Article
Chemistry, Organic
Jiying Liang, Han Jia, Lan Li, Xiang Li, Ying Li
Summary: A novel beta-difluoroalkylamine was designed for capturing RNAs and proteins with high tempospatial resolution via proximity labeling mediated by photoinduced singlet oxygen. The appended azide group enables RNA biotinylation and downstream analysis through both SPAAC and CuAAC, with the beta-difluoroalkylazide motif exhibiting an enhanced CuAAC reaction rate for preserving good RNA integrity.
Article
Biochemical Research Methods
Alexandra Bristiel, Manon Cadinot, Mathieu Pizzonero, Frederic Taran, Dominique Urban, Raphael Guignard, Dominique Guianvarc'h
Summary: The researchers developed a facile method for conjugating relevant probes, ligands, or delivery agents onto oligonucleotides (ONs), which is important for both fundamental studies in chemical biology and improving the pharmacology of ONs in medicinal chemistry. They introduced novel 2'-functionalized nucleoside phosphoramidite monomers that contain bioorthogonal methylcyclopropene or sydnone moieties for the first time to ON solid-phase synthesis, allowing traceless ON postsynthetic modifications with reactive complementary probes through inverse electron-demand Diels-Alder reactions or strain-promoted sydnone-alkyne cycloaddition. These findings expand the bioorthogonal phosphoramidite building blocks and provide a new method for generating labeled ONs.
BIOCONJUGATE CHEMISTRY
(2023)
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, Analytical
Yuanyu Huang, Quanqing Zhang, Lujie Yang, Ling Lin, Juanjuan Xie, Jun Yao, Xinwen Zhou, Lei Zhang, Huali Shen, Pengyuan Yang
Summary: The PMSNP method was developed for efficient capture and analysis of nascent proteins, achieving a modification efficiency of 91.8% on silica microspheres through click reaction. After optimization, more than 3500 and 3900 nascent proteins could be rapidly identified, demonstrating the sensitivity and immediacy of this method in exploring changes in the translation process.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Chijioke N. Umunnakwe, Alice Duchon, Olga A. Nikolaitchik, Sheikh Abdul Rahman, Yang Liu, Jianbo Chen, Sheldon Tai, Vinay K. Pathak, Wei-Shau Hu
Summary: This study aimed to investigate the cis-acting elements in the HIV-2 genome important for genome packaging, revealing a hierarchical nature of guanosine-containing sites with mutations at different sites affecting RNA packaging efficiency differently. Additionally, mutations at multiple sites can act synergistically to cause defects in genome packaging, providing key insights into the replication mechanisms of HIV-2.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Polymer Science
Himani Bisht, Jaehoon Jeong, Yubin Hong, Suho Park, Daewha Hong
Summary: A tyrosine-based azido derivative (TBAD) that can perform substrate-independent surface coating and clickable film functionalization is synthesized. The TBAD remains stable under alkaline and neutral conditions and is oxidized by tyrosinase to initiate melanin-like polymerization. The resulting poly(TBAD) film can be formed on various substrates and undergo click reaction with terminal alkyne moieties. This clickable coating technique could be significant for bioconjugation, soft lithography, and labeling techniques.
MACROMOLECULAR RAPID COMMUNICATIONS
(2022)
Article
Chemistry, Applied
Haotian Gao, Zhemiao Lu, Yin Xiao
Summary: In this study, two series of thiophene-based copolymers with cyclodextrins (CDs) grafted on the side chain were synthesized to achieve efficient enantio-recognition of amino acids. The copolymers showed a reverse interaction preference for D- and L-isomers due to the different interaction modes of native and substituted CDs. The content of the CD block in the copolymer was found to affect the sensitivity and chiral selectivity of the electrochemical sensor.
CARBOHYDRATE POLYMERS
(2022)
Article
Chemistry, Multidisciplinary
Hao Yu, Ziteng Guo, Ningxu Han, Junjuan Shi, Xin Jiang, Qixia Bai, Zhe Zhang, Pingshan Wang, Ming Wang
Summary: This study proposes a strategy for synthesizing molecular cages by endo-modification of steric hindrance groups on dissymmetrical ligands. The resulting cages have low symmetry and dissimilar chemical environments, which has significant implications for constructing new supramolecular systems.
