Article
Medicine, Research & Experimental
Oleksandr Zavoiura, Bodo Brunner, Peter Casteels, Luciana Zimmermann, Matthias Ozog, Carlo Boutton, Mike W. Helms, Timothy Wagenaar, Volker Adam, Josefine Peterka, Christiane Metz-Weidmann, Pieter Deschaght, Sabine Scheidler, Kerstin Jahn-Hofmann
Summary: Targeted delivery of siRNA to specific cells remains challenging, but using anti-EGFR Nanobodies for delivery shows promise. The siRNA-conjugated Nanobodies retain their binding and activity in EGFR-positive cells, inducing mRNA cleavage. Comparing different linkers for siRNA conjugation provides insights into improving Nanobody-mediated siRNA delivery.
MOLECULAR PHARMACEUTICS
(2021)
Article
Chemistry, Multidisciplinary
Yanpei Wang, Yulin Huang, Tingting Huang, Jun Zhang, Teng Luo, Yong Ni, Bo Li, Sheng Xie, Zebing Zeng
Summary: We report a stepwise solution-synthesis of linear nonalternant nanoribbons with pentagonal rings fused onto the repeating perylene unit. The nanoribbons have a twisted ribbon structure with a maximum crystalline length of 3.9 nm. They exhibit orange to deep-red photoluminescence even under room light. Benefiting from the enlarged size and antiaromatic character of pentagons, all the nanoribbons possess ambipolar redox properties.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Physical
Sophie Wintermans, Jordi F. Keijzer, Marte Dros, Han Zuilhof, Bauke Albada
Summary: The aptamer-functionalized hGQ DNAzymes enhance the bioconjugation of N-methyl luminol to tyrosine-containing residues and peptides, with a 12-fold increase in the catalytic rate constant. When applied for modifying Tyr-containing peptides, the nucleoapzymes not only recognize the ligand structure embedded in a larger peptide structure, but also show that distant residues in the peptide substrate can influence the conversion.
Article
Chemistry, Multidisciplinary
Blaise R. Kimmel, Milan Mrksich
Summary: This paper introduces an enzyme building block for assembling megamolecules, which inhibits protein CRABP2 to control protein domains. By conjugating the inhibitor and a fluorescent tag to a backbone, precise control over the placement of protein domains within a single molecule is achieved.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Inorganic & Nuclear
Aleksandra Tobolska, Nina E. Wezynfeld, Urszula E. Wawrzyniak, Wojciech Bal, Wojciech Wroblewski
Summary: Electrochemical and spectroscopic studies showed that the N-truncated amyloid beta peptide A β(5-9) containing histidine at position 2 formed ternary complexes with copper(ii) and phosphate anions or groups. The recognition ability of Cu(ii)-A β(5-9) towards phosphate species opens up new possibilities for designing phosphate-selective molecular receptors.
DALTON TRANSACTIONS
(2021)
Article
Chemistry, Multidisciplinary
Zhiheng Zhang, Jie Lu, Kai Yang, Jiayu Cao, Yi Zhao, Kai Ge, Shuang Wang, Yang Yang, Yue Zhang, Yongfang Yang
Summary: The study synthesizes porphyrinic covalent organic frameworks (COFs) with and without copper (Cu) and successfully forms tubular microstructures. The copper-containing tubular structure exhibits high activity in CO2 photoreduction due to its large specific surface area, strong absorption of visible light, and fast separation and transfer of electrons and holes.
Article
Chemistry, Multidisciplinary
Zichen Liu, Irene Lepori, Mahendra D. Chordia, Brianna E. Dalesandro, Taijie Guo, Jiajia Dong, M. Sloan Siegrist, Marcos M. Pires
Summary: A novel assay combining metabolic tagging, click chemistry, and fluorescent labeling was developed to measure the permeation of small molecules in Mycobacterium tuberculosis. The assay proved to be robust and compatible with high-throughput analysis, providing insights into drug uptake in mycobacteria.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Organic
Ana Da Lama, Beatrice Bartolomei, Cristian Rosso, Giacomo Filippini, M. Montserrat Martinez, Luis A. Sarandeses, Maurizio Prato
Summary: Boron-dipyrromethene complexes (BODIPYs) with notable photophysical properties have attracted increasing interest, particularly in organic photocatalysis. This study investigated the relationship between their chemical composition and photocatalytic activity through a rationally designed structure-activity relationship study using atom transfer radical addition (ATRA) reaction as a benchmark. It was demonstrated that the presence of heavy atoms in the chromophore's core is essential for achieving high reactivity levels, while electron-withdrawing groups at position 8 (meso) undermine the catalytic performances.
