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1. Fluorescent Platforms for RNA Chemical Biology Research

   https://doi.org/10.3390/genes13081348  

   Du, Jinxi; Dartawan, Ricky; Rice, William; Gao, Forrest; Zhou, Joseph H.; Sheng, Jia (August 2022, Genes)

   Efficient detection and observation of dynamic RNA changes remain a tremendous challenge. However, the continuous development of fluorescence applications in recent years enhances the efficacy of RNA imaging. Here we summarize some of these developments from different aspects. For example, single-molecule fluorescence in situ hybridization (smFISH) can detect low abundance RNA at the subcellular level. A relatively new aptamer, Mango, is widely applied to label and track RNA activities in living cells. Molecular beacons (MBs) are valid for quantifying both endogenous and exogenous mRNA and microRNA (miRNA). Covalent binding enzyme labeling fluorescent group with RNA of interest (ROI) partially overcomes the RNA length limitation associated with oligonucleotide synthesis. Forced intercalation (FIT) probes are resistant to nuclease degradation upon binding to target RNA and are used to visualize mRNA and messenger ribonucleoprotein (mRNP) activities. We also summarize the importance of some fluorescence spectroscopic techniques in exploring the function and movement of RNA. Single-molecule fluorescence resonance energy transfer (smFRET) has been employed to investigate the dynamic changes of biomolecules by covalently linking biotin to RNA, and a focus on dye selection increases FRET efficiency. Furthermore, the applications of fluorescence assays in drug discovery and drug delivery have been discussed. Fluorescence imaging can also combine with RNA nanotechnology to target tumors. The invention of novel antibacterial drugs targeting non-coding RNAs (ncRNAs) is also possible with steady-state fluorescence-monitored ligand-binding assay and the T-box riboswitch fluorescence anisotropy assay. More recently, COVID-19 tests using fluorescent clustered regularly interspaced short palindromic repeat (CRISPR) technology have been demonstrated to be efficient and clinically useful. In summary, fluorescence assays have significant applications in both fundamental and clinical research and will facilitate the process of RNA-targeted new drug discovery, therefore deserving further development and updating. 

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2. Chemical Approaches To Investigate Post-transcriptional RNA Regulation

   https://doi.org/10.1021/acschembio.3c00406  

   Kleiner, Ralph E. (August 2023, ACS Chemical Biology)
3. Chemical Method to Sequence 5-Formylcytosine on RNA

   https://doi.org/10.1021/acschembio.1c00707  

   Li, Ang; Sun, Xuemeng; Arguello, A. Emilia; Kleiner, Ralph E. (March 2022, ACS Chemical Biology)
4. RNAvigate: efficient exploration of RNA chemical probing datasets

   https://doi.org/10.1093/nar/gkae089  

   Irving, Patrick S.; Weeks, Kevin M. (February 2024, Nucleic Acids Research)

   Abstract Chemical probing technologies enable high-throughput examination of diverse structural features of RNA, including local nucleotide flexibility, RNA secondary structure, protein and ligand binding, through-space interaction networks, and multistate structural ensembles. Deep understanding of RNA structure–function relationships typically requires evaluating a system under structure- and function-altering conditions, linking these data with additional information, and visualizing multilayered relationships. Current platforms lack the broad accessibility, flexibility and efficiency needed to iterate on integrative analyses of these diverse, complex data. Here, we share the RNA visualization and graphical analysis toolset RNAvigate, a straightforward and flexible Python library that automatically parses 21 standard file formats (primary sequence annotations, per- and internucleotide data, and secondary and tertiary structures) and outputs 18 plot types. RNAvigate enables efficient exploration of nuanced relationships between multiple layers of RNA structure information and across multiple experimental conditions. Compatibility with Jupyter notebooks enables nonburdensome, reproducible, transparent and organized sharing of multistep analyses and data visualization strategies. RNAvigate simplifies and accelerates discovery and characterization of RNA-centric functions in biology. 

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5. Carbon‐13 chemical shift tensor measurements for nitrogen‐dense compounds

   https://doi.org/10.1002/mrc.5422  

   Holmes, Sean T.; Boley, Cameron M.; Dewicki, Angelika; Gardner, Zachary T.; Vojvodin, Cameron S.; Iuliucci, Robbie J.; Schurko, Robert W. (January 2024, Magnetic Resonance in Chemistry)

   Abstract This paper reports the principal values of the¹³C chemical shift tensors for five nitrogen‐dense compounds (i.e., cytosine, uracil, imidazole, guanidine hydrochloride, and aminoguanidine hydrochloride). Although these are all fundamentally important compounds, the majority do not have¹³C chemical shift tensors reported in the literature. The chemical shift tensors are obtained from¹H→¹³C cross‐polarization magic‐angle spinning (CP/MAS) experiments that were conducted at a high field of 18.8 T to suppress the effects of¹⁴N‐¹³C residual dipolar coupling. Quantum chemical calculations using density functional theory are used to obtain the¹³C magnetic shielding tensors for these compounds. The best agreement with experiment arises from calculations using the hybrid functional PBE0 or the double‐hybrid functional PBE0‐DH, along with the triple‐zeta basis sets TZ2P or pc‐3, respectively, and intermolecular effects modeled using large clusters of molecules with electrostatic embedding through the COSMO approach. These measurements are part of an ongoing effort to expand the catalog of accurate¹³C chemical shift tensor measurements, with the aim of creating a database that may be useful for benchmarking the accuracy of quantum chemical calculations, developing nuclear magnetic resonance (NMR) crystallography protocols, or aiding in applications involving machine learning or data mining. This work was conducted at the National High Magnetic Field Laboratory as part of a 2‐week school for introducing undergraduate students to practical laboratory experience that will prepare them for scientific careers or postgraduate studies. 

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