Capillary electrophoretic analysis of synthetic short-chain oligoribonucleotides

Investigating the Merits of Microfluidic Capillary Zone Electrophoresis-Mass Spectrometry (CZE-MS) in the Bottom-Up Characterization of Larger RNAs

Established bottom-up approaches for the characterization of nucleic acids (NAs) rely on the strand-cleavage activity of nucleotide-specific endonucleases to generate smaller oligonucleotides amenable to gas-phase sequencing. The complexity of these hydrolytic mixtures calls for the utilization of a front-end separation to facilitate full mass spectrometric (MS) characterization. This report explored the merits of microfluidic capillary zone electrophoresis (CZE) as a possible alternative to common liquid chromatography techniques. An oligonucleotide ladder was initially employed to investigate the roles of fundamental analyte features and experimental parameters in determining the outcome of CZE-MS analyses. The results demonstrated the ability to fully resolve the various rungs into discrete electrophoretic peaks with full-width half-height (FWHH) resolution that was visibly affected by the overall amount of material injected into the system. Analogous results were obtained from a digestion mixture prepared by treating yeast tRNAPhe (75 nt) with RNase T1, which provided several well-resolved peaks in spite of the increasing sample heterogeneity. The regular shapes of such peaks, however, belied the fact that most of them contained sets of comigrating species, as shown by the corresponding MS spectra. Even though it was not possible to segregate each species into an individual electrophoretic peak, the analysis still proved capable of unambiguously identifying a total of 29 hydrolytic products, which were sufficient to cover 96% of the tRNAPhe's sequence. Their masses accurately reflected the presence of modified nucleotides characteristic of this type of substrate. The analysis of a digestion mixture obtained from the 364 nt HIV-1 5'-UTR proved to be more challenging. The electropherogram displayed fewer well-resolved peaks and significantly greater incidence of product comigration. In this case, fractionating the highly heterogeneous mixture into discrete bands helped reduce signal suppression and detection bias. As a result, the corresponding MS data enabled the assignment of 248 products out of the possible 513 predicted from the 5'-UTR sequence, which afforded 100% sequence coverage. This figure represented a significant improvement over the 36 total products identified earlier under suboptimal conditions, which afforded only 57% coverage, or the 83 observed by direct infusion nanospray-MS (72%). These results provided a measure of the excellent potential of the technique to support the bottom-up characterization of progressively larger NA samples, such as putative NA therapeutics and mRNA vaccines.

Discovered triethylamine as impurity in synthetic DNAs for and by electrochemiluminescence techniques

The purity of the synthetic oligonucleotides is very important because it is crucial for the accuracy of the established biological assays. Herein, it was discovered that one impurity in synthetic DNAs might affect the experiment results of electrochemiluminescence (ECL) detection techniques, which was never reported before. According to a series of experiments using ECL detection methods combined with capillary electrophoresis (CE) (CE-ECL), the impurity was identified as triethylamine (TEA), which came from incomplete removal after HPLC purification of synthetic DNAs. Moreover, CE-ECL technique was for the first time to be proposed for discovering, identifying and sensitive determining the possible impurity such as TEA in various DNA samples, which was usually neglected by other detection techniques for purification quality control of synthetic oligonucleotides. A detection range from 5.00×10(-10) to 2.00×10(-5) M with a detection limit as low as 50 nM (S/N=3) was reached for TEA. Through further designed ECL methods and data analysis, situations which would be really affected by the impurity of TEA were studied. To avoid or eliminate the impact of the TEA impurity on ECL applications, judgment basis for choosing purification ways was discussed according to individual requirements.

RNA structure analysis assisted by capillary electrophoresis

Although most capillary electrophoresis (CE) applications in the nucleic acid field performed so far address DNA analysis, various RNA assays by CE have also been done. Both natural and synthetic RNAs have been examined to evaluate their quantities, sizes and interactions. In this report, we show a novel application of CE in RNA research for the analysis of RNA stable conformers. First, we present a successful adaptation of two different enzymatic methods for the 3'-end labeling of RNAs with commercially available fluorescent probes. Then, we show the high performance of CE with laser-induced fluorescence detection (CE-LIF) assisting the structural studies of transcripts. Using the example of regulatory elements present in the breast cancer gene transcript BRCA1, we demonstrate-by direct comparisons-the advantages of CE-LIF over the traditional slab-gel electrophoresis. These include a better and more reproducible separation of conformers, shorter analysis time and higher detection sensitivity.

Capillary electrophoresis of RNA in dilute and semidilute polymer solutions

We report separations of RNA molecules (281-6583 nucleotides) by capillary electrophoresis in dilute and semidilute solutions of aqueous hydroxyethylcellulose (HEC) ether in varying buffers. RNA mobility and peak band widths are examined under both nondenaturing and also denaturing conditions. From studies of sieving polymer concentration and chain length, it is found that good separations can be obtained in semidilute solutions as well as in dilute solutions. The dependence of RNA mobility on its chain length is consistent with separation by a similar to transient entanglement mechanism in dilute solutions. In semidilute entangled solutions the separation proceeds by segmental motion.

Capillary electrophoresis of high-molecular chitosan: the natural carbohydrate biopolymer

Due to its high resolving power and diverse application range, capillary electrophoresis (CE) has been successfully applied to the analysis of carbohydrates. In this paper, a method for the determination of high-molecular chitosan (Mr 200,000) using CE is presented. We studied the optimal condition of buffer pH and type, and column type for determination of chitosan. Optimal CE performance was found when employing 100 mM triethylamine (TEA)-phosphate buffer, pH 2.0 and untreated fused-silica capillary (50 microm x 27 cm) for the chitosan analysis. Under optimum conditions, excellent linear responses were obtained in the concentration range of 1.25-20 microM, with a linear correlation coefficient of 0.9983. The standard deviations of the migration time and peak area were found to be 2.5 and 6.4%, respectively. This method could be readily applied to chitosan determination in real biological samples and commercial products.