Article
Chemistry, Multidisciplinary
Miao Wang, Donglei Yang, Qin Lu, Lin Liu, Zixin Cai, Yirong Wang, Hong-Hui Wang, Pengfei Wang, Zhou Nie
Summary: This study presents a DNA nanoplatform called DOTA that can program receptor oligomerization and control cellular signaling response. It allows for artificial signaling induction or natural activation simulation by arraying aptamer ligands. Furthermore, DOTA can function as a signaling switch to control cellular behaviors.
Article
Chemistry, Multidisciplinary
Trixy Fang, Jonatan Alvelid, Joel Spratt, Elena Ambrosetti, Ilaria Testa, Ana Teixeira
Summary: The spatial organization of PD-L1 plays a crucial role in regulating T-cell signaling, with PD-L1 ligands at 200 nm distance being more effective in inhibiting T-cell activation and reducing IL-2 expression compared to closer distances. These findings may guide the development of nanomedicine-based immunomodulatory therapies in the future.
Article
Multidisciplinary Sciences
Jean-Philippe Guegan, Justine Pollet, Christophe Ginestier, Emmanuelle Charafe-Jauffret, Marcus E. Peter, Patrick Legembre
Summary: Our study reveals that the interaction between CD95 and KPC2 leads to the degradation of NF-kappa B1, resulting in the repression of NF-kappa B-driven gene expression through the formation of p50 homodimers. Loss of CD95 in TNBC cells releases KPC2, promoting NF-kappa B activation and the production of pro-inflammatory cytokines.
Article
Chemistry, Multidisciplinary
Yang Wang, Igor Baars, Ferenc Fordos, Bjorn Hogberg
Summary: The nanoscale spatial organization of TNF receptors on cell surfaces plays a crucial role in regulating cellular fate. The use of DNA origami nanostructures to pattern TNF-related apoptosis-inducing ligand-mimicking peptides has shown potential in inducing death receptor clustering and apoptosis in human breast cancer cells, offering a new strategy to improve TNF superfamily activation methods.
Review
Biochemistry & Molecular Biology
Layla Haymour, Mickael Jean, Cristian Smulski, Patrick Legembre
Summary: The interaction between CD95L and CD95 plays a crucial role in maintaining tissue homeostasis and eliminating infected and cancer cells. However, this interaction can also activate non-apoptotic signaling pathways that contribute to cancer metastasis and auto-immune disorders. Moreover, CD95 expression itself may promote oncogenesis independently of CD95L, and both ligand and receptor can interact with other partners to modulate their physiological functions. Therefore, understanding these non-canonical responses is essential for elucidating the functions of the CD95L-CD95 pair.
BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER
(2023)
Article
Multidisciplinary Sciences
Kelly J. Culhane, Tejas M. Gupte, Indrani Madhugiri, Chetan J. Gadgil, Sivaraj Sivaramakrishnan
Summary: This study proposes a kinetic model to simulate the interactions between hormone, G protein coupled receptor (GPCR), and G protein. Experimental validation reveals the phenomenon of GPCR priming and the temporary enhancement of GPCR ternary complex formation by allokairic effectors. This study uncovers the kinetic mechanisms of ternary complex formation and downstream signaling.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Arivazhagan Rajendran, Kirankumar Krishnamurthy, Seojeong Park, Eiji Nakata, Youngjoo Kwon, Takashi Morii
Summary: DNA minicircles are important for studying DNA-protein interactions, and their topological features play a significant role in these interactions.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Nanoscience & Nanotechnology
Melika Shahhosseini, Peter E. Beshay, Ehsan Akbari, Niksa Roki, Christopher R. Lucas, Alex Avendano, Jonathan W. Song, Carlos E. Castro
Summary: This study presents a method to monitor the interactions between cells and molecules in their surrounding environment in a three-dimensional tissue model. By utilizing a DNA origami cell sensing platform, specific nucleic acid sequences on the cell membrane were detected in real-time, and biomolecules on the cell surface were also detected in a 3D microfluidic tissue model.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Pharmacology & Pharmacy
Elizabeth K. M. Johnstone, Rekhati S. Abhayawardana, Heng B. See, Ruth M. Seeber, Shannon L. O'Brien, Walter G. Thomas, Kevin D. G. Pfleger
Summary: TRIO acts as an intermediate in the transactivation process of EGFR mediated by AngII/AT(1) receptor, with its proximity to other proteins confirmed through BRET assays. The existence of the AT(1)-EGFR heteromer was further supported by Receptor-Heteromer Investigation Technology, revealing potential mechanisms of TRIO contribution to this process.
