Article
Engineering, Biomedical
Mathaeus Tschaikowsky, Tanja Neumann, Sofia Brander, Heiko Haschke, Bernd Rolauffs, Bizan N. Balzer, Thorsten Hugel
Summary: Understanding the function and dysfunction of hierarchically organized biomaterials or tissues requires studying different length scales. Atomic force microscopy (AFM) combined with fluorescence microscopy can provide detailed information from millimeter to nanometer scales. This approach is not only applicable to cartilage but also useful for characterizing native biological tissues from macro- to nanoscale.
ACTA BIOMATERIALIA
(2021)
Review
Chemistry, Analytical
Agnieszka Nawrocka, Ireneusz Piwonski, Salvatore Sauro, Annalisa Porcelli, Louis Hardan, Monika Lukomska-Szymanska
Summary: This paper conducted a literature review on four microscopic methods commonly used in dental research, which are confocal laser scanning microscopy (CLSM), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and atomic force microscopy (AFM). These microscopic techniques differ in their principles and require specific protocols for specimen preparation, but all play a significant role in describing and evaluating the adhesive bonding process and enamel surface condition.
Article
Biochemistry & Molecular Biology
Karen Zagorski, Tommy Stormberg, Mohtadin Hashemi, Anatoly B. Kolomeisky, Yuri L. Lyubchenko
Summary: The interplay between the mechanical properties of double-stranded and single-stranded DNA plays an important role in genetic processes. In this study, DNA nanorings were designed to investigate the stretching effect of double-stranded DNA on single-stranded DNA. The results showed that the stretching effect was consistent with theoretical estimates. Furthermore, time-lapse observations revealed dynamic behavior of the DNA rings, allowing for the formation of various morphologies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Virology
Brian Mondeja, Odalys Valdes, Sonia Resik, Ananayla Vizcaino, Emilio Acosta, Adelmo Montalvan, Amira Paez, Mayra Mune, Roberto Rodriguez, Juan Valdes, Guelsys Gonzalez, Daisy Sanchez, Viviana Falcon, Yorexis Gonzalez, Vivian Kouri, Angelina Diaz, Maria Guzman
Summary: The study collected nasopharyngeal swabs from 12 Cuban individuals, processed them with various microscopy techniques, and found that positive samples showed characteristic coronavirus-like particles with evident destruction of microvilli, potentially explaining anosmia in some patients.
Article
Biochemistry & Molecular Biology
Md. Saddam Husain Ansari, Naveen Kumar, Sriyans Jain, N. Yogesh Balakarthick, Ranjan Sen
Summary: We screened a clone from a genomic library of mycobacteriophages and found it to have mycobactericidal properties. This clone codes for a protein called Gp49, which is highly conserved among mycobacteriophages and likely plays a role in phage DNA replication. Gp49 is a high-affinity heparin-binding protein that can bind to both linear dsDNA and ssDNA/cooperatively, inhibiting transcription and displacing DNA-binding proteins. Its heparin-binding ability could have therapeutic/diagnostic applications in bacterial sepsis treatment.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Materials Science, Multidisciplinary
Frederico Tremoco, Ana I. Gomez-Varela, Adelaide Miranda, Martin Lopez-Garcia, Ana G. Silva, Pieter A. A. De Beule
Summary: The study found that sample heating is an important issue that needs to be considered in experimental setups involving intense light illumination of AFM cantilevers, especially when conducting single molecule investigations.
RESULTS IN PHYSICS
(2022)
Article
Biology
Fatima El Alaoui, Ignacio Casuso, David Sanchez-Fuentes, Charlotte Arpin-Andre, Raissa Rathar, Volker Baecker, Anna Castro, Thierry Lorca, Julien Viaud, Stephane Vassilopoulos, Adrian Carretero-Genevrier, Laura Picas
Summary: Clathrin-mediated endocytosis (CME) is a central trafficking pathway in eukaryotic cells regulated by phosphoinositides. The study reveals the molecular dynamics of FCHo2 self-assembly on membranes, showing that it forms ring-like-shaped protein patches and enhances PI(4,5)P-2 clustering, leading to increased clathrin assembly.
