Strategies for Covalent Labeling of Long RNAs

EPR distance measurements on long non-coding RNAs empowered by genetic alphabet expansion transcription

(2020) Christof Domnick et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Repurposing antiviral drugs for orthogonal RNA‐catalyzed labeling of RNA

(2020) Mohammad Ghaem Maghami et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Postsynthetic Modifications of DNA and RNA by Means of Copper-Free Cycloadditions as Bioorthogonal Reactions

(2020) Katja Krell et al.   BIOCONJUGATE CHEMISTRY

Optimization and characterization of position-selective labelling of RNA (PLOR) for diverse RNA and DNA sequences

(2020) Xiaoyu Zhang et al.   RNA Biology

Tag‐free internal RNA labeling and photocaging based on mRNA methyltransferases

(2020) Anna Ovcharenko et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Site-Selective RNA Functionalization via DNA-Induced Structure

(2020) Lu Xiao et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Hachimoji DNA and RNA: A genetic system with eight building blocks

(2019) Shuichi Hoshika et al.   SCIENCE

Multiple covalent fluorescence labeling of eukaryotic mRNA at the poly(A) tail enhances translation and can be performed in living cells

(2019) Lea Anhäuser et al.   NUCLEIC ACIDS RESEARCH

Chemical methods for the modification of RNA

(2019) Marie Flamme et al.   METHODS

Heavy-atom labeling of RNA by PLOR for de novo crystallographic phasing

(2019) Jason R. Stagno et al.   PLoS One

Genetic code expansion facilitates position‐selective labeling of RNA for biophysical studies

(2019) Andreas Hegelein et al.   CHEMISTRY-A EUROPEAN JOURNAL

Direct in Vitro Selection of Trans-Acting Ribozymes for Posttranscriptional, Site-Specific, and Covalent Fluorescent Labeling of RNA

(2019) Mohammad Ghaem Maghami et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The chemistry and applications of RNA 2′-OH acylation

(2019) Willem A. Velema et al.   Nature Reviews Chemistry

Catalytic RNA, ribozyme, and its applications in synthetic biology

(2019) Soyeon V. Park et al.   BIOTECHNOLOGY ADVANCES

RNA Cloaking by Reversible Acylation

(2018) Anastasia Kadina et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Light-Activated Control of Translation by Enzymatic Covalent mRNA Labeling

(2018) Dongyang Zhang et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Enzymatic or In Vivo Installation of Propargyl Groups in Combination with Click Chemistry for the Enrichment and Detection of Methyltransferase Target Sites in RNA

(2018) Katja Hartstock et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

T7 RNA Polymerase Discriminates Correct and Incorrect Nucleoside Triphosphates by Free Energy

(2018) Shaogui Wu et al.   BIOPHYSICAL JOURNAL

CCR 5 RNA Pseudoknots: Residue and Site-Specific Labeling correlate Internal Motions with microRNA Binding

(2018) Bin Chen et al.   CHEMISTRY-A EUROPEAN JOURNAL

A Cytidine Phosphoramidite with Protected Nitroxide Spin Label: Synthesis of a Full-Length TAR RNA and Investigation by In-Line Probing and EPR Spectroscopy

(2018) Timo Weinrich et al.   CHEMISTRY-A EUROPEAN JOURNAL

Incorporation of isotopic, fluorescent, and heavy-atom-modified nucleotides into RNAs by position-selective labeling of RNA

(2018) Yu Liu et al.   Nature Protocols

Animal Hen1 2′-O-methyltransferases as tools for 3′-terminal functionalization and labelling of single-stranded RNAs

(2018) Milda Mickutė et al.   NUCLEIC ACIDS RESEARCH

Post-transcriptional labeling by using Suzuki–Miyaura cross-coupling generates functional RNA probes

(2018) Manisha B Walunj et al.   NUCLEIC ACIDS RESEARCH

Enzymatic synthesis of base-modified RNA by T7 RNA polymerase. A systematic study and comparison of 5-substituted pyrimidine and 7-substituted 7-deazapurine nucleoside triphosphates as substrates

(2018) Nemanja Milisavljevic et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Hierarchical mechanism of amino acid sensing by the T-box riboswitch

(2018) Krishna C. Suddala et al.   Nature Communications

Structural Basis for Regulation of METTL16, an S-Adenosylmethionine Homeostasis Factor

(2018) Katelyn A. Doxtader et al.   MOLECULAR CELL

Structural insights into the RNA methyltransferase domain of METTL16

(2018) Agnieszka Ruszkowska et al.   Scientific Reports

N6-Allyladenosine: A New Small Molecule for RNA Labeling Identified by Mutation Assay

