Direct Immunodetection of Global A-to-I RNA Editing Activity with a Chemiluminescent Bioassay

Spatial Visualization of A-to-I Editing in Cells Using Endonuclease V Immunostaining Assay (EndoVIA)

Adenosine-to-inosine (A-to-I) editing is one of the most widespread post-transcriptional RNA modifications and is catalyzed by adenosine deaminases acting on RNA (ADARs). Varying across tissue types, A-to-I editing is essential for numerous biological functions, and dysregulation leads to autoimmune and neurological disorders, as well as cancer. Recent evidence has also revealed a link between RNA localization and A-to-I editing, yet understanding of the mechanisms underlying this relationship and its biological impact remains limited. Current methods rely primarily on in vitro characterization of extracted RNA that ultimately erases subcellular localization and cell-to-cell heterogeneity. To address these challenges, we have repurposed endonuclease V (EndoV), a magnesium-dependent ribonuclease that cleaves inosine bases in edited RNA, to selectively bind and detect A-to-I edited RNA in cells. The work herein introduces an endonuclease V immunostaining assay (EndoVIA), a workflow that provides spatial visualization of edited transcripts, enables rapid quantification of overall inosine abundance, and maps the landscape of A-to-I editing within the transcriptome at the nanoscopic level.

Spatial visualization of A-to-I Editing in cells using Endonuclease V Immunostaining Assay (EndoVIA)

Adenosine-to-Inosine (A-to-I) editing is one of the most widespread post-transcriptional RNA modifications and is catalyzed by adenosine deaminases acting on RNA (ADARs). Varying across tissue types, A-to-I editing is essential for numerous biological functions and dysregulation leads to autoimmune and neurological disorders, as well as cancer. Recent evidence has also revealed a link between RNA localization and A-to-I editing, yet understanding of the mechanisms underlying this relationship and its biological impact remains limited. Current methods rely primarily on in vitro characterization of extracted RNA that ultimately erases subcellular localization and cell-to-cell heterogeneity. To address these challenges, we have repurposed Endonuclease V (EndoV), a magnesium dependent ribonuclease that cleaves inosine bases in edited RNA, to selectively bind and detect A-to-I edited RNA in cells. The work herein introduces Endonuclease V Immunostaining Assay (EndoVIA), a workflow that provides spatial visualization of edited transcripts, enables rapid quantification of overall inosine abundance, and maps the landscape of A-to-I editing within the transcriptome at the nanoscopic level.

Is Metal Stabilization of the Leaving Group Required or Can Lysine Facilitate Phosphodiester Bond Cleavage in Nucleic Acids? A Computational Study of EndoV

Endonuclease V (EndoV) is a single-metal-dependent enzyme that repairs deaminated DNA nucleobases in cells by cleaving the phosphodiester bond, and this enzyme has proven to be a powerful tool in biotechnology and medicine. The catalytic mechanism used by EndoV must be understood to design new disease detection and therapeutic solutions and further exploit the enzyme in interdisciplinary applications. This study has used a mixed molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) approach to compare eight distinct catalytic pathways and provides the first proposed mechanism for bacterial EndoV. The calculations demonstrate that mechanisms involving either direct or indirect metal coordination to the leaving group of the substrate previously proposed for other nucleases are unlikely for EndoV, regardless of the general base (histidine, aspartate, and substrate phosphate moiety). Instead, distinct catalytic pathways are characterized for EndoV that involve K139 stabilizing the leaving group, a metal-coordinated water stabilizing the transition structure, and either H214 or a substrate phosphate group activating the water nucleophile. In silico K139A and H214A mutational results support the newly proposed roles of these residues. Although this is a previously unseen combination of general base, general acid, and metal-binding architecture for a one-metal-dependent endonuclease, our proposed catalytic mechanisms are fully consistent with experimental kinetic, structural, and mutational data. In addition to substantiating a growing body of literature, suggesting that one metal is enough to catalyze P-O bond cleavage in nucleic acids, this new fundamental understanding of the catalytic function will promote the exploration of new and improved applications of EndoV.