Article
Biophysics
Kaizhu Guo, Zongbo Li, Allison Win, Roxana Coreas, Gary Brent Adkins, Xinping Cui, Dong Yan, Minghui Cao, Shizhen Emily Wang, Wenwan Zhong
Summary: The ultrasensitive method reported in this study can detect single EVs with an input as low as 100 vesicles/µL by using DNA nanostructure labeling and EV membrane staining. It allows calibration-free analysis of protein profiles among different EV samples, differentiation of EVs by their cell of origin, and co-localization of dual protein markers on the same EV. The method shows great potential for non-invasive detection of EV-based protein biomarkers for cancer diagnosis and treatment monitoring.
BIOSENSORS & BIOELECTRONICS
(2021)
Article
Chemistry, Multidisciplinary
Sara Cavallaro, Federico Pevere, Fredrik Stridfeldt, Andre Gorgens, Carolina Paba, Siddharth S. Sahu, Doste R. Mamand, Dhanu Gupta, Samir El Andaloussi, Jan Linnros, Apurba Dev
Summary: This study for the first time simultaneously investigated multiple parameters on small extracellular vesicles (sEVs) to identify both common and cell line-specific subpopulations, providing insights into their biology and functions.
Article
Chemistry, Multidisciplinary
Heba Khateb, Rasmus S. Sorensen, Kimberly Cramer, Alexandra S. Eklund, Jorgen Kjems, Rikke L. Meyer, Ralf Jungmann, Duncan S. Sutherland
Summary: This study investigates the interaction between Staphylococcus aureus and fibronectin, and its impact on bacterial adhesion. The results show that the adhesion of S. aureus is regulated by the size of fibronectin patches, and the engagement of at least two receptors is required for strong adhesion.
Article
Genetics & Heredity
Ingrid Tessmer
Summary: A variety of DNA lesions are constantly introduced into our cells, and their efficient repair is crucial for maintaining genomic stability and cell viability. Different DNA repair systems, involving various protein factors and strategies, play essential roles in targeting and repairing different types of DNA lesions. Interestingly, certain specialized DNA repair proteins form non-functional complexes with their target lesions, marking them for repair and facilitating recruitment of DNA repair cascades. These proteins also establish connections between DNA repair mechanisms and transcription regulation. Recent single molecule analyses have provided insights into the function of alkyltransferase-like protein ATL in initiating nucleotide excision repair (NER) of non-native NER target lesions, and the recruitment of the base excision repair (BER) enzyme hOGG1 by the oncogene transcription factor Myc during oxidative stress.
Article
Energy & Fuels
Wentong Zhang, Zhengfu Ning, Shaohua Gai, Jie Zhu, Fan Fan, Zongke Liu, Hengli Wang
Summary: The study introduces nanoindentation technology to create a marked district, allowing fast and effective observations of the pore structure of tight sandstones at the same location of the same sample by combining AFM and CF-SEM technologies.
JOURNAL OF PETROLEUM SCIENCE AND ENGINEERING
(2022)
Article
Chemistry, Multidisciplinary
Do Hyung Chun, Seongchan Kim, Jumi Park, SunJe Lee, Wook Kim, Jung Hwan Lee, Ryan Rhee, Tae Gyun Kim, Dae Geun Choi, Dukhyun Choi, Dongho Kim, Jeong Ho Cho, Jong Hyeok Park
Summary: Nanoimprinting lithography (NIL) technique is widely used for nanostructure engineering of soft materials. In this study, a defect-free nanopatterned-(FAPbI(3))(0.85)(MAPbBr(3))(0.15) (NP-FAMA) film is successfully developed by optimizing the NIL process. Surface energy control plays a crucial role in NIL process, and treatment of the polymeric mold prevents peeling-off issues. NP-FAMA shows enhanced crystallographic and photophysical properties, and the photoresponsivity of NP-FAMA-based photodetectors outperform other devices.
