Article
Chemistry, Multidisciplinary
Christopher D. Reinkemeier, Christine Koehler, Paul F. Sauter, Nataliia V. Shymanska, Cecile Echalier, Anna Rutkowska, David W. Will, Carsten Schultz, Edward A. Lemke
Summary: This study presents the synthesis of four new SPIEDAC reactive ncAAs that do not undergo beta-elimination and a fluorescence flow cytometry based FRET-assay to measure reaction kinetics inside living cells. The results capture specific experimental conditions that are not taken into account in other assays, demonstrating conflicting findings with some previous studies.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Biotechnology & Applied Microbiology
Simon K. Krebs, Nathanael Rakotoarinoro, Marlitt Stech, Anne Zemella, Stefan Kubick
Summary: Incorporation of noncanonical amino acids with bioorthogonal reactive groups allows the generation of synthetic proteins with novel properties. This study investigates the positions of these amino acids in a cell-free system and their impact on incorporation efficiency and protein functionality.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Wenbing Cao, Haoyu Wang, Mao Quan, Yuxuan Li, Yeyu Su, Yuhang Li, Wei Jiang, Tao Liu
Summary: We identified a high-affinity host-guest pair and developed a molecular-recognition strategy to control tetrazine reactions. This strategy efficiently and reversibly regulates the reactivity of tetrazine, enabling site-specific protein labeling and dual conjugate formation in living organisms.
Article
Biochemistry & Molecular Biology
Marcel Streit, Mareike Hemberger, Stephanie Haefner, Felix Knote, Tobias Langenhan, Gerti Beliu
Summary: The introduction of an engineered aminoacyl-tRNA synthetase/tRNA pair allows for the site-specific incorporation of unnatural amino acids into proteins. This method, called Genetic Code Expansion (GCE), can also be used to control the temporal incorporation of genetically encoded elements into proteins. In this study, an optimized GCE system (GCEXpress) was developed for efficient and fast incorporation of unnatural amino acids. The GCEXpress system was used to alter the subcellular localization of proteins and to study protein-protein interactions involved in immune functions and oncological processes. The results suggest that GCE, combined with biophysical measurements, is a valuable approach for analyzing the properties of proteins and their interactions with ligands.
Review
Polymer Science
Jie Zhang, Zhiming Zhang, Jia Wang, Qiguang Zang, Jing Zhi Sun, Ben Zhong Tang
Summary: The amino-yne click reaction has rapidly developed as a useful tool for scientists in various fields since its first report in 2017, with the advantages of spontaneity, ubiquity of amines, and cleavability of products under specific stimuli.
Article
Chemistry, Multidisciplinary
Gangam Srikanth Kumar, Stefano Racioppi, Eva Zurek, Qing Lin
Summary: This article reports the design of a super fast bioorthogonal ligation reactant pair, enabling rapid bioorthogonal labeling on live cells.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Wenbing Cao, Xuewen Qin, Yong Wang, Zhen Dai, Xianyin Dai, Haoyu Wang, Weimin Xuan, Yingming Zhang, Yu Liu, Tao Liu
Summary: A general host-guest molecular recognition approach involving modification of protein functional surfaces with genetically encoded unnatural amino acids has been developed in this study, which can reversibly regulate protein function through molecular recognition, providing valuable tools for studying protein functions.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Qianqian Qi, Yutong Zhang, Wei Xiong, Xingyu Liu, Shuangyu Cui, Xiaofang Ye, Kaisong Zhang, Tian Tian, Xiang Zhou
Summary: In this study, the norbornene-tetrazine ligation chemistry is used to develop clickable RNA switches in biological contexts, and its potential applications are explored. The application of RNA-based norbornene-tetrazine ligation chemistry in controlling CRISPR systems and manipulating gene editing in human cells is successfully demonstrated.
Article
Chemistry, Multidisciplinary
Cayo Lee, Brodie J. Thomson, Glenn M. Sammis
Summary: A novel method for the generation of thionyl fluoride (SOF2) has been developed, allowing access to both aliphatic and aromatic acyl fluorides in moderate to high yields. The method shows potential for amino acid couplings and peptide synthesis, both in liquid phase and solid phase, without the need for column chromatography.