CELL REPORTS PHYSICAL SCIENCE
(2023)
Article
Biochemical Research Methods
Anjalee N. Wijetunge, Garrett J. Davis, Mehrdad Shadmehr, Julia A. Townsend, Michael T. Marty, John C. Jewett
Summary: The novel TBD described in this study allows for efficient protein labeling with cyclooctyne installation on protein surfaces, enabling later copper-free click reactions involving functional azides across a wide pH range. The orthogonality of the cyclooctyne modification was demonstrated, and the azobenzene modification was shown to be cleavable with sodium dithionite treatment.
BIOCONJUGATE CHEMISTRY
(2021)
Review
Chemistry, Analytical
Feiyu Wang, Yiwen Xie, Weijie Zhu, Tianxiang Wei
Summary: The functionalization of biosensor interfaces is crucial for improving key characteristics of biosensing systems. The click reaction, particularly the electro-click reaction, has gained significant attention and is widely regarded as a promising approach for modifying electrodes and sensing films. It offers advantages such as reagent-free functionalization, high speed, selectivity, and minimal pollution. This review discusses the latest advancements in functionalized biosensor interfaces, categorizing the strategies based on the mediators used, and provides a comprehensive summary of electro-click strategies for functionalizing electrochemical and optical biosensor interfaces.
Article
Biochemistry & Molecular Biology
Paloma Lozano-Picazo, Cristina Castro-Dominguez, Augusto Luis Bruno, Alejandro Baeza, Adelia S. Martinez, Patricia A. Lopez, Angela Castro, Yassmin Lakhal, Elena Montero, Luis Colchero, Daniel Gonzalez-Nieto, Francisco Javier Rojo, Fivos Panetsos, Milagros Ramos, Rafael Daza, Alfonso M. Ganan-Calvo, Manuel Elices, Gustavo Victor Guinea, Jose Perez-Rigueiro
Summary: High-performance regenerated silk fibers can be efficiently produced through straining flow spinning technique. These fibers not only have enhanced biocompatibility but also can be conveniently functionalized, such as producing fluorescent fibers for tracking, combining fibers with enzymes for catalytic properties, and modifying fibers with cell-adhesion motifs for modulating cell adherence.
Article
Chemistry, Multidisciplinary
Olga A. Krasheninina, Julia Thaler, Matthias D. Erlacher, Ronald Micura
Summary: This study introduces a new method for metal-free diazotransfer on native RNA, which can be used for tagging and developing other RNA tools. The azido-RNA obtained by this method can be further processed through well-established bioorthogonal reactions, expanding its applications.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Agricultural Engineering
Xiao-Man Fan, Jia-Jia Shen, Yuan-Yuan Xu, Jian Gao, Ye-Wang Zhang
Summary: A method for specific immobilization of whole-cell was developed through a click reaction between alkyne and azide groups, showing significantly higher activity, operational stability, and reusability compared to free cells.
BIORESOURCE TECHNOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Kai Klein, Kateryna Loza, Marc Heggen, Matthias Epple
Summary: In this study, glutathione-functionalized gold nanoparticles were azidated and covalently functionalized through a click reaction successfully coupling alkyne-functionalized dyes. The surface composition and successful azidation were confirmed by NMR and UV/vis spectroscopy. The dye-clicked nanoparticles exhibited high fluorescence, high yield, and applicability for metallic nanoparticles.
Article
Chemistry, Inorganic & Nuclear
Shamna Muhamed, Ravari Kandy Aparna, Arun Karmakar, Subrata Kundu, Sukhendu Mandal
Summary: NU-1000, a hydrothermally stable metal-organic framework, was functionalized with thiol moieties using a solvent-assisted ligand incorporation strategy. The thiolated NU-1000 can immobilize gold nanoparticles and exhibit catalytic activity for the hydrogen evolution reaction. The catalyst showed sustainable performance and holds potential as a catalyst for hydrogen production.