ADVANCED FUNCTIONAL MATERIALS
(2022)
Article
Chemistry, Multidisciplinary
Christopher M. Green, William L. Hughes, Elton Graugnard, Wan Kuang
Summary: The study utilized correlative microscopy techniques to investigate DNA nanostructures, finding that over 75% of defective docking sites were incorporated but inactive, with unincorporated strands playing a minor role in limiting the availability of addressable sites. Further exploration of the effects of strand purification, UV irradiation, and photooxidation on availability provided insights into potential sources of defects and pathways to improving the fidelity of DNA nanostructures.
Article
Chemistry, Multidisciplinary
Joschka Hellmeier, Rene Platzer, Vanessa Muehlgrabner, Magdalena C. Schneider, Elke Kurz, Gerhard J. Schuetz, Johannes B. Huppa, Eva Sevcsik
Summary: DNA origami structures provide flexible scaffolds for organizing biomolecules with nanometer precision, but functionalizing them with proteins while maintaining stoichiometry and protein functionality remains challenging. This study systematically evaluated different strategies for site-specific decoration of DNA origami structures, with a focus on efficiency, stoichiometry, and protein functionality. The study found that using charge-neutral peptide nucleic acid emerged as the best strategy for achieving high yield and preserving protein functionality.
Editorial Material
Chemistry, Multidisciplinary
Stefan Howorka
NATURE REVIEWS CHEMISTRY
(2022)
Article
Nanoscience & Nanotechnology
Yongzheng Xing, Adam Dorey, Lakmal Jayasinghe, Stefan Howorka
Summary: Rational design with DNA can greatly expand the structural and functional range of membrane nanopores, allowing for customizable pore shapes and lumen widths of up to tens of nanometres. These designer nanopores demonstrate how DNA nanotechnology can provide functional biomolecular structures for use in synthetic biology, single-molecule enzymology, biophysical analysis, portable diagnostics, and environmental screening.
NATURE NANOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Swarup Dey, Adam Dorey, Leeza Abraham, Yongzheng Xing, Irene Zhang, Fei Zhang, Stefan Howorka, Hao Yan
Summary: Artificial systems to control the transport of molecules across biomembranes can be useful for biosensing or drug delivery. Here, the authors assemble a DNA channel enabling the precisely timed, stimulus-controlled transport of functional proteins across bilayer membranes.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Jeroen F. van Dyck, Jonathan R. Burns, Kyle I. P. Le Huray, Albert Konijnenberg, Stefan Howorka, Frank Sobott
Summary: Recent interest in oligonucleotide nanostructures has led to the use of mass spectrometry and ion mobility to study their assembly. In this study, the authors use these techniques to characterize the structure of a hexameric DNA barrel and its intermediates and byproducts. They demonstrate the ability of these methods to determine the mass, charge state, and size of noncovalent DNA assemblies and reveal the role of ionic strength in their assembly. They also identify previously undetected higher-order assemblies and assign them to larger geometric structures.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Daniel Offenbartl-Stiegert, Alexia Rottensteiner, Adam Dorey, Stefan Howorka
Summary: Controlling biological processes with light allows precise and selective activation in a non-invasive and non-toxic manner. Researchers have developed a synthetic light-gated nanostructure that controls membrane transport through a controllable lid, with potential applications in biotechnology, drug release, and synthetic cells.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Ammar Alkhalde, Hannah Seferovic, Ali Abri, Alvana Simbrunner, Peter Hinterdorfer, Yoo Jin Oh
Summary: A new corneal crosslinking method called Bubble-CXL was introduced, which used intracameral oxygen as an additional oxygen source during the treatment. The use of intracameral oxygen resulted in increased biomechanical stability of the cornea.