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Daniel F. Earley, Amaury Guillou, Dion van der Born, Alex J. Poot, Jason P. Holland
Summary: The study examines the potential of using a microfluidic photochemical flow reactor to prepare Zr-89-radiolabelled proteins, showing that photochemical labeling in flow is a feasible platform for the automated production of protein-based Zr-89-radiotracers. However, further refinement of the apparatus and optimization of the method are required before the flow process can compete with manual reactions.
Article
Chemistry, Multidisciplinary
Serena Gentile, Erica Del Grosso, Leonard J. Prins, Francesco Ricci
Summary: We introduce a strategy for programmable and autonomous reorganization of self-assembled DNA polymers using redox chemistry. Different DNA monomers are designed to co-assemble into tubular structures, which can be orthogonally activated/deactivated with disulfide-linked DNA fuel strands that are degraded over time upon reduction. The concentration of the disulfide fuels controls the activation kinetics of each DNA tile, thus regulating the degree of order/disorder in the formed co-polymer. By combining the disulfide-reduction pathway with enzymatic fuel-degradation pathways, the re-organization of DNA structures can be further controlled. The pH sensitivity of the disulfide-thiol and enzymatic reactions allows for pH-dependent control over the order in DNA-based co-polymers.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Weifeng Lin, Louis P. Conway, Miroslav Vujasinovic, J-Matthias Lohr, Daniel Globisch
Summary: The study developed a new chemical biology tool to overcome analytical challenges in metabolite analysis, enabling detection of over 200 metabolites in human fecal, urine, and plasma samples. This comprehensive mass spectrometric analysis enhances metabolomics-driven biomarker discovery.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Review
Biochemistry & Molecular Biology
Cheng Giuseppe Chen, Alessandro Nicola Nardi, Andrea Amadei, Marco D'Abramo
Summary: The estimation of redox potentials in biologically relevant systems is challenging due to the complexity and size of these systems. Various theoretical-computational approaches have been developed to overcome the limitations of full quantum-mechanical treatment. This review provides an overview of these approaches, discussing their physical principles, advantages, and limitations. Examples of their application in estimating redox potentials of proteins and nucleic acids are described and critically discussed. Finally, general considerations on the most promising strategies are reported.
Article
Chemistry, Medicinal
Alberto Ongaro, Giovanni Desiderati, Erika Oselladore, Davide Auricchio, Maurizio Memo, Giovanni Ribaudo, Claudia Sissi, Alessandra Gianoncelli
Summary: This study found that guanine-rich sequences can form G-quadruplex structures in oncogenes and telomeres, inhibiting immortalization of cancer cells. Researchers improved ligand design based on an anthraquinone scaffold using click chemistry to enhance side chain length and interactions with nucleobases, leading to increased stability and selectivity towards G4 DNA.
Review
Biochemistry & Molecular Biology
Vincent Joseph, Mindy Levine
Summary: The article reviews key research accomplishments of Professor Ronald Charles D. Breslow throughout his more than 60 year research career, covering a wide range of topics including physical organic chemistry, medicinal chemistry, bioorganic chemistry, molecular electronics, and origin of chirality. Breslow's contributions to the broader chemistry profession are also briefly reviewed, including his work for the American Chemical Society and gender equity promotion.
BIOORGANIC CHEMISTRY
(2021)
Article
Chemistry, Analytical
Yan Shan Ang, Lin-Yue Lanry Yung
Summary: Protein-oligonucleotide conjugates are crucial in various biological applications. This study demonstrates the importance of high-quality conjugate probes for achieving consistent performance. A streamlined workflow was developed to obtain pure subpopulations of protein probes carrying a specific number of oligonucleotide strands. This workflow was successfully applied to a wide range of binders and showed robust assay performance with just a single reaction step and short reaction time.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Martin Peng, Dominik L. Siebert, Martin K. M. Engqvist, Christof M. Niemeyer, Kersten S. Rabe
Summary: A novel thermostable benzaldehyde lyase ReBAL was discovered, showing structural differences from PfBAL but with higher thermostability and different activity in rational design-generated variants. Using the most stable variant, (R)-benzoin was successfully synthesized, providing new insights for the production of alpha-hydroxy ketones and APIs.
