Article
Chemistry, Multidisciplinary
Dzung Nguyen, Dinar Abdullin, Caspar A. Heubach, Toni Pfaffeneder, Andreas Nguyen, Andreas Heine, Klaus Reuter, Francois Diederich, Olav Schiemann, Gerhard Klebe
Summary: Mechanistic insights into protein-ligand interactions can provide chemical tools for modulating protein function. The type of ligand can affect the equilibrium between functional and twisted dimers in the homodimeric enzyme TGT. The experiments suggest a dissociation-association mechanism for the formation of the twisted dimer upon ligand binding.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Organic
Yuliya F. Polienko, Natalia M. Kuprikova, Dmitriy A. Parkhomenko, Yuriy Gatilov, Elena Chernyak, Igor A. Kirilyuk
Summary: Nitroxides with spirocyclic moieties adjacent to the N-O group exhibit longer spin echo dephasing times between 80 and 295 K compared to tetramethyl nitroxides. New spin labels for site-directed spin labeling have been developed from 2,5-bis(spirocyclohexane)-substituted nitroxides of the pyrroline series, showing advantages in reduction stability and relaxation rates when compared to tetramethyl nitroxides.
Article
Chemistry, Multidisciplinary
Shutian Lu, Catherine R. R. Fowler, Brian Ream, Sheela M. M. Waugh, Theresa M. M. Russell, John C. C. Rohloff, Larry Gold, Jason P. P. Cleveland, Stefan Stoll
Summary: Recent developments in aptamer chemistry have provided new opportunities for protein biosensing tools. This study presents a method that uses immobilized slow off-rate modified aptamers (SOMAmers) labeled with a nitroxide radical to detect protein binding. The rotational mobility of the spin label is changed by protein binding, which is detected using solution-state electron paramagnetic resonance (EPR) spectroscopy.
Article
Chemistry, Multidisciplinary
Yunfan Qiu, Asif Equbal, Chenjian Lin, Yuheng Huang, Paige J. Brown, Ryan M. Young, Matthew D. Krzyaniak, Michael R. Wasielewski
Summary: Photoexcited organic chromophores combined with stable radicals can be used as candidates for quantum information applications. In this study, the synthesis and characterization of 1,6,7,12-Tetra-(4-tert-butylphenoxy)-perylene-3,4 : 9,10-bis(dicarboximide) (tpPDI) linked to a partially deuterated alpha,gamma-bisdiphenylene-beta-phenylallyl radical (BDPA-d(16)) were performed using time-resolved optical and electron paramagnetic resonance (EPR) spectroscopies. The results showed efficient generation of a quartet state (Q) followed by a spin-polarized doublet ground state (D-0) upon photoexcitation of tpPDI-BDPA-d(16).
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Arianna Actis, Michele Melchionna, Giacomo Filippini, Paolo Fornasiero, Maurizio Prato, Enrico Salvadori, Mario Chiesa
Summary: This study assesses the influence of morphology and light-excitation on the number and chemical nature of radical defects in carbon nitride (CN) and derives the spatial distribution of native radicals in CN using magnetic dipole-dipole coupling.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Polymer Science
Uwe Lappan, Carolin Naas, Ulrich Scheler
Summary: This study utilizes cationic charged chitosan and weak polyacid poly(ethylene-alt-maleic acid) to create polyelectrolyte multilayers (PEMs). By attaching a nitroxide spin-label to the polyacid, the rotational dynamics of the polymer backbone in the swollen state of the PEMs are studied using electron paramagnetic resonance spectroscopy. The study reveals that PEMs with an even number of layers exhibit a superposition of two spectral components, a major slow-motion component from protonated amino groups compensating chain segments of the chitosan, and a minor fast-motion component believed to originate from loops and tails of the polyacid chain at the PEMs' surface.