INORGANIC CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Florian Richter, Johanna E. Plehn, Larissa Bessler, Jasmin Hertler, Marko Joerg, Cansu Cirzi, Francesca Tuorto, Kristina Friedland, Mark Helm
Summary: The research revealed significant differences in RNA degradation rates and modification patterns in different tissues after death, with RNA integrity correlated with co-varying rRNA markers. Therefore, careful execution of RNA and tissue preparations is crucial for interpreting modification patterns in tRNA and small RNA.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cell Biology
Yuri Motorin, Mark Helm
Summary: RNA methylation has re-emerged as an important mechanism in gene regulation, leading to new insights in RNA research; the presence of methyltransferases in disease models and clinical investigations has significantly contributed to the field's progress; the concept of reversibility and dynamics in RNA modification has replaced the previous perception of irreversible RNA maturation, potentially resulting in diverse populations of RNA variants.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2022)
Editorial Material
Multidisciplinary Sciences
Mark Helm, Yuri Motorin
Summary: For the first time, a comprehensive study has described the phosphorylation in the core of a transfer RNA molecule and characterized the enzymes responsible for adding and removing the phosphate group.
Article
Biochemistry & Molecular Biology
Tim R. Fischer, Laurenz Meidner, Marvin Schwickert, Marlies Weber, Robert A. Zimmermann, Christian Kersten, Tanja Schirmeister, Mark Helm
Summary: RNA methyltransferases (MTases) are widely present enzymes that have gained increasing interest in the field of RNA methylation. This article discusses the development of small molecules for targeted transfer of functional groups and labels, as well as the investigation of SAM-derived compounds as inhibitors of RNA MTases.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Damien Bregeon, Ludovic Pecqueur, Sabrine Toubdji, Claudia Sudol, Murielle Lombard, Marc Fontecave, Valerie de Crecy-Lagard, Yuri Motorin, Mark Helm, Djemel Hamdane
Summary: Recent studies have revealed that RNA molecules undergo post-transcriptional modifications, including dihydrouridine modifications that were originally believed to be specific to tRNA. These modifications have been found not only in tRNA but also in mRNA, and they play important roles in meiotic chromosome segregation, protein translation rates, and cell proliferation. Dihydrouridine modifications are introduced by dihydrouridine synthases.
ACS CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Medicinal
Elisabeth Kallert, Tim R. Fischer, Simon Schneider, Maike Grimm, Mark Helm, Christian Kersten
Summary: This study reveals the potential of protein-based docking programs to reproduce native binding modes of small-molecule RNA ligands and to distinguish known binders from decoys. A prospective virtual screening experiment demonstrates the feasibility of this approach.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Biochemistry & Molecular Biology
Larissa Bessler, Navpreet Kaur, Lea-Marie Vogt, Laurin Flemmich, Carmen Siebenaller, Marie-Luise Winz, Francesca Tuorto, Ronald Micura, Ann E. Ehrenhofer-Murray, Mark Helm
Summary: This study successfully incorporated an azide-containing derivative into tRNA via transglycosylation, resulting in a semi-synthetic RNA modification called Q-L1. The incorporation of this clickable chemical entity was demonstrated in vitro and in vivo, indicating its functional integration into translation and recruitment to the ribosome. The Q-L1 modification facilitated analytics through click conjugation, and was shown to maintain tRNA substrate specificity and promote further modification in cellular systems. This study represents the first in vivo integration of a synthetic moiety into an RNA modification circuit.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Jasmin Hertler, Kaouthar Slama, Benedikt Schober, Zeynep Ozrendeci, Virginie Marchand, Yuri Motorin, Mark Helm
Summary: Techniques have been developed to isolate long, translatable, and internally point-modified mRNA, enabling functional analysis of these modified mRNAs.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Larissa Bessler, Lea-Marie Vogt, Marc Lander, Christina Dal Magro, Patrick Keller, Jonas Kuehlborn, Christopher J. Kampf, Till Opatz, Mark Helm
Summary: Both RNA modification and RNA damage involve non-canonical nucleoside structures. While RNA modifications improve function, RNA damage has detrimental effects. This study identified and characterized a new structure, 2-methylthio-1,N6-ethenoadenosine (ms(2)epsilon A), related to a lesion resulting from exposure to alkylating chemicals. The formation of ms(2)epsilon A involves cleavage of a prenyl moiety in a known transfer RNA modification.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Florian Pichot, Marion C. Hogg, Virginie Marchand, Valerie Bourguignon, Elisabeth Jirstrom, Cliona Farrell, Hesham A. Gibriel, Jochen H. M. Prehn, Yuri Motorin, Mark Helm
Summary: Modification of tRNA is crucial for generating RNA expression diversity. In this study, the stoichiometry of incompletely modified sites in human tRNAs was investigated, and it was found that up to 75% of sites can be incompletely modified. The modification patterns of tRNA populations can provide information to differentiate different cell lines.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Chemistry, Medicinal
Robert Alexander Zimmermann, Marvin Schwickert, J. Laurenz Meidner, Zarina Nidoieva, Mark Helm, Tanja Schirmeister
Summary: This study explores the applicability of a novel fluorescent tracer for human RNA methyltransferase DNMT2 and establishes a new screening method using microscale thermophoresis. The results overcome some limitations of traditional methods and provide additional information.