BIOCHEMICAL PHARMACOLOGY
(2021)
Article
Environmental Sciences
Haojie Li, Junjiang Fan, Yangfei Zhao, Jiarong Yang, Huimiao Xu, Ram Kumar Manthari, Xiaofang Cheng, Jundong Wang, Jinming Wang
Summary: The study shows that long-term excessive intake of fluoride can cause kidney damage and apoptosis, while dietary calcium supplementation can alleviate this damage. Calcium supplementation mitigates fluoride-induced kidney apoptosis through various signaling pathways.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Article
Anatomy & Morphology
Zhengguang Wang, Yongfang Tan, Fei Xu
Summary: This study aimed to investigate the effects of zonisamide (ZNS) on a degenerative cervical myelopathy (DCM) rat model and explore the potential mechanisms. The results showed that ZNS promoted motor recovery, reversed histopathological injury and cell apoptosis in DCM rats. Additionally, ZNS attenuated DCM injury through the regulation of Fas and FasL signaling. Therefore, this study provided a new theoretical approach for subsequent academic and clinical research on DCM injury.
Article
Multidisciplinary Sciences
Ying Chen, Jinyi Zhang, Yuan Weng, Yueming Xu, Weiqiang Lu, Wei Liu, Mingyao Liu, Tian Hua, Gaojie Song
Summary: This study presents the structures of the human adenosine A2B receptor (A2BR) bound to its agonists NECA and BAY60-6583, elucidating the orthosteric binding pockets and their subtle differences. Selectivity is mainly determined by regions extended from the orthosteric pocket, and the key determinants for BAY60-6583's selectivity against A2BR are identified. This study provides a better understanding of ligand selectivity in the adenosine receptor family and offers a structural template for the development of A2BR ligands for related diseases.
Article
Biology
Shimaa A. Abdellatef, Hisashi Tadakuma, Kangmin Yan, Takashi Fujiwara, Kodai Fukumoto, Yuichi Kondo, Hiroko Takazaki, Rofia Boudria, Takuo Yasunaga, Hideo Higuchi, Keiko Hirose, Andrew P. Carter
Summary: The bending of cilia and flagella is caused by the oscillatory movement of dynein molecules. Researchers constructed a simple model system to study the oscillation of dynein and found that it can cause repetitive bending motions even without additional regulatory structures.
Article
Cell Biology
Pengxiang Huang, Bradley M. Wierbowski, Tengfei Lian, Charlene Chan, Sara Garcia-Linares, Jiansen Jiang, Adrian Salic
Summary: This study reveals a unique role for GAS1 in catalyzing the assembly of the SHH-PTCH1 complex by transferring SHH from the extracellular carrier SCUBE2 to PTCH1 in vertebrate cells. Structure-guided experiments elucidate the mechanism of SHH movement and PTCH1 internalization, providing insights into morphogen reception and regulation.
DEVELOPMENTAL CELL
(2022)
Review
Pharmacology & Pharmacy
Yuyu Feng, Yumeng Yan, Jiahua He, Huanyu Tao, Qilong Wu, Sheng-You Huang
Summary: Nucleic acid-ligand interactions play crucial roles in cellular processes and have attracted significant interest in drug discovery. However, traditional docking algorithms and scoring functions for protein-ligand interactions may not be applicable to nucleic acid-ligand docking due to the differences in their properties. This review discusses the current status, challenges, and limitations of docking algorithms and scoring functions for DNA/RNA-ligand interactions.
DRUG DISCOVERY TODAY
(2022)
Article
Materials Science, Multidisciplinary
Christoph Pauer, Aron Venczel, Mihir Dass, Tim Liedl, Joe Tavacoli
Summary: Eukaryotic cells that swim by the beating of nanoscale elastic filaments called flagella provide a promising locomotion paradigm. This study demonstrates the fabrication of custom-made nanoscale filaments using the DNA-origami technique. The study shows that these filaments, when attached to magnetic beads, can cause them to move in a ballistic fashion under an external magnetic field. This proof-of-concept work paves the way for the design of purpose-built appendages using DNA self-assembly for more complex locomotion on the nano and microscale.