MACROMOLECULAR CHEMISTRY AND PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Samuel F. Haysom, Jonathan Machin, James M. Whitehouse, Jim E. Horne, Katherine Fenn, Yue Ma, Hassane El Mkami, Nils Boehringer, Till F. Schaeberle, Neil A. Ranson, Sheena E. Radford, Christos Pliotas
Summary: The BAM complex is crucial for folding outer membrane proteins in Gram-negative bacteria and can be a potential target for antimicrobial agents. Using PELDOR spectroscopy, we investigated the conformational changes of BAM complex in E. coli cells and found that BAM adopts a variety of conformations in the outer membrane, but shifts to a restricted ensemble consistent with a closed state in the presence of the antibiotic DAR-B. Our findings are supported by cryoEM structures of BAM with and without DAR-B.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Frank Kaiser, Burkhard Endeward, Alberto Collauto, Ute Scheffer, Thomas F. Prisner, Michael W. Gobel
Summary: This article introduces a synthetic method for phosphoramidite that reduces the complexity and special equipment requirement of previous methods by using a photocaged benzyl group to attach the TPA spin label. A doubly spin-labeled 27mer neomycin sensing riboswitch was synthesized using this method and studied by PELDOR. The results showed that while TPA does not significantly affect the overall thermal stability of the fold, changes in local mobility were detected by in-line probing.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Applied
Jacqueline Lux, Mykhailo Azarkh, Laura Fitzner, Julia K. Keppler, Karin Schwarz, Malte Drescher, Anja Steffen-Heins
Summary: SDSL of natural beta-lactoglobulin revealed that different spin labels bind to specific sites to varying extents, affecting the formation of amyloid-like structures. The spatial distribution of labels within protein aggregates was confirmed to be similar to a string of pearls, indicating a potential mechanism for amyloid formation.
FOOD HYDROCOLLOIDS
(2021)
Article
Biology
Maria F. Vicino, Tobias Hett, Olav Schiemann
Summary: Understanding the function of oligonucleotides on a molecular level requires studying their structure, conformational changes, and internal dynamics. Various biophysical methods, including PELDOR, allow for analysis of distances between electron spins in biomolecules and the introduction of spin labels. This process involves attaching nitroxide spin labels to oligonucleotides using Click chemistry, running PELDOR experiments to derive coarse-grained structures, and emphasizing the limitations and requirements for data interpretation.
Article
Chemistry, Physical
Joshua L. Wort, Swati Arya, Katrin Ackermann, Alan J. Stewart, Bela E. Bode
Summary: Pulse-dipolar EPR is an attractive method for structural characterization in solution, especially when paired with genetically encoded self-assembling spin labels and Cu-II-chelates. The combination of room-temperature isothermal titration calorimetry and cryogenic relaxation-induced dipolar modulation enhancement showed that the double-histidine motif spin labeling with Cu-II-nitrilotriacetic acid is robust against competition from Zn-II-NTA and maintains high nM binding affinity even under acidic and basic conditions. The strategy is well-suited for diverse biological applications, with the requirement of other metal ion cofactors or slightly acidic pH not necessarily being prohibitive.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Daniel L. Drew, Tanbi Ahammad, Rachel A. Serafin, Indra D. Sahu, Rasal H. Khan, Emily Faul, Robert M. McCarrick, Gary A. Lorigan
Summary: Advances have been made in detecting local secondary structures of membrane proteins using electron paramagnetic resonance (EPR) methods. A three pulsed electron spin echo envelope modulation (ESEEM) approach was used to determine the local helical secondary structure of the small hole forming membrane protein, S-21 pinholin. Circular dichroism (CD) spectroscopy was also used to study the overall global helical structure of S-21 pinholin.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2022)
Article
Chemistry, Multidisciplinary
Fangbai Xie, Haochuan Mao, Chenjian Lin, Yuanning Feng, J. Fraser Stoddart, Ryan M. Young, Michael R. Wasielewski
Summary: This study demonstrates that a photogenerated spin-correlated radical ion pair can be used to sense an electric field change through molecular recognition. The experiment shows that the distance between the two charges decreases when a certain molecule encapsulates one of the charges, indicating that the system can function as a quantum sensor to detect electric field changes.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Multidisciplinary Sciences
Ryan D. D. Dill, Kori E. E. Smyser, Brandon K. K. Rugg, Niels H. H. Damrauer, Joel D. D. Eaves
Summary: Singlet fission is important for next-generation solar cells. The authors design a molecular system with specific spin sub-levels that can produce highly entangled states. They demonstrate that the coherence between magnetic sub-levels of that state can be preserved at higher temperatures than conventional superconducting quantum hardware.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Viranga W. Wimalasiri, Kinga A. Jurczak, Monika K. Wieliniec, Thushani D. Nilaweera, Robert K. Nakamoto, David S. Cafiso
Summary: Pulse EPR measurements provide information on distances and distance distributions in proteins. In this study, in vivo labeling of the E. coli outer membrane proteins BtuB and FecA were achieved using strains defective in the disulfide bond formation system. The in vivo measurements showed that the cellular environment affects the behavior of the extracellular loops of FecA, and the use of a DsbA minus strain improved the EPR signals and data obtained in vitro from BtuB.