(2017) Xiao Shu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Iluminated by foreign letters – Strategies for site-specific cyclopropene modification of large functional RNAs via in vitro transcription

(2017) Frank Eggert et al.   METHODS

Posttranscriptional chemical labeling of RNA by using bioorthogonal chemistry

(2017) Jerrin Thomas George et al.   METHODS

Site-Specific Covalent Conjugation of Modified mRNA by tRNA Guanine Transglycosylase

(2017) Fabian Ehret et al.   MOLECULAR PHARMACEUTICS

Single-molecule FRET reveals the energy landscape of the full-length SAM-I riboswitch

(2017) Christoph Manz et al.   Nature Chemical Biology

Site-specific dual-color labeling of long RNAs for single-molecule spectroscopy

(2017) Meng Zhao et al.   NUCLEIC ACIDS RESEARCH

Fluorescent turn-on probes for wash-free mRNA imaging via covalent site-specific enzymatic labeling

(2017) Cun Yu Zhou et al.   Chemical Science

A benzylic linker promotes methyltransferase catalyzed norbornene transfer for rapid bioorthogonal tetrazine ligation

(2017) F. Muttach et al.   Chemical Science

S -Adenosylmethionine Synthesis Is Regulated by Selective N 6 -Adenosine Methylation and mRNA Degradation Involving METTL16 and YTHDC1

(2017) Hiroki Shima et al.   Cell Reports

FRET Characterization of Complex Conformational Changes in a Large 16S Ribosomal RNA Fragment Site-Specifically Labeled Using Unnatural Base Pairs

(2016) Thomas Lavergne et al.   ACS Chemical Biology

Sequence-Specific Post-Synthetic Oligonucleotide Labeling for Single-Molecule Fluorescence Applications

(2016) David Egloff et al.   ACS Chemical Biology

Modifying the 5′-Cap for Click Reactions of Eukaryotic mRNA and To Tune Translation Efficiency in Living Cells

(2016) Josephin M. Holstein et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Conformational Flexibility and Dynamics of the Internal Loop and Helical Regions of the Kink–Turn Motif in the Glycine Riboswitch by Site-Directed Spin-Labeling

(2016) Jackie M. Esquiaqui et al.   BIOCHEMISTRY

A cyclopropene-modified nucleotide for site-specific RNA labeling using genetic alphabet expansion transcription

(2016) F. Eggert et al.   CHEMICAL COMMUNICATIONS

Synthesis of a Cytidine Phosphoramidite with Protected Nitroxide Spin Label for EPR Experiments with RNA

(2016) Timo Weinrich et al.   EUROPEAN JOURNAL OF ORGANIC CHEMISTRY

Applications of PLOR in labeling large RNAs at specific sites

(2016) Yu Liu et al.   METHODS

Structural Basis for Cooperative Function of Mettl3 and Mettl14 Methyltransferases

(2016) Ping Wang et al.   MOLECULAR CELL

Metal dependence and branched RNA cocrystal structures of the RNA lariat debranching enzyme Dbr1

(2016) Nathaniel E. Clark et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Expanded Genetic Alphabet

(2015) Denis A. Malyshev et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

A Biocatalytic Cascade for Versatile One-Pot Modification of mRNA Starting from Methionine Analogues

(2015) Fabian Muttach et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

A Covalent Approach for Site-Specific RNA Labeling in Mammalian Cells

(2015) Fahui Li et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Site-specific enzymatic introduction of a norbornene modified unnatural base into RNA and application in post-transcriptional labeling

(2015) Christof Domnick et al.   CHEMICAL COMMUNICATIONS

Site-Specific Covalent Labeling of RNA by Enzymatic Transglycosylation

(2015) Seth C. Alexander et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Synthesis and applications of RNAs with position-selective labelling and mosaic composition

(2015) Yu Liu et al.   NATURE

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

Site-specific labeling of RNA by combining genetic alphabet expansion transcription and copper-free click chemistry

(2015) Tatsuhiko Someya et al.   NUCLEIC ACIDS RESEARCH

Engineering Giardia lamblia trimethylguanosine synthase (GlaTgs2) to transfer non-natural modifications to the RNA 5'-cap

(2015) Josephin Marie Holstein et al.   PROTEIN ENGINEERING DESIGN & SELECTION

A triazole linkage that mimics the DNA phosphodiester group in living systems

(2015) Afaf H. El-Sagheer et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Enzymatic modification of 5′-capped RNA with a 4-vinylbenzyl group provides a platform for photoclick and inverse electron-demand Diels–Alder reaction