Article
Chemistry, Multidisciplinary
Birthe Meineke, Johannes Heimgartner, Alexander J. Craig, Michael Landreh, Lindon W. K. Moodie, Simon J. Elsasser
Summary: Bioorthogonal chemistry enables rapid and highly selective reactions in biological environments, with the CuAAC reaction commonly used to modify azides or alkynes introduced into biomolecules. Incorporating chemical handles into proteins via amber suppression, specifically introducing ncAAs in response to an amber stop codon, has proven useful for CuAAC chemistry on proteins. The incorporation of copper-chelating azides into proteins has not been explored extensively but using ncAA PazK has shown efficient protein labeling and improved reactivity with alkyne reagents in CuAAC.
FRONTIERS IN CHEMISTRY
(2021)
Article
Chemistry, Organic
Zoeisha S. Chinoy, Kelley W. Moremen, Frederic Friscourt
Summary: This study reports a new chemical tool, sydnone-aglycon, that can be used for the synthesis of O-glycans and the high-throughput screening of O-glycan-lectin interactions.
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Bo Li, Jie Zhang, Li Li, Gong Chen
Summary: A practical method for chiroptical sensing of free alpha amino acids has been developed, utilizing a three-component labeling reaction to derivatize analytes into an isoindole for sensitive CD and UV readouts. The assay shows high selectivity and accuracy across a wide range of concentrations, with a unprecedented lower limit of 10 micromolar concentration.
Article
Biochemical Research Methods
Bhargavi Narayanan, Fiddia Zahra, Russell A. Reeves, Akanksha Aggarwal, Robert N. O'Meally, Roger K. Henry, Megan Craven, Avital Jacobson, Robert N. Cole, Mark J. Kohr, Priya Umapathi, Natasha E. Zachara
Summary: This study aims to optimize the detection of O-GlcNAc in heart lysates by immunoblotting. The results demonstrate that two commercially available antibodies (CTD110.6 and RL2) display differential detection capability for contractile proteins in the heart, with RL2 providing a better assessment of cardiac O-GlcNAcylation in total tissue lysates.
ANALYTICAL BIOCHEMISTRY
(2023)
Article
Biochemical Research Methods
Cheng-Yueh Ting, Paul T. Kolbeck, Raffaele Colombo, Chacko Chakiath, Megan Rice, Marcello Marelli, R. James Christie
Summary: The study aims to expand the bioconjugation toolbox for cyclopentadiene by identifying reactive groups that can couple with antibodies bearing cyclopentadiene amino acids through normal electron demand (NED) or inverse electron demand (IED) mechanisms in aqueous solution. The researchers discovered 12 NED dienophiles and 4 tetrazine-based IED substrates that can be practically used for biocoupling.
BIOCONJUGATE CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Natalie Elia
Summary: GFP revolutionized cell biology by enabling protein visualization in living cells, but newer imaging technologies face limitations due to size and photophysics of fluorescent proteins. An alternative approach of direct protein labeling with fluorescent dyes has been introduced, allowing for live-cell and super-resolution imaging without the need for protein-labeling tags.
Article
Biochemistry & Molecular Biology
Simon Veth, Adrian Fuchs, Dilara Oezdemir, Clemens Dialer, David Jan Drexler, Fabian Knechtel, Gregor Witte, Karl-Peter Hopfner, Thomas Carell, Evelyn Ploetz
Summary: The cGAS-STING pathway plays a crucial role in sensing cytosolic DNA. Research on the development of fluorescent moieties and synthesis of fluorescent molecules for detection is important for the therapeutic potential of this pathway.