ACS PHARMACOLOGY & TRANSLATIONAL SCIENCE
(2022)
Article
Chemistry, Medicinal
Marvin Schwickert, Robert A. Zimmermann, Tanja Habeck, Sabrina N. Hoba, Zarina Nidoieva, Tim R. Fischer, Martin M. Stark, Christian Kersten, Frederik Lermyte, Mark Helm, Tanja Schirmeister
Summary: The DNA methyltransferase 2 (DNMT2) is an RNA modifying enzyme that plays a role in various pathophysiological processes, including mental and metabolic disorders and cancer. In this study, covalent SAH-based DNMT2 inhibitors were developed and tested for their effectiveness. A 4-bromo-3-nitrophenylsulfonamide-decorated SAH derivative (80) was found to be the most potent and selective inhibitor, with confirmed covalent reaction with the catalytically active cysteine-79.
ACS MEDICINAL CHEMISTRY LETTERS
(2023)
Review
Genetics & Heredity
Sylvain Delaunay, Mark Helm, Michaela Frye
Summary: Chemical modifications of nucleotides in RNA can alter its properties and are used for clinical purposes in stable artificial RNAs. These modifications also regulate cellular processes and their study has led to the understanding of disease mechanisms and innovative clinical approaches. The ability to manipulate RNA modifications offers therapeutic potential and has paved the way for novel clinical strategies.
NATURE REVIEWS GENETICS
(2023)
Article
Biochemical Research Methods
Anna Wierczeiko, Stefan Pastore, Stefan Muendnich, Anne M. Busch, Vincent Dietrich, Mark Helm, Tamer Butto, Susanne Gerber
Summary: Oxford Nanopore Technologies' sequencing platform allows for real-time analysis, providing early insights and accelerating decision-making for further analysis. NanopoReaTA is introduced as a user-friendly toolbox for real-time analysis of RNA-sequencing data from ONT, offering visual snapshots and enabling interactive sequencing and rapid decision-making.
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)
Review
Chemistry, Multidisciplinary
Dan He, Yawen Li, Fuwen Zhao, Yuze Lin
Summary: High trap density in organic solar cells leads to localized charge carriers and reduced carrier lifetime, limiting device efficiency. This feature article summarizes the recent advances of trap suppression by material design and device engineering.
CHEMICAL COMMUNICATIONS
(2024)
Review
Chemistry, Multidisciplinary
Olivier Monfort, Arshitha Madhusudhan, Martin Motola
Summary: This article presents the advantages of coupling photocatalysis and Fenton-based processes for environmental remediation and discusses their synergy. It critically examines the simultaneous triggering of these two processes and provides insights into research approaches. The study aims to enhance understanding of this complex process and highlight the potential integration of new catalysts in current wastewater treatment technology.
CHEMICAL COMMUNICATIONS
(2024)
Article
Chemistry, Multidisciplinary
Manideepa Dhar, Chittaranjan Mishra, Avijit Das, Uttam Manna
Summary: An approach of 'polymerization of monomers in its aggregated form' has been introduced to tailor the water wettability of fibrous and porous substrates, achieving hydrophobicity to superhydrophobicity transition, as well as patterned wettability. This facile chemical method provides a durable coating with adjustable and patterned wettability for various potential applications.