Surface Oxygen Vacancy-Rich Co3O4 Nanowires as an Effective Catalyst of Luminol-H2O2 Chemiluminescence for Sensitive Immunoassay

Oxygen vacancy is one intrinsic defect in metal oxide materials. Interestingly, we herein found that the surface oxygen vacancy can significantly enhance the catalytic activity of Co3O4 nanowires in the luminol-H2O2 chemiluminescence (CL) reaction. 0.1 ng/mL Co3O4 nanowires containing 51.3% surface oxygen vacancies possessed ca. 2.5-fold catalytic activity of free Co2+ (the best metal ionic catalyst for the luminol-H2O2 CL reaction). The superior catalytic efficiency is attributed to the enhanced adsorption of H2O2 by surface oxygen vacancies, which in turn accelerates the cleavage of O-O bonds and generates •OH radicals. More importantly, the surface oxygen vacancy-rich Co3O4 nanowires retained about 90% catalytic activity after modification with antibodies. The surface oxygen vacancy-rich Co3O4 nanowires were used to label the secondary antibody, and one sandwich-type CL immunoassay of carcinoembryonic antigen was established. The detection limit was 0.3 ng/mL with a linear range of 1-10 ng/mL. This proof-of-concept work proves that surface oxygen vacancy-rich Co3O4 nanowires are suitable for labeling biomolecules in CL bioanalysis and biosensing.

Carbon Vacancy-Enhanced Activity of Fe-N-C Single Atom Catalysts toward Luminol Chemiluminescence in the Absence of H2O2

The classic luminol-H2O2 chemiluminescence (CL) systems suffer from easy self-decomposition of H2O2 at room temperature, hindering the practical applications of the luminol-H2O2 CL system. In this work, unexpectedly, we found that the carbon vacancy-modified Fe-N-C single atom catalysts (VC-Fe-N-C SACs) can directly trigger a luminol solution to generate strong CL emission in the absence of H2O2. The Fe-based SACs were prepared through the conventional pyrolysis of zeolitic imidazolate frameworks. The massive carbon vacancies were readily introduced into Fe-N-C SACs through a tannic acid-etching process. Carbon vacancy significantly enhanced the catalytic activity of Fe-N-C SACs on the CL reaction of luminol-dissolved oxygen. The VC-Fe-N-C SACs performed a 13.4-fold CL enhancement compared with the classic luminol-Fe2+ system. It was found that the introduction of a carbon vacancy could efficiently promote dissolved oxygen to convert to reactive oxygen species. As a proof of concept, the developed CL system was applied to detect alkaline phosphatase with a linear range of 0.005-1 U/L as well as a detection limit of 0.003 U/L. This work demonstrated that VC-Fe-N-C SAC is a highly efficient CL catalyst that can promote the analytic application of the luminol CL system.

Harnessing Nature's Molecular Recognition Capabilities to Map and Study RNA Modifications

RNA editing or "epitranscriptomic modification" refers to the processing of RNA that occurs after transcription to alter the sequence or structure of the nucleic acid. These chemical alterations can be found on either the ribose sugar or the nucleobase, and although many are "silent" and do not change the Watson-Crick-Franklin code of the RNA, others result in recoding events. More than 170 RNA modifications have been identified so far, each having a specific biological purpose. Additionally, dysregulated RNA editing has been linked to several types of diseases and disorders. As new modifications are discovered and our understanding of their functional impact grows, so does the need for selective methods of identifying and mapping editing sites in the transcriptome.The most common methods for studying RNA modifications rely on antibodies as affinity reagents; however, antibodies can be difficult to generate and often have undesirable off-target binding. More recently, selective chemical labeling has advanced the field by offering techniques that can be used for the detection, enrichment, and quantification of RNA modifications. In our method using acrylamide for inosine labeling, we demonstrated the versatility with which this approach enables pull-down or downstream functionalization with other tags or affinity handles. Although this method did enable the quantitative analysis of A-to-I editing levels, we found that selectivity posed a significant limitation, likely because of the similar reactivity profiles of inosine and pseudouridine or other nucleobases.Seeking to overcome the inherent limitations of antibodies and chemical labeling methods, a more recent approach to studying the epitranscriptome is through the repurposing of proteins and enzymes that recognize modified RNA. Our laboratory has used Endonuclease V, a repair enzyme that cleaves inosine-containing RNAs, and reprogrammed it to instead bind inosine. We first harnessed EndoV to develop a preparative technique for RNA sequencing that we termed EndoVIPER-seq. This method uses EndoV to enrich inosine-edited RNAs, providing better coverage in RNA sequencing and leading to the discovery of previously undetected A-to-I editing sites. We also leveraged EndoV to create a plate-based immunoassay (EndoVLISA) to quantify inosine in cellular RNA. This approach can detect differential A-to-I editing levels across tissue types or disease states while being independent of RNA sequencing, making it cost-effective and high-throughput. By harnessing the molecular recognition capabilities of this enzyme, we show that EndoV can be repurposed as an "anti-inosine antibody" to develop new methods of detecting and enriching inosine from cellular RNA.Nature has evolved a plethora of proteins and enzymes that selectively recognize and act on RNA modifications, and exploiting the affinity of these biomolecules offers a promising new direction for the field of epitranscriptomics.

