Article
Chemistry, Multidisciplinary
Shuoxing Jiang, Nibedita Pal, Fan Hong, Nour Eddine Fahmi, Huiyu Hu, Matthew Vrbanac, Hao Yan, Nils G. Walter, Yan Liu
Summary: Controlling the nucleation step of a self-assembly system is crucial for engineering structural complexity and dynamic behaviors. This study investigates the inherent dynamics of three general nucleation modes in DNA tile-based self-assembly and reveals temperature-dependent kinetics and a nucleation-growth model are key factors. The assembly of tiles can be externally regulated by the hosting frame and an UV-responsive trigger, offering a general strategy for controlling the self-assembly process.
Article
Chemistry, Multidisciplinary
Kristina Huebner, Himanshu Joshi, Aleksei Aksimentiev, Fernando D. Stefani, Philip Tinnefeld, Guillermo P. Acuna
Summary: The study introduces a new technique to determine the orientation of single fluorophores in DNA origami structures, providing insights into the relationship between the fluorophores, environment, and structure. Results indicate that the orientation of fluorophores is influenced more by the specific molecular environment than the type of fluorophore.
Article
Nanoscience & Nanotechnology
Leo Sala, Tomas Perecko, Oto Mestek, Dominik Pinkas, Tomas Homola, Jaroslav Kocisek
Summary: In this study, cisplatin was utilized as a therapeutic and cross-linking agent for DNA origami nanostructures. The loading of cisplatin molecules onto the nanostructures showed time dependence and gradual release. Structural distortions were observed when the number of loaded cisplatin molecules exceeded a certain threshold. Cisplatin-loaded DNA origami nanostructures exhibited significant cytotoxicity against cancer cells, making them a promising drug carrier.
ACS APPLIED NANO MATERIALS
(2022)
Article
Chemistry, Multidisciplinary
Will T. Kaufhold, Wolfgang Pfeifer, Carlos E. Castro, Lorenzo Di Michele
Summary: The study utilizes metadynamics to sample the free energy landscapes of DNA nanostructures and demonstrates its ability to predict the mechanical response of DNA nanodevices. These findings are significant for the design and application of DNA nanostructures.
Article
Chemistry, Physical
Cecilia Zaza, German Chiarelli, Ludovit P. Zweifel, Mauricio Pilo-Pais, Evangelos Sisamakis, Fabio Barachati, Fernando D. Stefani, Guillermo P. Acuna
Summary: Fluorescence Resonance Energy Transfer (FRET)-based approaches are unique tools for sensing the immediate surroundings and interactions of (bio)molecules. FRET imaging and Fluorescence Lifetime Imaging Microscopy (FLIM) enable the visualization of the spatial distribution of molecular interactions and functional states. However, conventional FLIM and FRET imaging provide average information over an ensemble of molecules within a diffraction-limited volume, which limits the spatial information, accuracy, and dynamic range of the observed signals. Here, an approach to obtain super-resolved FRET imaging based on single-molecule localization microscopy using an early prototype of a commercial time-resolved confocal microscope is demonstrated. DNA Points Accumulation for Imaging in Nanoscale Topography with fluorogenic probes provides a suitable combination of background reduction and binding kinetics compatible with the scanning speed of usual confocal microscopes. A single laser is used to excite the donor, a broad detection band is employed to retrieve both donor and acceptor emission, and FRET events are detected from lifetime information.
Article
Chemistry, Multidisciplinary
Michael Scheckenbach, Tom Schubert, Carsten Forthmann, Viktorija Glembockyte, Philip Tinnefeld
Summary: Advancements in DNA nanotechnology and DNA origami techniques have enabled the easy design and synthesis of complex and functional nanostructures. Molecular devices are prone to rapid degradation, so self-repair mechanisms are desirable. By utilizing the self-assembly and reconfigurability of DNA origami nanostructures, self-repair of defects can be induced.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Aleksandra K. Adamczyk, Teun A. P. M. Huijben, Miguel Sison, Andrea Di Luca, Stefano Vanni, Sophie Brasselet, Kim I. Mortensen, Fernando D. Stefani, Mauricio Pilo-Pais, Guillermo P. Acuna
Summary: This study demonstrates a controlled orientation of single molecules in DNA origami by linking them to oligonucleotide strands and leaving unpaired bases. The number of unpaired bases affects the stretching and orientation of the fluorophore linkers. These findings expand the application of DNA origami in the fabrication of nanodevices involving orientation-dependent molecular interactions.