Article
Biochemistry & Molecular Biology
Stephan Werner, Aurellia Galliot, Florian Pichot, Thomas Kemmer, Virginie Marchand, Maksim Sednev, Tina Lence, Jean-Yves Roignant, Julian Koenig, Claudia Hoebartner, Yuri Motorin, Andreas Hildebrandt, Mark Helm
Summary: NOseq is a novel method for detecting m(6)A residues using chemical deamination with nitrous acid. It utilizes a mapping algorithm adapted to sequence degeneration caused by deamination, enabling detection of m(6)A sites with a modification level of around 50% in defined amplicons.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Goran Kokic, Hauke S. Hillen, Dimitry Tegunov, Christian Dienemann, Florian Seitz, Jana Schmitzova, Lucas Farnung, Aaron Siewert, Claudia Hoebartner, Patrick Cramer
Summary: Remdesivir is the only FDA-approved drug for treating COVID-19 patients, working by inhibiting the RNA-dependent RNA polymerase (RdRp) of coronaviruses. It hinders RNA synthesis and impairs proofreading by the viral 3'-exonuclease, leading to a stalled replication process.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Anam Liaqat, Maksim V. Sednev, Carina Stiller, Claudia Hoebartner
Summary: Deoxyribozymes have been identified as modification-specific endonucleases that selectively respond to different natural methylated cytidines, accelerating the cleavage of modified RNA. These deoxyribozymes can be programmed to interrogate natural RNAs of interest, demonstrating the potential of synthetic functional DNA in shaping highly selective active sites.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Bin Liu, Yvonne Vonhausen, Alexander Schulz, Claudia Hoebartner, Frank Wuerthner
Summary: The study demonstrated the suitability of the N-(2-aminoethyl)-glycine oligomers backbone for the formation of structurally defined dye stacks, but the peptide backbone cannot direct the formation of a defined duplex architecture upon further extension of the oligomer.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Julia Dietzsch, David Bialas, Johannes Bandorf, Frank Wuerthner, Claudia Hoebartner
Summary: This study reports the tuning of exciton coupling by changing the double helix conformation. Different arrangements of dyes were achieved by changing the backbone constitution and geometry of nucleic acids, resulting in distinct optical characteristics.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Maksim Sednev, Anam Liaqat, Claudia Hoebartner
Summary: DZ-seq is a new high-throughput sequencing method that allows for the direct measurement and localization of activity and cleavage sites of thousands of deoxyribozymes. It provides an effective tool for the discovery of novel catalytic motifs.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Multidisciplinary Sciences
Nicole Kleiber, Nicolas Lemus-Diaz, Carina Stiller, Marleen Heinrichs, Mandy Mong-Quyen Mai, Philipp Hackert, Ricarda Richter-Dennerlein, Claudia Hoebartner, Katherine E. Bohnsack, Markus T. Bohnsack
Summary: RNA modifications, specifically the enzyme METTL8, play a crucial role in regulating RNA functions and have significant impacts on tRNA structure and mitochondrial translation.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Carolin P. M. Scheitl, Mateusz Mieczkowski, Hermann Schindelin, Claudia Hoebartner
Summary: RNA-catalyzed RNA methylation has been found to be part of the catalytic repertoire of ribozymes. The crystal structure of methyltransferase ribozyme MTR1 has been determined, revealing a guanine-binding site similar to natural guanine riboswitches. The structure also suggests the involvement of a protonated cytidine in the methyl transfer reaction. The synergistic effect of 2'-O-methylated ribose residues in the active site accelerates methyl group transfer. These findings suggest that modified nucleotides may have played a role in early RNA catalysis and that metabolite-binding riboswitches resemble inactivated ribozymes.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Hermann Neitz, Irene Bessi, Valentin Kachler, Manuela Michel, Claudia Hoebartner