Article
Biotechnology & Applied Microbiology
Edina Klein, Janek Weiler, Michael Wagner, Minja Celikic, Christof M. Niemeyer, Harald Horn, Johannes Gescher
Summary: Aerobic granular sludge has become an increasingly popular method for wastewater treatment due to its ability to remove organic carbon, nitrogen, and phosphorus simultaneously. However, analyzing the processes and microbial population within the granules is challenging due to their microscale. In this study, a small-scale model system for aerobic granular sludge was introduced using a machine-assisted microfluidic cultivation platform. With this setup, it was possible to enrich specific microorganisms and investigate the influence of process parameters on wastewater treatment systems.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sabrina Gallus, Esther Mittmann, Kersten S. Rabe
Summary: Comparing different membrane anchor motifs for surface display of a protein is crucial, and using a modular display system allows for easy assembly of anchors and passengers without the need for direct genetic fusion constructs in each case. Membrane anchors not only impact cell growth and membrane integrity, but also affect surface display capacity and biocatalytic activity. The strategy can be applied to other anchor and passenger combinations for various applications involving cell surface display.
Article
Instruments & Instrumentation
I Zoi, A. Ebrahimi, F. Feindt, E. Garutti, P. Gunnellini, A. Hinzmann, C. Niemeyer, D. Pitzl, J. Schwandt, G. Steinbruck
Summary: Pixelated silicon detectors are advanced technology designed to accurately measure the hit position of incoming particles in high rate and radiation environments. Operation requirements become extremely demanding at the High-Luminosity LHC due to multiple interactions and radiation, affecting sensor performance and resolution.
NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION A-ACCELERATORS SPECTROMETERS DETECTORS AND ASSOCIATED EQUIPMENT
(2022)
Article
Nanoscience & Nanotechnology
Esther Mittmann, Frank Mickoleit, Denis S. Maier, Sabrina Y. Staebler, Marius A. Klein, Christof M. Niemeyer, Kersten S. Rabe, Dirk Schueler
Summary: This study demonstrates that using magnetosomes as an alternative for immobilizing biocatalysts can achieve high and stable conversion rates. By genetically engineering foreign proteins onto the surface of magnetosomes, stable functionality of the particles is achieved. Results show that SpyCatcher magnetosomes significantly expand the genetic toolbox for particle surface functionalization.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Chemistry, Multidisciplinary
Carmen M. Dominguez, Miguel Garcia-Chame, Ulrike Mueller, Andreas Kraus, Klavdiya Gordiyenko, Ahmad Itani, Heiko Haschke, Peter Lanzerstorfer, Kersten S. Rabe, Christof M. Niemeyer
Summary: This article reports on the high dynamic interaction between streptavidin and DNA origami nanostructures, and provides detailed insights into this interaction using a novel high-speed atomic force microscope. The study also demonstrates a correlation between this interaction and cellular activation. This work is significant for further standardizing the use of DNA nanostructures in the study of biological processes.