Article
Chemistry, Multidisciplinary
Jiajia Zou, Ashley C. Stammers, Andrea Taladriz-Sender, Jamie M. Withers, Iain Christie, Marina Santana Vega, Badri L. Aekbote, William J. Peveler, David A. Rusling, Glenn A. Burley, Alasdair W. Clark
Summary: An orthogonal, noncovalent approach is presented for the assembly of higher-order DNA origami nanostructures. By incorporating perfluorinated tags into DNA origami tiles, their hierarchical assembly is controlled via fluorous-directed recognition. This integrated catch-and-latch approach combining fluorous effect with base-pairing specificity enables increased assembly efficiency and requires fewer DNA sequences, providing a cheap and efficient means for producing discrete superstructures in DNA nanotechnology.
Article
Chemistry, Multidisciplinary
Xinpei Dai, Xiaoliang Chen, Xinxin Jing, Yinan Zhang, Muchen Pan, Mingqiang Li, Qian Li, Pi Liu, Chunhai Fan, Xiaoguo Liu
Summary: Integrating dissimilar materials at the nanoscale is crucial for modern electronics and optoelectronics. Researchers have developed a DNA origami-encoded strategy for integrating silica-metal heterostructures and revealed the underlying mechanisms. By programming the densities and lengths of protruding dsDNA strands on DNA origami, high site-addressability of material deposition was achieved.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Physical
Denis Selnihhin, Kim Mortensen, Jannik B. Larsen, Jens B. Simonsen, Finn Skou Pedersen
Summary: In this study, DNA-origami nanobeads were designed and constructed using DNA nanotechnology for fluorescence/antigen quantification in flow cytometry. The effectiveness of the bead design was verified through various microscopy techniques. The results demonstrate that DNA beads can accelerate quantitative studies of the biology of individual particles in flow cytometry.
Article
Biochemistry & Molecular Biology
Marcel Hanke, Niklas Hansen, Emilia Tomm, Guido Grundmeier, Adrian Keller
Summary: The study investigated the denaturation of DNA origami nanostructures by different Gdm salts, with guanidinium thiocyanate being the most potent denaturant. The results also revealed a non-monotonous temperature dependence of DNA origami denaturation in guanidinium sulfate, emphasizing the complexity of Gdm-DNA interaction.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Yuchen Wang, Anjelica Kucinic, Lilly Des Rosiers, Peter E. Beshay, Nicholas Wile, Michael W. Hudoba, Carlos E. Castro
Summary: DNA origami nanotechnology has potential for diverse applications, but its use in education is limited due to high cost and time requirements. We developed an experiment module for classroom implementation, focusing on a deformable hinge joint, that can be evaluated within 120 minutes using cost-effective equipment. Two beam-based models were presented to describe the joint deformation. This module can broaden access to and interest in the mechanical design of DNA origami.
APPLIED SCIENCES-BASEL
(2023)
Article
Chemistry, Multidisciplinary
Marco Lolaico, Sebbe Blokhuizen, Boxuan Shen, Yang Wang, Bjorn Hogberg
Summary: Interest in wireframe DNA origami has been growing, with different designs and software emerging rapidly. In this study, we enhance the design options for A-trail routed wireframe DNA structures by introducing four-helix bundles. We develop software for designing these structures, successfully create and fold a library of structures, and investigate the mechanical rigidity of the reinforced ones. The scaffold routing allows for easy incorporation of reinforced edges and flexible single helix edges, enabling customization of structure stiffness.