(2015) Josephin Marie Holstein et al.   Chemical Science

Probing Xist RNA Structure in Cells Using Targeted Structure-Seq

(2015) Rui Fang et al.   PLoS Genetics

Sequence-Specific Generation of 1,N6-Ethenoadenine and 3,N4-Ethenocytosine in Single-Stranded Unmodified DNA

(2014) David Egloff et al.   ACS Chemical Biology

Fluorescent RNA Labeling Using Self-Alkylating Ribozymes

(2014) Ashwani K. Sharma et al.   ACS Chemical Biology

The T box riboswitch: A novel regulatory RNA that utilizes tRNA as its ligand

(2014) Tina M. Henkin   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Diels–Alder Cycloadditions on Synthetic RNA in Mammalian Cells

(2014) Anna Maria Pyka et al.   BIOCONJUGATE CHEMISTRY

Site-specific fluorescence labelling of RNA using bio-orthogonal reaction of trans-cyclooctene and tetrazine

(2014) P. N. Asare-Okai et al.   CHEMICAL COMMUNICATIONS

Bioorthogonal site-specific labeling of the 5′-cap structure in eukaryotic mRNAs

(2014) Josephin Marie Holstein et al.   CHEMICAL COMMUNICATIONS

Synthesis of Nucleoside Phosphate and Phosphonate Prodrugs

(2014) Ugo Pradere et al.   CHEMICAL REVIEWS

Site-Specific Labeling of RNA at Internal Ribose Hydroxyl Groups: Terbium-Assisted Deoxyribozymes at Work

(2014) Lea Büttner et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Selective Covalent Labeling of miRNA and siRNA Duplexes Using HEN1 Methyltransferase

(2014) Alexandra Plotnikova et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway

(2014) Ashton Trey Belew et al.   NATURE

Electrophilic activity-based RNA probes reveal a self-alkylating RNA for RNA labeling

(2014) Richard I McDonald et al.   Nature Chemical Biology

A fully enzymatic method for site-directed spin labeling of long RNA

(2014) Isabelle Lebars et al.   NUCLEIC ACIDS RESEARCH

Preparation of modified long-mer RNAs and analysis of FMN binding to theypaAaptamer fromB. subtilis

(2014) Jennifer Frommer et al.   RNA Biology

A Chemo-Enzymatic Approach for Site-Specific Modification of the RNA Cap

(2013) Daniela Schulz et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Synthesis of spin-labeled riboswitch RNAs using convertible nucleosides and DNA-catalyzed RNA ligation

(2013) Lea Büttner et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Bioorthogonal chemistry: strategies and recent developments

(2013) Carlo P. Ramil et al.   CHEMICAL COMMUNICATIONS

A modified dinucleotide for site-specific RNA-labelling by transcription priming and click chemistry

(2013) Ayan Samanta et al.   CHEMICAL COMMUNICATIONS

Inverse electron demand Diels–Alder (iEDDA)-initiated conjugation: a (high) potential click chemistry scheme

(2013) Astrid-Caroline Knall et al.   CHEMICAL SOCIETY REVIEWS

Lanthanide Cofactors Accelerate DNA-Catalyzed Synthesis of Branched RNA

(2013) Fatemeh Javadi-Zarnaghi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Natural-like Replication of an Unnatural Base Pair for the Expansion of the Genetic Alphabet and Biotechnology Applications

(2013) Lingjun Li et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Production of pure and functional RNA for in vitro reconstitution experiments

(2013) Franziska Theresia Edelmann et al.   METHODS

2′-Azido RNA, a Versatile Tool for Chemical Biology: Synthesis, X-ray Structure, siRNA Applications, Click Labeling

(2012) Katja Fauster et al.   ACS Chemical Biology

Optimization of acetonitrile co-solvent and copper stoichiometry for pseudo-ligandless click chemistry with nucleic acids

(2012) Eduardo Paredes et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons

(2012) Kate D. Meyer et al.   CELL

Chemical Reporters for Monitoring RNA Synthesis and Poly(A) Tail Dynamics

(2012) Markus Grammel et al.   CHEMBIOCHEM

A Selenium-Based Click AdoMet Analogue for Versatile Substrate Labeling with Wild-Type Protein Methyltransferases

(2012) Sophie Willnow et al.   CHEMBIOCHEM

Site-specific functionalization of RNA molecules by an unnatural base pair transcription system via click chemistry

(2012) Takumi Ishizuka et al.   CHEMICAL COMMUNICATIONS

Synthesis and Characterization of RNA Containing a Rigid and Nonperturbing Cytidine-Derived Spin Label

