Article
Multidisciplinary Sciences
Yang-Ha Lee, Eunsoo Yu, Cheol-Min Park
Summary: Researchers have reported a chemo- and regioselective method for modifying unpaired guanosines in single- and double-stranded oligonucleotides, based on Rh(I)-carbene catalysis.
NATURE COMMUNICATIONS
(2021)
Review
Biochemistry & Molecular Biology
Barry S. Cooperman
Summary: The introduction of fluorophores into RNA for both in vitro and in cellulo studies of RNA function and cellular distribution is a subject of great current interest. Various methods for site-specific fluorescent labeling of RNAs are reviewed, including the utilization of natural posttranslational modifications, enzymatic transferase reactions, nucleic acid-assisted labeling, and de novo preparation of specifically labeled RNAs.
Article
Biochemical Research Methods
Moon Hyeok Choi, Van Thang Nguyen, Guralamatta Siddappa Ravi Kumara, Young Jun Seo
Summary: This study presents a stepwise RNA-primed RNA polymerization method for the site-specific incorporation of multiple fluorescent moieties into RNA, using T7 RNA polymerase. The resulting RNA exhibited fluorescence resonance energy transfer (FRET) between the multiple fluorescent labels, with the FRET signal increasing upon structural changes in the RNA. This approach suggests the possibility of performing diverse site-specific modifications in RNA using RNA polymerase.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Quentin Vicens, Jeffrey S. Kieft
Summary: Recent events have brought RNA research into the spotlight, igniting a new passion for understanding the diverse functions and structure of RNA. However, there is a misunderstanding of the foundational characteristics of RNA structure, often viewed as a single floppy strand. The purpose of this article is to help adjust mental models, better utilize RNA structural information, and provide suggestions for future efforts.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Monika K. Singha, Jan Zimak, Samantha R. Levine, Nan Dai, Chan Hong, Cecily Anaraki, Mrityunjay Gupta, Christopher J. Halbrook, Scott X. Atwood, Robert C. Spitale
Summary: In this study, a modified RNA metabolic labeling method with improved cell-specificity is described, which utilizes the in vivo expression of an optimized UPRT enzyme. The results demonstrate the selective incorporation of a modified nucleobase into nascent RNA, as validated by various tests. This approach is also successfully used for profiling cell-specific nascent RNA in a metastatic human breast cancer mouse model.
Article
Biochemical Research Methods
Micha Hersch, Adriano Biasini, Ana C. Marques, Sven Bergmann
Summary: In this study, a new method is proposed to estimate RNA synthesis, processing and degradation rates from a single sample. The method was validated on mouse embryonic stem cells and compared with other methods. The results show that the method is computationally efficient, reliable and correlates well with previous data sets. Furthermore, the application of this method reveals differences between dynamic and stable biological processes.
BMC BIOINFORMATICS
(2022)
Article
Chemistry, Multidisciplinary
Kuei C. Tang, Monika Raj
Summary: This study presents a novel strategy for the efficient chemical modification of proteins and enhancement of mass-detection sensitivity, which can be used for protein analysis in complex mixtures.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Inorganic & Nuclear
Bin-Bin Ruan, Jun-Nan Sun, Meng-Hu Zhou, Qing-Song Yang, Ya-Dong Gu, Gen-Fu Chen, Lei Shan, Zhi-An Ren
Summary: Compared with phosphorus, the study of arsenic doping in silicides is relatively less explored. In this study, superconductivity is successfully achieved by doping arsenic into Mo5Si3, with a superconducting transition temperature (T-c) of 7.7 K, which is higher than previously known W5Si3-type superconductors. Mo5Si2As is identified as a type-II BCS superconductor with upper and lower critical fields of 6.65 T and 22.4 mT, respectively. The selective occupation of 8h sites by arsenic atoms in Mo5Si2As is observed. The emergence of superconductivity is attributed to the shift of the Fermi level caused by arsenic doping, as evidenced by specific heat measurements and first-principles calculations. This work not only presents another example of arsenic doping, but also provides a practical strategy for achieving superconductivity in silicides through Fermi level engineering.
INORGANIC CHEMISTRY
(2022)
Review
Biochemistry & Molecular Biology
Keyun Huang, Xianyang Fang
Summary: RNAs are essential biomolecules that are closely associated with various cellular processes and human diseases. Investigating the structure, dynamics, and functional connections of RNA using magnetic resonance techniques such as NMR and EPR spectroscopies is crucial for understanding their biological functions and developing RNA-based therapeutics.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Chemistry, Multidisciplinary
Guralamatta Siddappa Ravi Kumara, Anup Pandith, Young Jun Seo
Summary: The method enables direct fluorescence labeling of natural unmodified DNA and RNA through selective N-6-arylation of adenosine moieties, although it favors single-stranded structures.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Philipp Innig Aguion, John Kirkpatrick, Teresa Carlomagno, Alexander Marchanka
Summary: Knowledge of RNA structure, whether in isolation or in complex, is crucial for understanding cellular processes. Solid-state NMR has been used to study high molecular-weight complexes, and recent developments in H-1 detection at fast MAS rates have overcome sensitivity and resolution limitations, allowing for more efficient analysis of RNA structures in protein-RNA complexes of any size.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Erin E. Doherty, Agya Karki, Xander E. Wilcox, Herra G. Mendoza, Aashrita Manjunath, Victorio Jauregui Matos, Andrew J. Fisher, Peter A. Beal
Summary: ADARs, which correct disease-causing mutations at the RNA level, can be targeted to sites in the transcriptome using complementary guide strands. However, ADARs have bias against editing adenosines with a guanosine 5' nearest neighbor, limiting its effectiveness. This study reveals that certain nucleosides and specific duplex structures can enhance ADAR editing efficiency at 5'-GA sites, providing insights for the design of therapeutic RNA editing strategies.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Physical
Kathiravan Murugesan, Karsten Donabauer, Rok Narobe, Volker Derdau, Armin Bauer, Burkhard Koenig
Summary: This study describes the selective activation of a C(sp3 )-H bond in the alpha-position to an amine via a carbanion intermediate. Only one specific position is activated among multiple alpha-amine sites. This method allows for the synthesis of various compounds, late-stage modification of drug derivatives, and gram-scale synthesis. Detailed mechanistic investigation has been conducted to support the proposed hypothesis.
Article
Chemistry, Multidisciplinary
Kenta Tanaka, Yoshiya Hatano, Junko Ohkanda
Summary: The 14-3-3 family of proteins plays a central role in regulating signaling pathways driven by serine/threonine kinases. Although there are seven highly conserved isoforms of 14-3-3 in humans, the specific functions of each isoform are still not fully understood. This study focused on evaluating the sigma isoform of 14-3-3 and designing a fluorescent labeling agent using a natural product as a base. The results showed that the labeled agent exhibited selective fluorescent detection of 14-3-3 sigma, indicating its potential use for studying the biological roles of this isoform.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Lukasz T. Olenginski, Owen B. Becette, Serge L. Beaucage, Theodore K. Dayie
Summary: The study introduces a novel isotope-labeled CEM amidite for efficient solid-phase synthesis of large, position-specifically labeled RNAs for NMR analysis. The unique properties of CEM amidite allow for the synthesis of large RNAs with high yield and purity. This advancement enables the study of RNA structures without complications from resonance overlap and couplings, offering valuable insights for research.
MONATSHEFTE FUR CHEMIE
(2021)