Article
Chemistry, Multidisciplinary
Marco Lolaico, Sebbe Blokhuizen, Boxuan Shen, Yang Wang, Bjorn Hogberg
Summary: In recent years, there has been a growing interest in wireframe DNA origami, with various designs, software, and applications emerging rapidly. This study focuses on increasing the design options for A-trail routed wireframe DNA structures by incorporating four-helix bundles (4HB). The researchers developed software for designing these structures, successfully demonstrated the design and folding of a library of structures, and investigated the mechanical rigidity of the reinforced structures. The scaffold routing technique allows for the easy incorporation of reinforced edges and flexible single helix edges, enabling customization of the desired structure's stiffness. The successful folding of hybrid structures and the characterization of different stiffness levels using computational and experimental approaches were demonstrated.
Article
Biochemistry & Molecular Biology
Yang Xin, Amir Ardalan Zargariantabrizi, Guido Grundmeier, Adrian Keller
Summary: This study evaluated three approaches for efficiently immobilizing DNA origami nanostructures (DONs) on mica surfaces under essentially Mg2+-free conditions, finding that pre-adsorption of different multivalent cations can replace Mg2+ and successfully immobilize DONs.
Article
Biochemistry & Molecular Biology
Patrick Walter, Ariel Mechaly, Julien Bous, Ahmed Haouz, Patrick England, Josephine Lai-Kee-Him, Aurelie Ancelin, Sylviane Hoos, Bruno Baron, Stefano Trapani, Patrick Bron, Gilles Labesse, Helene Munier-Lehmann
Summary: Tuberculosis claims over one million lives each year. Developing new antibiotics is a feasible approach to address drug resistance. Bacterial UMP kinase, which is essential for bacterial survival and has no human counterpart, serves as a promising target for novel antibiotic discovery. This study provides a detailed description of the UTP-binding site of a typical Gram-positive behaving UMP kinase, shedding light on the allosteric regulation of this enzyme and offering valuable insights for future drug discovery strategies.
Article
Biology
Emmanuel Saridakis, Rishi Vishwakarma, Josephine Lai-Kee-Him, Kevin Martin, Isabelle Simon, Martin Cohen-Gonsaud, Franck Coste, Patrick Bron, Emmanuel Margeat, Marc Boudvillain
Summary: Cryo-EM structure determination reveals that M. tuberculosis Rho-factor adopts an open, ring-shaped hexamer conformation and exhibits steric bulk in the cavity for bicyclomycin binding, leading to resistance to the antibiotic. The study also uncovers a leucine-to-methionine substitution that creates a steric bulk in the binding cavities, resulting in resistance to bicyclomycin at the expense of motor efficiency. This work contributes to understanding the unique features of M. tuberculosis Rho and provides insights for future antibiotic development.
COMMUNICATIONS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
A. Mills, N. Aissaoui, D. Maurel, J. Elezgaray, F. Morvan, J. J. Vasseur, E. Margeat, R. B. Quast, J. Lai Kee-Him, N. Saint, C. Benistant, A. Nord, F. Pedaci, G. Bellot
Summary: This study introduces a programmable DNA origami-based molecular actuator called Nano-winch, which can manipulate multiple mechanoreceptors by exerting fine-tuned forces. This device provides a tool-free approach to control and explore mechanotransduction circuits on living cells.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Brandon Huntington, Lingyun Zhao, Patrick Bron, Umar F. Shahul F. Hameed, Stefan T. T. Arold, Bilal M. M. Qureshi
Summary: This study investigated how to solve the issues of aggregation, dissociation, and particle orientation in sample preparation for cryo-EM analysis of CDC48A. By improving purification methods and selecting optimal ice thickness for grid freezing, high-quality data was obtained under standard laboratory and microscope settings.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Multidisciplinary Sciences
Julien Bous, Aurelien Fouillen, Helene Orcel, Stefano Trapani, Xiaojing Cong, Simon Fontanel, Julie Saint-Paul, Josephine Lai-Kee-Him, Serge Urbach, Nathalie Sibille, Remy Sounier, Sebastien Granier, Bernard Mouillac, Patrick Bron
Summary: Recent structural studies have provided insights into the molecular mechanisms of GPCR-arrestin coupling, but it is unclear whether this process is conserved among different GPCRs. In this study, the cryo-electron microscopy active structure of the wild-type arginine-vasopressin V2 receptor (V2R) in complex with beta-arrestin1 was determined, revealing a unique arrangement of beta-arrestin1 and an interface involving all receptor intracellular loops. These findings suggest a significant structural variability among GPCR-arrestin signaling complexes.
