with 0.1 M hydrochloric acid between injections and (ii) a running buffer composed of Tris-phosphate-ethylenediamine tetraacetic acid (EDTA) and 4.5% of 2-hydroxyethyl cellulose (HEC) as sieving polymer. The use of this new CGE procedure gives highly resolved and reproducible separations of DNA fragments ranging from 50 to 750 bp. The separation of these DNA fragments is accomplished in less than 30 min with efficiencies up to 1.7 x 10(6) plates/m. Reproducibility values of migration times (given as %RSD) for the analyzed DNA fragments are better than 1.0% (n = 4) for the same day, 2.2% (n = 16) for four different days, and 2.3% (n = 16) for four different capillaries. The usefulness of this separation method is demonstrated by detecting genetically modified maize and genetically modified soy after DNA amplification by PCR. This new CGE procedure together with LIF as detector provides sensitive analysis of 0.9% of Bt11 maize, Mon810 maize, and Roundup Ready soy in flours with S/ N up to 542. These results demonstrate the usefulness of this procedure to fulfill the European regulation on detection of genetically modified organisms in foods.

A new PCR-CGE (size and color) method for simultaneous detection of genetically modified maize events

We present a novel multiplex PCR assay for simultaneous detection of multiple transgenic events in maize. Initially, five PCR primers pairs specific to events Bt11, GA21, MON810, and NK603, and Zea mays L. (alcohol dehydrogenase) were included. The event specificity was based on amplification of transgene/plant genome flanking regions, i.e., the same targets as for validated real-time PCR assays. These short and similarly sized amplicons were selected to achieve high and similar amplification efficiency for all targets; however, its unambiguous identification was a technical challenge. We achieved a clear distinction by a novel CGE approach that combined the identification by size and color (CGE-SC). In one single step, all five targets were amplified and specifically labeled with three different fluorescent dyes. The assay was specific and displayed an LOD of 0.1% of each genetically modified organism (GMO). Therefore, it was adequate to fulfill legal thresholds established, e.g., in the European Union. Our CGE-SC based strategy in combination with an adequate labeling design has the potential to simultaneously detect higher numbers of targets. As an example, we present the detection of up to eight targets in a single run. Multiplex PCR-CGE-SC only requires a conventional sequencer device and enables automation and high throughput. In addition, it proved to be transferable to a different laboratory. The number of authorized GMO events is rapidly growing; and the acreage of genetically modified (GM) varieties cultivated and commercialized worldwide is rapidly increasing. In this context, our multiplex PCR-CGE-SC can be suitable for screening GM contents in food.

pH effect on dynamic coating for capillary electrophoresis of DNA

A buffer consisting of tris(hydroxymethyl)aminomethane, 2-(N-moropholino)ethanesulfonic acid (Mes) and EDTA with constant ion strength was used to investigate the effect of buffer pH on the dynamic coating behavior of poly(N-isopropylacrylamide) (PNIPAM) for DNA separation. The atomic force microscopy (AFM) image illustrated that PNIPAM in lower-pH buffer was much more efficient in covering a silica wafer than that in higher-pH buffer. The coating performance of PNIPAM was also quantitatively analyzed by Fourier transform IR attenuated total reflectance spectroscopy and by measuring the electroosmotic flow (EOF). These results indicated that the stability of the dynamic coating was dependent on the pH of the sieving matrix and was improved by reducing the pH to the weak-acid range. The lower pH of the sieving buffer may induce the polymer more efficiently to adsorb on the capillary wall to suppress EOF and DNA-capillary wall interaction for DNA separation. The enhanced dynamic coating capacity of PNIPAM in lower-pH buffer may be attributed to the hydrogen bonds between the hydroxyl groups of the silica surface and the oxygen atom of the carbonyl groups of PNIPAM.

Analytical approaches to expanding the use of capillary electrophoresis in routine food analysis

Capillary Electrophoresis (CE) is becoming an ever more powerful analytical technique for the separation, identification, and quantification of a wide variety of compounds of interest in many application fields. Particularly in food analysis this technique can offer interesting advantages over chromatographic techniques because of its greater simplicity and efficiency. Nevertheless, CE needs to advance with regard to compatibility with sample matrices, sensitivity, and robustness of the methodologies in order to gain even wider acceptance in food analysis laboratories, specially for routine work. This article presents various approaches to expanding the analytical usefulness of CE in food analysis, discussing their advantages over conventional CE. These approaches focus on sample screening, automated sample preparation with on-line CE arrangements, and the automatic integration of calibration in routine analytical work with CE.

DNA separation by capillary electrophoresis with hydrophilic substituted celluloses as coating and sieving polymers. Application to the analysis of genetically modified meals

A coating procedure based on the physical adsorption of hydroxypropyl cellulose onto the wall of a capillary column has been successfully used for the separation of DNA fragments up to 500 bp. The method uses a running Tris-phosphate-EDTA buffer containing 2-hydroxyethyl cellulose as sieving polymer. The separation procedure shows good reproducibility (measured as RSD%) for consecutive runs (<0.64), for different days (< 1.15) and capillaries (<2.15), short analysis times, and a long coating lifetime. Good reproducibility and efficiency are even achieved by performing the separation in the presence of additives such as ethidium bromide and mannitol. The method is applied to the detection of GMOs in soybean and maize meals with an accurate evaluation of the length of DNA sequences, previously amplified by polymerase chain reaction.

Detection of Genetically Modified Organisms in Foods by DNA Amplification Techniques

In this article, the different DNA amplification techniques that are being used for detecting genetically modified organisms (GMOs) in foods are examined. This study intends to provide an updated overview (including works published till June 2002) on the principal applications of such techniques together with their main advantages and drawbacks in GMO detection in foods. Some relevant facts on sampling, DNA isolation, and DNA amplification methods are discussed. Moreover; these analytical protocols are discuissed from a quantitative point of view, including the newest investigations on multiplex detection of GMOs in foods and validation of methods.

Quantitation of Transgenic Bt Event-176 Maize Using Double Quantitative Competitive Polymerase Chain Reaction and Capillary Gel Electrophorsesis Laser-Induced Fluorescence

In this work, a new procedure useful to quantitatively analyze genetically modified organisms (GMOs) in foods is described and applied to analyze transgenic Bt Event-176 maize. The method developed consists of coamplifications of specific DNA maize sequences with internal standards using quantitative competitive PCR (QC-PCR). The QC-PCR products are quantitatively analyzed using a capillary gel electrophoresis (CGE) with laser-induced fluorescence detection (LIF) method developed at our laboratory that utilizes a physically adsorbed coating. The CGE-LIF procedure allows the use of internal standards differing by only 10 bp from the original target fragments, to our knowledge, the smallest size difference that can be found in the bibliography for QC-PCR of GMOs. A spectrofluorometric procedure using ROX reference dye is proposed to solve calibration problems of input DNA concentration. It is demonstrated that the use of ROX drastically enhances the accuracy of the quantitative analysis by QC-PCR. Reproducibility of analysis times and corrected peak areas (measured as target/competitor PCR products ratio) for the CGE-LIF separations are determined to be better than 0.91 and 1.93% (RSD, n = 15) respectively, for three different days. It is shown that CGE-LIF provides better resolution and a signal/noise ratio improvement of approximately 700-fold compared to slab gel electrophoresis. The good possibilities in terms of quantitative analysis of GMOs provided by this new method are confirmed by determining the Bt Event-176 maize content in certified reference maize powder and food samples of known composition. This procedure opens the possibility for accurate quantitation of multiple GMOs in a single run.