ADVANCED MATERIALS TECHNOLOGIES
(2022)
Article
Chemistry, Multidisciplinary
Kevin Martens, Timon Funck, Eva Y. Santiago, Alexander O. Govorov, Sven Burger, Tim Liedl
Summary: Chirality is a fundamental feature in various domains of nature, and this study explores the interaction between light and chiral nanostructures. Using DNA origami, the researchers assembled plasmonic nanoparticles to investigate their impact on optical near fields. They also designed and implemented sign-flipping signals through the addition or removal of particles. The study revealed the previously unrecognized phenomenon of chiral plasmonic-dielectric coupling in DNA-based plasmonic nanostructures.
Article
Biophysics
Luzia Kilwing, Pascal Lill, Bhavik Nathwani, Jasleen Kaur Daljit Singh, Tim Liedl, William M. Shih
Summary: Nanoscale stepper motors are important in natural processes and biomimetic technologies. A DNA-origami based stepper motor was studied, with innovative features including octapedal walking, orthogonal sequences, and small step sizes. Although cyclic actuation was achieved, control over movement directionality was not successful.
BIOPHYSICAL JOURNAL
(2022)
Article
Biophysics
Heini Ijas, Tim Liedl, Veikko Linko, Gregor Posnjak
Summary: DNA self-assembly and DNA origami are reliable methods for organizing materials. We use temperature-controlled sample holders and standard spectrometers to monitor the assembly process in real time and determine the folding and melting temperatures of different DNA structures. Additionally, we investigate the digestion of DNA structures in the presence of DNase I.
BIOPHYSICAL JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Gaspard Junot, Sergi G. Leyva, Christoph Pauer, Carles Calero, Ignacio Pagonabarraga, Tim Liedl, Joe Tavacoli, Pietro Tierno
Summary: In this study, we demonstrate the transport of lithographically shaped magnetic microtriangles in viscous fluids using a precessing magnetic field. The microtriangles undergo complex transport modes, including a surfing-like drift and a transversal drift, which is generated by the asymmetric shape of the triangles. We explain this phenomenon with a minimal numerical model and suggest that this method can be extended to other anisotropic-shaped magnetic materials.
Article
Multidisciplinary Sciences
Martina F. Ober, Anna Baptist, Lea Wassermann, Amelie Heuer-Jungemann, Bert Nickel
Summary: In this study, silica deposition on DNA origami structures was investigated using in situ small-angle X-ray scattering. The results revealed that silica formation led to condensation and shrinkage of the DNA origami structures. Silicification increased the stability of the structures and provided chemical protection. The study also found that silica not only formed an outer shell, but also penetrated the internal structure of the origami.
NATURE COMMUNICATIONS
(2022)
Article
Nanoscience & Nanotechnology
Veit Giegold, Karol Kolataj, Tim Liedl, Achim Hartschuh
Summary: This study demonstrates that Miller's rule still holds for ultra-broadband excitation pulses, and the nonlinear response of nanoantennas can be deterministically controlled and optimized by varying the spectral phase of the laser pulse. The positioning of the nanoantenna with respect to the laser spectrum affects the ND-FWM signal, and phase control enables chirp-selective confocal imaging.
Article
Chemistry, Multidisciplinary
Kateryna Trofymchuk, Karol Kolataj, Viktorija Glembockyte, Fangjia Zhu, Guillermo P. Acuna, Tim Liedl, Philip Tinnefeld
Summary: DNA origami has become a leading technology for organizing materials at the nanoscale, particularly for manipulating light using plasmonic nanoparticles. In this study, gold nanorods were arranged in a plasmonic nanoantenna dimer, resulting in a 1600-fold enhancement of fluorescence from a conventional near-infrared dye located at the plasmonic hotspot between the nanorods. Various characterization techniques and numerical simulations provided insights into the heterogeneity of the observed enhancement values. The use of a recently introduced design called NAnoantenna with Cleared HotSpot (NACHOS) enabled the creation of a hotspot region with a size of approximately 12 nm, which allows for the incorporation of tailored bioassays. The possibility of synthesizing nanoantennas in solution opens the potential for large-scale production.