Article
Multidisciplinary Sciences
Zakia Morichaud, Stefano Trapani, Rishi K. Vishwakarma, Laurent Chaloin, Corinne Lionne, Josephine Lai-Kee-Him, Patrick Bron, Konstantin Brodolin
Summary: Researchers discovered that a stress-response factor called sigma(B) from Mycobacterium tuberculosis can induce the oligomerization of RNA polymerase (RNAP), resulting in the formation of a supramolecular complex composed of eight RNAP units. This finding reveals how sigma(B) can regulate gene expression by modulating the assembly and hibernation of RNAP holoenzyme.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Sandy Ibanes, Fatima El-Alaoui, Josephine Lai-Kee-Him, Chantal Cazevieille, Francois Hoh, Sebastien Lyonnais, Patrick Bron, Luca Cipelletti, Laura Picas, Simonetta Piatti
Summary: This study reveals that Syp1 is able to align and pack septin filaments laterally, aiding in the assembly of septin collar. It also emphasizes the conserved protein functions and the functional diversity of unstructured protein domains.
Article
Microbiology
Stefano Trapani, Eijaz Ahmed Bhat, Michel Yvon, Josephine Lai-Kee-Him, Francois Hoh, Marie-Stephanie Vernerey, Elodie P. Pirolles, Melia Bonnamy, Guy P. Schoehn, Jean-Louis Zeddam, Stephane P. Blanc, Patrick Bron
Summary: The genome of multipartite viruses is divided into segments that are encapsidated separately. There are two hypothesis about how these viral systems maintain genome integrity. After studying a nanovirus (FBNSV), it was found that there were no major structural differences depending on the encapsidated segment. Further experiments demonstrated that the viral genome moves long distance as assembled viral particles, suggesting independent and random propagation of the distinct segments.
Review
Materials Science, Biomaterials
Allan Mills, Nesrine Aissaoui, Julie Finkel, Juan Elezgaray, Gaetan Bellot
Summary: This review highlights the ability of DNA nanodevices to self-assemble and respond to the local environment, and discusses their potential applications and challenges in fields such as mechanobiology and nanomedicine.
Review
Biochemistry & Molecular Biology
Aurelien Fouillen, Julien Bous, Sebastien Granier, Bernard Mouillac, Remy Sounier
Summary: G-protein coupled receptors (GPCRs) are versatile signaling proteins that regulate key physiological processes in response to a wide variety of extracellular stimuli. Recent advancements in structural biology, cryo-electron microscopy, NMR development, and molecular dynamic simulations have provided better insight into the regulation of GPCRs by ligands of different efficacy and bias. These developments have fostered a renewed interest in GPCR drug discovery and the identification of biased ligands that can selectively promote specific regulations.
Article
Virology
Justine Girard, Celia Jakob, Lina Kathrin Toews, Jonas Fuchs, Anne Pohlmann, Kati Franzke, Larissa Kolesnikova, Csaba Jeney, Martin Beer, Patrick Bron, Martin Schwemmle, Hardin Bolte
Summary: This study reveals the phenomenon of vRNA loss and replacement by host RNA caused by mutations in the influenza virus. The disruption of two packaging signals in a model H7N7 influenza A virus leads to a mixture of virions with different vRNA content, including empty virions, virions with one to four vRNAs, and virions with octameric complexes composed of vRNA duplicates. These results suggest that the assembly of complete octameric complexes proceeds through a series of defined vRNA sub-complexes and that virions can bud without incorporating complete octameric complexes.
JOURNAL OF VIROLOGY
(2023)