Article
Nanoscience & Nanotechnology
Ahmed E. Zoheir, Laura Meisch, Marta Velaz Martin, Christoph Bickmann, Alexei Kiselev, Florian Lenk, Anne-Kristin Kaster, Kersten S. Rabe, Christof M. Niemeyer
Summary: This study presents the fabrication and application of a novel device for decoding microbial dark matter (MDM) in environmental microbiomes. The device, which is low-cost and easily scalable, allows for rapid colonization and enrichment of microorganisms. The results highlight the potential of this device for systematic study of MDM and cultivation of previously unculturable microorganisms.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Chemistry, Multidisciplinary
Patrick Bitterwolf, Ahmed E. Zoheir, Julian Hertel, Sandra Kroll, Kersten S. Rabe, Christof M. Niemeyer
Summary: An intracellular approach to produce all-enzyme hydrogel particles has been developed, enabling efficient and sustainable biocatalysis. By using gene engineering, the researchers were able to simplify the construction of biocatalytic reactors and improve the stability and continuity of the reactions. This study provides a novel method for optimizing sustainable biocatalytic processes.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Biotechnology & Applied Microbiology
Lukas Wenger, Carsten P. Radtke, Eva Gerisch, Max Kollmann, Christof M. Niemeyer, Kersten S. Rabe, Juergen Hubbuch
Summary: This study compares the suitability and performance of different concentrations of low-melting agarose or agar-based inks in bioprinting. It was found that agarose bioinks with at least 4.5% polymer were the most suitable for printing biocatalytic reactors.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Engineering, Biomedical
Bingquan Yang, Klavdiya Gordiyenko, Andreas Schaefer, Seyed Mohammad Mahdi Dadfar, Wenwu Yang, Kristina Riehemann, Ravi Kumar, Christof M. Niemeyer, Michael Hirtz
Summary: In this study, three different surface coatings were compared to investigate their influence on DNA hybridization behavior. The structures and chemical properties of the coatings were characterized using various methods. The results showed that one of the coatings (PBAG) exhibited the highest hybridization efficiency, which has significant implications for the fabrication of DNA sensors.
ADVANCED NANOBIOMED RESEARCH
(2023)
Article
Nanoscience & Nanotechnology
Enrico Domenico Lemma, Roberta Tabone, Kai Richler, Ann-Kathrin Schneider, Claudia Bizzarri, Franco Weth, Christof M. Niemeyer, Martin Bastmeyer
Summary: Three-dimensional microscaffolds have shown great potential in mimicking physiological environments and simulating complex multicellular constructs in cell biology. However, controlling the precise localization of cells on microfabricated structures is still complex and limited to two-dimensional assays. This study presents a novel method using two-photon lithography and UV-mediated click reactions to selectively target different cell types to specific regions of a 3D microscaffold through DNA hybridization, enabling controlled cocultures of eukaryotic cells in 3D.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Chemistry, Multidisciplinary
Leonie Schneider, Kersten S. Rabe, Carmen M. Dominguez, Christof M. Niemeyer
Summary: The immunological response of mast cells is regulated by the binding of antigens to IgE antibodies bound to the Fc epsilon RI receptor on the cell membrane surface. However, the organization and structural requirements of these antigen-antibody-receptor complexes at the nanometer scale are not fully understood. In this study, DNA nanostructures were used to generate multivalent artificial antigens, allowing for control over valency and nanoscale architecture. The results showed that the assembly of antibody-receptor complexes is critical for mast cell activation, and the affinity and nanoscale distance between the binding partners have less influence on the activation process.
Article
Chemistry, Multidisciplinary
Leonie Schneider, Kersten S. Rabe, Carmen M. Dominguez, Christof M. Niemeyer
Summary: This study utilizes DNA nanostructures to create multivalent artificial antigens and investigates the spatial requirements and critical factors for mast cell activation. It reveals the importance of antigen-directed assembly of antibody-receptor complexes in triggering degranulation.
Article
Chemistry, Multidisciplinary
Sandra Kroell, Leonie Schneider, Parvesh Wadhwani, Kersten S. Rabe, Christof M. Niemeyer
Summary: We propose an efficient and readily applicable strategy for covalently linking proteins to DNA origami using the SpyCatcher-SpyTag (SC-ST) connector system. This method exhibits orthogonality with other covalent connectors and has been successfully used to immobilize and study stereoselective ketoreductases on DNA nanostructures, providing insights into enzyme spatial arrangement.
CHEMICAL COMMUNICATIONS
(2022)
Article
Nanoscience & Nanotechnology
Ahmed E. Zoheir, Laura Meisch, Marta Velaz Martin, Christoph Bickmann, Alexei Kiselev, Florian Lenk, Anne-Kristin Kaster, Kersten S. Rabe, Christof M. Niemeyer
Summary: Natural evolution has generated a wide variety of microorganisms that are still largely unknown. In order to exploit the potential of these microbial dark matter (MDM) in biotechnology, a new chip design has been developed. This chip allows for rapid decoding of MDM and efficient enrichment of microorganisms in various habitats. The initial case studies demonstrate the chip's suitability for systematic study and cultivation of previously unculturable microorganisms.
ACS APPLIED MATERIALS & INTERFACES
(2022)