Endonuclease V from the archaeon Thermococcus kodakarensis is an inosine-specific ribonuclease

Endonuclease V (EndoV) is an inosine-specific endonuclease which is highly conserved in all domains of life: Bacteria, Archaea, and Eukarya; and, therefore, may play an important role in nucleic acid processes. It is currently thought that bacterial EndoVs are involved in DNA repair, while eukaryotic EndoVs are involved in RNA editing based on the differences in substrate preferences. However, the role of EndoV proteins, particularly in the archaeal domain, is still poorly understood. Here, we explored the biochemical properties of EndoV from the hyperthermophilic archaeon Thermococcus kodakarensis (TkoEndoV). We show that TkoEndoV has a strong preference for RNA over DNA. Further, we synthesized 1-methylinosine-containing RNA that is a simple TΨC loop mimic of archaeal tRNA and found that TkoEndoV discriminates between 1-methylinosine and inosine, and selectively acts on inosine. Our findings suggest a potential role of archaeal EndoV in the regulation of inosine-containing RNA.

Highly Sensitive Chemiluminescent Immunoassay of Mycotoxins Using ZIF-8-Derived Yolk-Shell Co Single-Atom Site Catalysts as Superior Fenton-like Probes

Superior to traditional nanoscale catalysts, single-atom site catalysts (SASCs) show such merits as maximal catalysis efficiency and outstanding catalytic activity for the construction of analytical methodological platforms. Hereby, an in situ etching strategy was designed to prepare yolk-shell Co SASCs derived from ZIF-8@SiO₂ nanoparticles. On the basis of direct chemical interactions between precursors and supports, the Co element with isolated atomic dispersion was anchored on ZIF-8@SiO₂ nanoparticles. The Co SASCs possess high Fenton-like activity and thus can catalyze the decomposition of H₂O₂ to produce massive superoxide radical anions instead of singlet oxygen and hydroxyl radicals. With the activity for producing superoxide radical anion, Co SASCs can greatly improve the chemiluminescent (CL) response of a luminol system by 3133.7 times. Furthermore, the SASCs with active sites of Co-O₅ moieties were utilized as the CL probes for establishment of an immunoassay method for sensitive detection of mycotoxins by adopting aflatoxin B1 as a mode analyte. The quantitation range is 10-1000 pg/mL, and the limit of detection is 0.44 pg/mL (3σ) for aflatoxin B1. The proof-of-principle work elucidates the practicability of direct chemical interactions between precursors and supports for forming SASCs with ultrahigh CL response, which can be extended to the exploitation of more sorts of SASCs for tracing biological binding events.

Emitter-Quencher Pair of Single Atomic Co Sites and Monolayer Titanium Carbide MXenes for Luminol Chemiluminescent Reactions

A facile, one-step doping protocol was adopted to synthesize Co single atomic site catalysts (SASCs) in UiO-66 metal-organic frameworks. In view of highly uniform active sites of Co-O₆ moieties, the SASCs specifically contribute to catalyzing the generation of a large amount of singlet oxygen instead of superoxide or hydroxyl radicals, which endows Co SASCs with a the remarkable enhancement effect (∼3775 times) on luminol chemiluminescent (CL) emission. Interestingly, monolayer titanium carbide MXenes can drastically quench the CL signal of the Co SASC-boosted luminol reaction by ∼94.6% as highly efficient luminescent absorbents. Furthermore, the emitter-quencher pair of Co SASCs and titanium carbide MXenes was successfully adopted to develop an immunoassay method for cardiac troponin I (cTnI) on an immunochromatographic test strip platform. With a sandwich immunoreaction mode, a titanium carbide MXene-labeled cTnI tracer antibody was captured on the test line of a test strip, which significantly inhibited the CL response of the Co SACs-boosted luminol system. The dynamic range for quantitating cTnI is 1.0-100 pg mL^-1, with a detection limit of 0.33 pg mL^-1 (3σ). The test strip was successfully used to detect cTnI in human serum samples collected from cardiopathy patients. This proof-of-principle work manifests both the CL enhancement of SASCs and the quenching behavior of MXenes, which shows the thrilling prospects of combinational usage of the two functionalized nanomaterials for tracking biological recognition events.