Summary: This study demonstrates the use of tolane-perfluorotolane interaction as a base pair replacement in DNA by modifying the DNA backbone. Thermodynamic analyses show that only THH/TFF heteropairs connected to the BuNA backbone significantly stabilize the DNA duplex, while no such effect is observed with the shorter GNA linker. NMR studies confirm the preference of the BuNA backbone for enhanced polar pi-stacking. This work defines the principles of tailoring orthogonal supramolecular interactions by small structural changes in the DNA backbone and inspires future studies of arene-fluoroarene-programmed assembly of DNA.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Carolin P. M. Scheitl, Takumi Okuda, Juliane Adelmann, Claudia Hoebartner
Summary: This article reports a method for synthesizing aldehyde-functionalized RNA by directly converting a purine nucleobase using a ribozyme-based approach. The modified nucleotide can react with aldehyde-reactive probes, allowing for the conjugation of biotin or fluorescent dyes to short synthetic RNAs and tRNA transcripts. The condensation of a 2,3,3-trimethylindole with the modified RNA generates a novel hemicyanine chromophore directly on the RNA. This work expands the application of the MTR1 ribozyme from a methyltransferase to a tool for site-specific late-stage functionalization of RNA.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Hermann Neitz, Irene Bessi, Jochen Kuper, Caroline Kisker, Claudia Hoebartner
Summary: Covalent crosslinking of DNA strands using modified nucleoside PhedU enables light-induced interstrand DNA crosslinking reaction. The crosslinking ability is controlled by base pairing and metal ion interaction, allowing efficient formation of PhedU dimer within DNA duplex. The covalent crosslink prevents DNA unwinding, suggesting potential applications in biochemistry or structural biology.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Physical
Mirco Zerbetto, Christine Saint-Pierre, Andrea Piserchia, Simona Torrengo, Serge Gambarelli, Daniel Abergel, Antonino Polimeno, Didier Gasparutto, Giuseppe Sicoli
Summary: This study proposes an integrated approach for structural characterization of DNA tetrahedron structures. Through self-assembly and electron paramagnetic resonance spectroscopy analysis of spin-labeled DNA sequences, the study reveals the dynamic heterogeneity and flexibility of the assembled structures. This method provides unprecedented resolution in accessing the main dynamic and structural features.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Julia Dietzsch, Ajay Jayachandran, Stefan Mueller, Claudia Hoebartner, Tobias Brixner
Summary: We synthesized and analyzed the spectroscopy of RNA with barbituric acid merocyanine rBAM2 as a nucleobase surrogate. Incorporating rBAM2 into RNA by solid-phase synthesis resulted in enhanced fluorescence compared to the free chromophore. Linear absorption studies showed the formation of an excitonically coupled H-type dimer in the hybridized duplex. Ultrafast transient absorption spectroscopy of the non-fluorescent dimer suggested immediate exciton transfer and annihilation within sub-200 fs due to the proximity of rBAM2 units.
CHEMICAL COMMUNICATIONS
(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, Physical
David Fischermeier, Christian Steinmetzger, Claudia Hoebartner, Roland Mitric
Summary: Forster resonant energy transfer (FRET) is used to study tertiary structures of RNA aptamers by binding specific fluorophoric ligands. This study combined classical molecular dynamics with Forster exciton theory to investigate the preferred orientation and exciton transfer efficiency in mutated RNA aptamers. The methodology presented here can reliably evaluate nucleobase analogues in terms of their structural behavior and exciton transfer properties.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