Article
Chemistry, Multidisciplinary
Yongzheng Xing, Adam Dorey, Stefan Howorka
Summary: In bioinspired design, synthetic structures with similar structures and functions to biological templates are created. This report presents DNA-based biomimetic nanopores that can switch between open and closed states in response to specific binding of molecules and high transmembrane voltage. These designer nanopores mimic several aspects of complex biological channels and offer easier control over pore size, shape and stimulus response. They are expected to be applied in biosensing and synthetic biology.
ADVANCED MATERIALS
(2023)
Review
Chemistry, Multidisciplinary
Yongzheng Xing, Alexia Rottensteiner, Jonah Ciccone, Stefan Howorka
Summary: Membrane-spanning nanopores have diverse applications in label-free single-molecule sensing, nucleic acid sequencing, and research in biology and biophysics. The limitations of naturally occurring and synthetic inorganic nanopores can be overcome by functionalizing existing pores with DNA strands and creating a new class of DNA nanopores. This review focuses on the progress and potential applications of functional DNA nanopores.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Saanfor Hubert Suh, Yongzheng Xing, Alexia Rottensteiner, Rong Zhu, Yoo Jin Oh, Stefan Howorka, Peter Hinterdorfer
Summary: This study investigates molecular recognition in a synthetic confined nanopore with controllable pore dimension and molecular DNA receptors at different depth positions. The results show that the association rates are slower and the dissociation rates are faster for receptors positioned deeper inside the pore lumen. This phenomenon can be explained by the steric constraints on molecular interactions in confinement.
Article
Virology
Antonio Real-Hohn, Martin Groznica, Georg Kontaxis, Rong Zhu, Otavio Augusto Chaves, Leonardo Vazquez, Peter Hinterdorfer, Heinrich Kowalski, Dieter Blaas
Summary: Rhinoviruses are the main cause of the common cold and can lead to complications in patients with other ailments. Colds have a significant socioeconomic impact, but there are no vaccines or approved treatments available.
Article
Multidisciplinary Sciences
Katya Ahmad, Abid Javed, Conor Lanphere, Peter V. Coveney, Elena V. Orlova, Stefan Howorka
Summary: DNA can be folded into rationally designed, unique, and functional materials. Here the authors analyse an archetypal DNA nanoarchitecture with single particle cryo-electron microscopy and molecular dynamics simulations.
NATURE COMMUNICATIONS
(2023)
Editorial Material
Nanoscience & Nanotechnology
Adam Dorey, Stefan Howorka
Summary: A modified nanopore allows for enzyme-free threading of single polypeptides to detect post-translational modifications.
NATURE NANOTECHNOLOGY
(2023)
Article
Virology
Markus Kastner, Andreas Karner, Rong Zhu, Qiang Huang, Andreas Geissner, Anne Sadewasser, Markus Lesch, Xenia Woermann, Alexander Karlas, Peter H. Seeberger, Thorsten Wolff, Peter Hinterdorfer, Andreas Herrmann, Christian Sieben
Summary: The study compared influenza virus receptor specificity with virus binding to live cells using glycan arrays and single-virus force spectroscopy. The findings revealed that the receptor binding preference of the virus does not necessarily reflect its specificity to cells. Single-virus force spectroscopy was proposed as a tool to understand the cell binding preference of influenza A viruses.
Review
Chemistry, Multidisciplinary
Zuzanna S. S. Siwy, Merlin L. L. Bruening, Stefan Howorka
Summary: Nanopores in thin membranes have significant roles in science and industry. Single nanopores have been crucial in portable DNA sequencing and understanding nanoscale transport, while multipore membranes facilitate food processing and water and medicine purification. Although both fields utilize nanopores, they differ in terms of materials, fabrication, analysis, and applications. This Viewpoint proposes synergistic crosstalk between the two fields to enhance fundamental understanding and the development of advanced membranes. By improving communication and harmonizing measurements and modeling, the rational design of porous membranes can be enhanced.
CHEMICAL SOCIETY REVIEWS
(2023)