Letter
Chemistry, Multidisciplinary
Pauline J. Kolbeck, Mihir Dass, Irina V. Martynenko, Relinde J. A. van Dijk-Moes, Kelly J. H. Brouwer, Alfons van Blaaderen, Willem Vanderlinden, Tim Liedl, Jan Lipfert
Summary: Atomic force microscopy (AFM) is a powerful technique for high-resolution imaging of molecules, macromolecular complexes, and nanoparticles. However, the shape of the AFM tip can distort the images. In this study, we use a 3D DNA origami structure as a fiducial for tip reconstruction and image correction. The fiducial has sharp steps at different heights, allowing reliable tip reconstruction with as few as ten fiducials. This fiducial enables accurate and precise AFM imaging for a wide range of applications.
Article
Chemistry, Physical
Mariana Alarcon-Correa, Luzia Kilwing, Florian Peter, Tim Liedl, Peer Fischer
Summary: The DNA origami technique allows for the creation of catalytic nanomachines by combining precise engineered DNA nanostructures, which have been shown to be surprisingly stable in up to 5% hydrogen peroxide.
Editorial Material
Chemistry, Physical
Anastassia N. Alexandrova, Julie S. Biteen, Sonia Coriani, Franz M. Geiger, Andrew A. Gewirth, Gillian R. Goward, Hua Guo, Libai Huang, Jian-Feng Li, Tim Liedl, Stephan Link, Zhi-Pan Liu, Sudipta Maiti, Andrew J. Orr-Ewing, David L. Osborn, Jim Pfaendtner, Benoit Roux, Friederike Schmid, J. R. Schmidt, William F. Schneider, Lyudmila V. Slipchenko, Gemma C. Solomon, Jeroen A. van Bokhoven, Veronique Van Speybroeck, Shen Ye, T. Daniel Crawford, Martin T. Zanni, Gregory V. Hartland, Joan-Emma Shea
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Editorial Material
Chemistry, Physical
Anastassia N. Alexandrova, Julie S. Biteen, Sonia Coriani, Franz M. Geiger, Andrew A. Gewirth, Gillian R. Goward, Hua Guo, Libai Huang, Jian-Feng Li, Tim Liedl, Stephan Link, Zhi-Pan Liu, Sudipta Maiti, Andrew J. Orr-Ewing, David L. Osborn, Jim Pfaendtner, Benoit Roux, Friederike Schmid, J. R. Schmidt, William F. Schneider, Lyudmila V. Slipchenko, Gemma C. Solomon, Jeroen A. van Bokhoven, Veronique Van Speybroeck, Shen Ye, T. Daniel Crawford, Martin T. Zanni, Gregory V. Hartland, Joan-Emma Shea
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Editorial Material
Chemistry, Physical
Anastassia N. Alexandrova, Julie S. Biteen, Sonia Coriani, Franz M. Geiger, Andrew A. Gewirth, Gillian R. Goward, Hua Guo, Libai Huang, Jian-Feng Li, Tim Liedl, Stephan Link, Zhi-Pan Liu, Sudipta Maiti, Andrew J. Orr-Ewing, David L. Osborn, Jim Pfaendtner, Benoit Roux, Friederike Schmid, J. R. Schmidt, William F. Schneider, Lyudmila V. Slipchenko, Gemma C. Solomon, Jeroen A. van Bokhoven, Veronique Van Speybroeck, Shen Ye, T. Daniel Crawford, Martin T. Zanni, Gregory V. Hartland, Joan-Emma Shea
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Multidisciplinary Sciences
Omar A. Saleh, Sam Wilken, Todd M. Squires, Tim Liedl
Summary: This study investigates the dynamics of dilute internal inclusions, called vacuoles, within liquid droplets of DNA nanostar particles. The researchers observe appearance, growth, and bursting of the vacuoles, and find that their growth follows a linear relationship with time. The vacuoles burst when they reach the droplet interface, causing droplet motion due to osmotic pressure. A diffusion-based model is developed to explain these behaviors quantitatively.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Francis Schuknecht, Karol Kolataj, Michael Steinberger, Tim Liedl, Theobald Lohmueller
Summary: The label-free identification of individual proteins from liquid samples by surface-enhanced Raman scattering (SERS) spectroscopy has been achieved using a DNA origami scaffold and gold nanorods, providing sufficient field enhancement for single-protein SERS spectroscopy with sub-second integration times.
NATURE COMMUNICATIONS
(2023)