CHEMICAL COMMUNICATIONS
(2024)
Article
Chemistry, Multidisciplinary
Saswat Ranjan Bhoi, Chhanda Debnath, Shikha Gandhi
Summary: In this article, a novel catalytic reaction using Pd(0) and Bronsted acid is reported for the synthesis of biologically important imidazolidinone-fused N-heterocycles through redox-neutral intramolecular N-allylation of indoles and pyrroles with alkynes. This atom-economical method is applicable to a wide range of substrates and eliminates the need for leaving groups or oxidizing agents commonly used in traditional allylation reactions.
CHEMICAL COMMUNICATIONS
(2024)
Article
Chemistry, Multidisciplinary
Longkun Chen, Mingshuai Zhang, Meichen Liu, Zhuoyuan Liu, Yuetong Qiu, Zhilai Zhang, Fuchao Yu, Jiuzhong Huang
Summary: In this study, an efficient Rh(III)-catalyzed selective mono- and dual-C-H bond functionalization/cyclization with iodonium ylide as the sole coupling partner was demonstrated. Fused benzodiazepine skeletons were obtained in excellent yields, providing an improved approach to dual C-H unsymmetrical functionalization.
CHEMICAL COMMUNICATIONS
(2024)
Article
Chemistry, Multidisciplinary
Alice Kennett, Sven Epple, Gabriella van der Valk, Irene Georgiou, Evelyne Gout, Romain R. Vives, Angela J. Russell
Summary: This study presents the design and synthesis of sulfated disaccharide inhibitors based on IdoA(2S)-GlcNS(6S), which showed potent inhibition of Sulf-2. The results suggest that IdoA(2S)-GlcNS(6S) is the shortest fragment size required for effective inhibition of Sulfs, and a trisulfated disaccharide is identified as the minimal fragment size of heparan sulfate for effective endosulfatase inhibition.
CHEMICAL COMMUNICATIONS
(2024)
Article
Chemistry, Multidisciplinary
Mauro Garbini, Andrea Brunetti, Riccardo Pedrazzani, Magda Monari, Massimo Marcaccio, Giulio Bertuzzi, Marco Bandini
Summary: The self-adaptability of galvanostatic electrolysis was found to be helpful in a multistage chemo- and diastereoselective electrochemically promoted cyclodimerization of chalcones. Through a series of reductive events, densely functionalized cyclopentanes with five contiguous stereocenters were obtained (25 examples, yields up to 95%, dr values up to >20:1). Further experimental and electrochemical investigations indicated the crucial role of dynamic kinetic resolution of the aldol intermediate in the reaction mechanism.
CHEMICAL COMMUNICATIONS
(2024)
Article
Chemistry, Multidisciplinary
Dhananjay S. Nipate, Neha Meena, Prakash N. Swami, Krishnan Rangan, Anil Kumar
Summary: In this study, the synthesis of functionalized benzo[a]phenazines and indazolo[2,3-a]quinolines was achieved through Rh(III)-catalyzed oxidative annulation of 2-arylquinoxalines and 2-aryl-2H-indazoles with allyl alcohols. The method showed a wide substrate scope, excellent functional group tolerance, good to high yields of annulated products, and the capability for scaled-up synthesis. A tentative mechanism of the annulation reaction was proposed based on a preliminary mechanistic investigation.
CHEMICAL COMMUNICATIONS
(2024)
Article
Chemistry, Multidisciplinary
Ruonan Zhang, Abudukadi Tudi, Xia Yang, Xuping Wang, Zhihua Yang, Shujuan Han, Shilie Pan
Summary: A new lead tellurium borate material with a unique fundamental building block [B4O10] was synthesized and found to exhibit high birefringence. The structure-property relationship was discussed using first-principles calculations.
CHEMICAL COMMUNICATIONS
(2024)
Article
Chemistry, Multidisciplinary
Amresh Kumar Singh, Baishali Thakurta, Anupam Giri, Monalisa Pal
Summary: This study introduces three key concepts for the quick synthesis of large-scale high-quality 2D materials films and their utilization in device fabrication.
CHEMICAL COMMUNICATIONS
(2024)
Article
Chemistry, Multidisciplinary
Reina Hagiwara, Shun Nishimura, Kosuke Okeyoshi
Summary: A copolymer-conjugated nanocatalytic system has been developed to improve electron transfer and enhance photoinduced H2 generation.
CHEMICAL COMMUNICATIONS
(2024)