Article
Chemistry, Multidisciplinary
Juraj Galeta, Veronika Slachtova, Martin Dracinsky, Milan Vrabel
Summary: A synthetic strategy for the formation of pyrrolo[2,1-f][1,2,4]triazines is presented. It is shown that various readily available 1,2,4-triazines can be efficiently alkylated under mild conditions to yield 1-alkyl-1,2,4-triazinium salts. These stable salts can serve as precursors for triazinium ylides, which undergo 1,3-dipolar cycloadditions with electron-poor dipolarophiles to afford polysubstituted pyrrolotriazines in a single step.
Article
Chemistry, Multidisciplinary
Luis Montiel, Fabio Spada, Antony Crisp, Sascha Serdjukow, Thomas Carell, Thomas Frischmuth
Summary: Biorthogonal labelling using fluorescent small molecules is crucial for diagnostic and biomedical applications. A new synthetic procedure was developed to produce pH-insensitive rhodamine dyes with outstanding brightness, outperforming other common dyes in DNA fluorescent imaging. Additionally, the fluorescence properties of these dyes were further explored using dendrimers with multiple fluorescein or rhodamine units, revealing fluorescence self-quenching effects.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Review
Chemistry, Multidisciplinary
Bethany Searle, Markus Mueller, Thomas Carell, Andrew Kellett
Summary: The discovery of epigenetic bases has greatly impacted our understanding of disease and development. One of the most studied epigenetic marks is the modification of cytosines at the 5 position. Determining the spatiotemporal distribution of these modifications within the genome is crucial for gaining insight into their biological significance. While third-generation sequencing platforms have the potential to directly detect epigenetic modifications, chemical or enzymatic derivatisation currently provides the most reliable method. This Review discusses techniques available for the detection of cytosine modifications on third-generation platforms.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Correction
Multidisciplinary Sciences
Maria Arroyo, Florian D. Hastert, Andreas Zhadan, Florian Schelter, Susanne Zimbelmann, Cathia Rausch, Anne K. Ludwig, Thomas Carell, M. Cristina Cardoso
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Johannes N. Singer, Felix M. Mueller, Ewa Wegrzyn, Christina Hoelzl, Hans Hurmiz, Chuyi Liu, Luis Escobar, Thomas Carell
Summary: RNA is a molecule that plays a significant role in the origin of life as it can store genetic information and catalyze reactions. Recent studies have shown that RNA can form chimeras with amino acids, combining the information-coding properties of RNA with the catalytic potential of amino acids, which may have been the structures from which life emerged. This study reports a prebiotic chemistry method that allows the loading of nucleosides and RNAs with amino acids, paving the way for RNA-based peptide synthesis in a hypothetical RNA-peptide world.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemical Research Methods
Ambra Spampinato, Erika Kuzmova, Radek Pohl, Veronika Sykorova, Milan Vrabel, Tomas Kraus, Michal Hocek
Summary: A series of modified dNTPs with different linkers were designed and synthesized as substrates for DNA polymerase. The reactivity of these modified nucleotides and DNA was systematically tested and compared in click reactions. The longer linker was found to be crucial for efficient labeling. These modified dNTPs were transported into live cells and successfully used for staining DNA and imaging DNA synthesis within short time periods. This method provides a new approach for in cellulo metabolic labeling and imaging of DNA synthesis that overcomes previous limitations.
BIOCONJUGATE CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Veronika Slachtova, Simona Bellova, Agustina La-Venia, Juraj Galeta, Martin Dracinsky, Karel Chalupsky, Alexandra Dvorakova, Helena Mertlikova-Kaiserova, Peter Rukovansky, Rastislav Dzijak, Milan Vrabel
Summary: The development of reagents selective in complex biological media is a significant challenge. We demonstrate that N1-alkylation of 1,2,4-triazines produces more reactive triazinium salts when reacting with strained alkynes compared to the parent 1,2,4-triazines. These salts facilitate efficient modification of peptides and proteins through a powerful bioorthogonal ligation. The positively charged N1-alkyl triazinium salts possess favorable cell permeability and outperform analogous 1,2,4,5-tetrazines for intracellular fluorescent labeling applications. These new ionic heterodienes exhibit high reactivity, stability, synthetic accessibility, and improved water solubility, making them valuable additions to the repertoire of modern bioorthogonal reagents.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Eva S. Schoenegger, Antony Crisp, Marco Radukic, Jonas Burmester, Thomas Frischmuth, Thomas Carell
Summary: Post-synthetic modification of nucleic acid structures with clickable functionality is a versatile tool that improves the performance and applicability of nucleic acids. This study presents a simple and feasible technology to modify DNA and RNA strands at both ends. This method helps to synthesize highly functionalized oligonucleotides, enhancing their therapeutic and diagnostic applications.
