Strategies to Avoid Artifacts in Mass Spectrometry-Based Epitranscriptome Analyses.

In this report, we perform structure validation of recently reported RNA phosphorothioate (PT) modifications, a new set of epitranscriptome marks found in bacteria and eukaryotes including humans. By comparing synthetic PT-containing diribonucleotides with native species in RNA hydrolysates by high-resolution mass spectrometry (MS), metabolic stable isotope labeling, and PT-specific iodine-desulfurization, we disprove the existence of PTs in RNA from E. coli, S. cerevisiae, human cell lines, and mouse brain. Furthermore, we discuss how an MS artifact led to the initial misidentification of 2'-O-methylated diribonucleotides as RNA phosphorothioates. To aid structure validation of new nucleic acid modifications, we present a detailed guideline for MS analysis of RNA hydrolysates, emphasizing how the chosen RNA hydrolysis protocol can be a decisive factor in discovering and quantifying RNA modifications in biological samples.

Benefits of stable isotope labeling in RNA analysis.

RNAs are key players in life as they connect the genetic code (DNA) with all cellular processes dominated by proteins. They contain a variety of chemical modifications and many RNAs fold into complex structures. Here, we review recent progress in the analysis of RNA modification and structure on the basis of stable isotope labeling techniques. Mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy are the key tools and many breakthrough developments were made possible by the analysis of stable isotope labeled RNA. Therefore, we discuss current stable isotope labeling techniques such as metabolic labeling, enzymatic labeling and chemical synthesis. RNA structure analysis by NMR is challenging due to two major problems that become even more salient when the size of the RNA increases, namely chemical shift overlaps and line broadening leading to complete signal loss. Several isotope labeling strategies have been developed to provide solutions to these major issues, such as deuteration, segmental isotope labeling or site-specific labeling. Quantification of modified nucleosides in RNA by MS is only possible through the application of stable isotope labeled internal standards. With nucleic acid isotope labeling coupled mass spectrometry (NAIL-MS), it is now possible to analyze the dynamic processes of post-transcriptional RNA modification and demodification. The trend, in both NMR and MS RNA analytics, is without doubt shifting from the analysis of snapshot moments towards the development and application of tools capable of analyzing the dynamics of RNA structure and modification profiles.

Introduction of electropolymerization of pyrrole as a coating method for stir bar sorptive extraction of estradiol followed by gas chromatography.

In this study, fabrication of a stir bar sorbent is presented by electropolymerization of pyrrole via cyclic voltametry for the first time. The fabricated stir bar was applied as an efficient sorbent for extraction and pre-concentration of trace amounts of estradiol in urine samples through stir bar sorptive extraction (SBSE) method followed by gas chromatography-flame ionization detector. For this purpose, first the surface of stainless steel rod was modified by hyroxide functional group. Then electropolymerization of pyrrole monomers took place on the surface of functionalized steel rod under the optimized conditions including pyrrole concentration of 0.03 mol L-1, equal concentration ratio of pyrrole to sodium dodecyl sulfate, 10 cycles of cyclic voltammetry and potential scan rate of 10 mV s-1. Characterization of the produced sorbent was confirmed by scanning electron microscope imaging and energy-dispersive X-ray and infrared spectroscopy. Evantually, under the optimized conditions, the stir bar sorbent was used for extraction of estradiol from human urine samples. The presented SBSE method showed a good linearity range of 50-700 ng mL-1 with coefficient of determination 0.9910, limit of detection 10 ng mL-1 and theoretical limit of quantification 33 ng mL-1. Moreover, better enrichment factor (87) and extraction recovery (43%) were obtained using the fabricated stir bar compared with two commercial stir bars for estradiol. The intra- and inter-bar relative recoveries were obtained 92.0% and their coefficient of variations were less than 5.4%.