(2012) Claudia Höbartner et al.   JOURNAL OF ORGANIC CHEMISTRY

Site-Specific Incorporation of Functional Components into RNA by an Unnatural Base Pair Transcription System

(2012) Nobuyuki Morohashi et al.   MOLECULES

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

(2012) Dan Dominissini et al.   NATURE

Programmable sequence-specific click-labeling of RNA using archaeal box C/D RNP methyltransferases

(2012) Miglė Tomkuvienė et al.   NUCLEIC ACIDS RESEARCH

Inverse electron-demand Diels–Alder reactions for the selective and efficient labeling of RNA

(2011) Juliane Schoch et al.   CHEMICAL COMMUNICATIONS

Cellular Consequences of Copper Complexes Used To Catalyze Bioorthogonal Click Reactions

(2011) David C. Kennedy et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Site-Specific Labeling of DNA and RNA Using an Efficiently Replicated and Transcribed Class of Unnatural Base Pairs

(2011) Young Jun Seo et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

RNA labeling, conjugation and ligation

(2011) Eduardo Paredes et al.   METHODS

Highly specific unnatural base pair systems as a third base pair for PCR amplification

(2011) Rie Yamashige et al.   NUCLEIC ACIDS RESEARCH

Multiple conformations of SAM-II riboswitch detected with SAXS and NMR spectroscopy

(2011) Bin Chen et al.   NUCLEIC ACIDS RESEARCH

RNA nucleotide methylation

(2011) Yuri Motorin et al.   Wiley Interdisciplinary Reviews-RNA

The Human HDV-likeCPEB3Ribozyme Is Intrinsically Fast-Reacting

(2010) Durga M. Chadalavada et al.   BIOCHEMISTRY

Site-Specific Chemical Labeling of Long RNA Molecules

(2010) Kasper Jahn et al.   BIOCONJUGATE CHEMISTRY

Click Chemistry for Rapid Labeling and Ligation of RNA

(2010) Eduardo Paredes et al.   CHEMBIOCHEM

Click chemistry with DNA

(2010) Afaf H. El-Sagheer et al.   CHEMICAL SOCIETY REVIEWS

Expanding the chemical scope of RNA:methyltransferases to site-specific alkynylation of RNA for click labeling

(2010) Y. Motorin et al.   NUCLEIC ACIDS RESEARCH

New strategy for the synthesis of chemically modified RNA constructs exemplified by hairpin and hammerhead ribozymes

(2010) A. H. El-Sagheer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Chemical Biology of Aptamers

(2009) Günter Mayer   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Bioorthogonal Chemistry: Fishing for Selectivity in a Sea of Functionality

(2009) Ellen M. Sletten et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Transcription of an Expanded Genetic Alphabet

(2009) Young Jun Seo et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Optimization of an Unnatural Base Pair toward Natural-Like Replication

(2009) Young Jun Seo et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Combined Approaches to Site-Specific Modification of RNA

(2008) Christine S. Chow et al.   ACS Chemical Biology

Postsynthetic DNA Modification through the Copper-Catalyzed Azide-Alkyne Cycloaddition Reaction

(2008) Philipp M. E. Gramlich et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Novel strategies for the site-specific covalent labelling of nucleic acids

(2008) Samuel H. Weisbrod et al.   CHEMICAL COMMUNICATIONS

Protecting groups for RNA synthesis: an increasing need for selective preparative methods

(2008) Álvaro Somoza   CHEMICAL SOCIETY REVIEWS

SELEX with modified nucleotides

(2008) Anthony D Keefe et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Tetrazine Ligation: Fast Bioconjugation Based on Inverse-Electron-Demand Diels−Alder Reactivity

(2008) Melissa L. Blackman et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Synthesis of biotin–AMP conjugate for 5′ biotin labeling of RNA through one-step in vitro transcription

(2008) Faqing Huang et al.   Nature Protocols

Displacement of protein-bound aptamers with small molecules screened by fluorescence polarization

(2008) Markus Hafner et al.   Nature Protocols

The preparation of site-specifically modified riboswitch domains as an example for enzymatic ligation of chemically synthesized RNA fragments

(2008) Kathrin Lang et al.   Nature Protocols

Synthesis of guanosine 5′-conjugates and their use as initiator molecules for transcription priming

(2008) Jörn Wolf et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Exploring RNA transcription and turnover in vivo by using click chemistry

(2008) C. Y. Jao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An important role of G638 in the cis-cleavage reaction of the Neurospora VS ribozyme revealed by a novel nucleotide analog incorporation method

(2008) D. Jaikaran et al.   RNA