Article
Biochemistry & Molecular Biology
Monika Witzenberger, Sandra Burczyk, David Settele, Wieland Mayer, Luisa M. Welp, Matthias Heiss, Mirko Wagner, Thomas Monecke, Robert Janowski, Thomas Carell, Henning Urlaub, Stefanie M. Hauck, Aaron Voigt, Dierk Niessing
Summary: 5-Methyluridine (m(5)U) is a common RNA modification in cytosolic tRNA, and tRNA methyltransferase 2 homolog A (hTRMT2A) is the enzyme responsible for m(5)U formation at position 54 of tRNA. Through structural and sequence analysis, it has been determined that hTRMT2A achieves specificity for tRNA modification through a combination of binding preference and the presence of a uridine at position 54. Additionally, hTRMT2A has been found to interact with proteins involved in RNA biogenesis and its knockdown has been shown to reduce translation fidelity.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Michael Kugler, Martin Hadzima, Rastislav Dzijak, Robert Rampmaier, Pavel Srb, Lukas Vrzal, Zdenek Voburka, Pavel Majer, Pavlina Rezacova, Milan Vrabel
Summary: The development of highly active and selective enzyme inhibitors is a priority in medicinal chemistry. Three selection strategies based on different principles have been compared, all leading to the identification of more potent and selective inhibitors compared to the parent compounds. Structural analysis revealed a novel exosite that could be used in the development of isoform specific inhibitors.
RSC MEDICINAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Mark Helm, Markus T. Bohnsack, Thomas Carell, Alexander Dalpke, Karl-Dieter Entian, Ann Ehrenhofer-Murray, Ralf Ficner, Christian Hammann, Claudia Ho''bartner, Andres Ja''schke, Albert Jeltsch, Stefanie Kaiser, Roland Klassen, Sebastian A. Leidel, Andreas Marx, Mario Mo''rl, Jochen C. Meier, Gunter Meister, Andrea Rentmeister, Marina Rodnina, Jean-Yves Roignant, Raffael Schaffrath, Peter Stadler, Thorsten Stafforst
Summary: This article describes the impact and subsequent effects of the DFG-funded priority program SPP1784 on the field of nucleic acid modifications. The program has facilitated interdisciplinary collaborations and contributed to the development of the nucleic acid chemistry community. The extension of funding during the COVID-19 pandemic has led to increased interest and research in the field of RNA and RNA modifications, particularly in the context of vaccination campaigns against SARS-CoV-2.
ACS CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Alexander Pichler, Markus Hillmeier, Matthias Heiss, Elsa Peev, Stylianos Xefteris, Barbara Steigenberger, Ines Thoma, Markus Mueller, Marco Borso, Axel Imhof, Thomas Carell
Summary: Queuosine is a highly complex hypermodified RNA nucleoside found in tRNAs. It has several derivatives, including glutamylated Queuosine (gluQ), which is only found in bacteria.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Genetics & Heredity
Paraskevi Karousi, Martina Samiotaki, Manousos Makridakis, Jerome Zoidakis, Diamantis C. Sideris, Andreas Scorilas, Thomas Carell, Christos K. Kontos
Summary: This study investigates the role of 3'-tRF-Cys(GCA) in gene expression regulation in HEK-293 cells and finds that it can regulate gene expression by affecting multiple cellular pathways. Additionally, the study identifies the direct interaction between 3'-tRF-Cys(GCA) and thymopoietin and its modulation of the protein's levels.
FUNCTIONAL & INTEGRATIVE GENOMICS
(2023)
