Review
Cell Biology
Jianquan Xu, Yang Liu
Summary: Chromatin organization plays a crucial role in gene regulation and genome maintenance. Disruption of chromatin structure is associated with various pathological processes and diseases. Recent advances in single molecule localization microscopy (SMLM) provide new opportunities to visualize chromatin architecture at nanometer resolution and improve our understanding of diseases.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Yang Zhang, Yeting Zheng, Andrea Tomassini, Ambarish Kumar Singh, Francisco M. Raymo
Summary: PALM uses fluorescence photoactivation and single-molecule localization to overcome optical diffraction and achieve nanoscale spatial resolution in imaging biological samples. Synthetic modifications of the BODIPY chromophore allow for photoactivation and precise localization of single molecules. In combination with targeting ligands, photoactivatable BODIPYs can label subcellular components and enable sub-diffraction imaging of live cells using PALM, making them valuable probes for bioimaging applications.
Review
Biochemistry & Molecular Biology
Yoonsuk Hyun, Doory Kim
Summary: With the development of super-resolution imaging techniques, understanding protein structure at the nanoscale in terms of clustering and organization in a cell is crucial. This review categorizes computational cluster analysis methods for single-molecule localization microscopy (SMLM) images into classical and machine learning-based methods, and discusses possible future directions for machine learning-based cluster analysis methods for SMLM data.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Review
Chemistry, Analytical
Hua Liu, Zhongju Ye, Yanan Deng, Jie Yuan, Lin Wei, Lehui Xiao
Summary: This review describes the basic principles of single-molecule localization microscopy (SMLM), factors affecting imaging quality, recent achievements in the development of fluorescent probes for SMLM, and challenges and future advances in SMLM for biological applications.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Xinyu Zhou, Rui Wang, Zijian Wan, Pengfei Zhang, Shaopeng Wang
Summary: In this study, we demonstrate multiplexed protein detection and parallel protein interaction analysis through evanescent scattering microscopy (ESM). ESM allows label-free digital single-molecule counting for binding kinetics measurement, improving counting efficiency and accuracy. We show that digital single-molecule counting can differentiate proteins with different molecular weights, enabling real-time monitoring of protein binding processes in solution. Additionally, we show that this strategy can analyze the kinetics of two different protein interaction processes simultaneously, both on surfaces and in solution. This work may provide a way to investigate complex protein interactions, such as the competition between biomarker-antibody binding in biofluids and biomarker-protein binding on cellular membranes.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Xinyu Zhou, Rui Wang, Zijian Wan, Pengfei Zhang, Shaopeng Wang
Summary: Multiplexed protein detection and parallel protein interaction analysis are achieved using evanescent scattering microscopy (ESM), enabling label-free digital single-molecule counting with high temporal resolution. This strategy allows for real-time tracking of protein binding processes and simultaneous analysis of multiple protein interactions.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Physical
John S. H. Danial, Yuri Quintana, Uris Ros, Raed Shalaby, Eleonora G. Margheritis, Sabrina Chumpen Ramirez, Christian Ungermann, Ana J. Garcia-Saez, Katia Cosentino
Summary: This study develops a high-throughput, automated computational pipeline for subunit counting of biomolecular complexes using single-molecule brightness analysis. It systematically analyzes the experimental conditions and accuracy of counting, and provides a simple software tool for stoichiometry analysis of such complexes.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Cell Biology
Nadine Weinelt, Christos Karathanasis, Sonja Smith, Juliane Medler, Sebastian Malkusch, Simone Fulda, Harald Wajant, Mike Heilemann, Sjoerd J. L. van Wijk
Summary: TNFR1 is a crucial regulator of proinflammatory cell survival and programmed cell death, and deregulation of TNFα and TNFR1 signaling underlies major diseases. Therefore, finding alternative approaches to directly antagonize TNFR1 is beneficial.
JOURNAL OF LEUKOCYTE BIOLOGY
(2021)
Review
Chemistry, Multidisciplinary
Shankar Mandal, Zi Li, Tanmay Chatterjee, Kunal Khanna, Karen Montoya, Liuhan Dai, Chandler Petersen, Lidan Li, Muneesh Tewari, Alexander Johnson-Buck, Nils G. Walter
Summary: Current methods for detecting disease biomarkers in biofluids face challenges such as insufficient analytical performance and high cost. SiMREPS, an amplification-free approach, overcomes these challenges by providing high specificity and sensitivity for detecting diverse biomarkers. Early proof-of-concept studies have shown its effectiveness in detecting miRNAs and rare mutant DNA alleles with high specificity and single-molecule sensitivity.
ACCOUNTS OF CHEMICAL RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Zhiwei Ye, Wei Yang, Ying Zheng, Shujing Wang, Xiaodong Zhang, Haibo Yu, Shuangshuang Li, Chunxiong Luo, Xiaojun Peng, Yi Xiao
Summary: In this study, a new membrane probe and microfluidic platform were developed to enable synchronous use of super-resolution imaging and single-molecule tracking. This method allows high-throughput observation and analysis of the ultrastructural and dynamic details of living red blood cell membranes, providing new perspectives for future disease diagnostics.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Analytical
Jinxiu Wei, Siyao Zhang, Jiangnan Yuan, Zhuyuan Wang, Shenfei Zong, Yiping Cui
Summary: Tumor cell exosomes play a vital role in tumor cell proliferation and metastasis, but we still lack a comprehensive understanding of their appearance and biological characteristics due to their nanoscale size and high heterogeneity. We propose an imaging method called Expansion SMLM (ExSMLM) that combines Expansion Microscopy (ExM) and Single Molecule Localization Microscopy (SMLM) to achieve the expansion and super-resolution imaging of tumor cell exosomes.
Review
Cell Biology
Mark Tingey, Steven J. Schnell, Wenlan Yu, Jason Saredy, Samuel Junod, Dhrumil Patel, Abdullah A. Alkurdi, Weidong Yang
Summary: The transient nature of RNA and temporal constraints within cells make it difficult to image RNA, especially endogenous RNA in transfected cells. However, recent advances have provided researchers with the tools to image endogenous RNA at the cellular and single-molecule level.
Article
Biochemical Research Methods
Vincent Ebert, Patrick Eiring, Dominic A. Helmerich, Rick Seifert, Markus Sauer, Soren Doose
Summary: Characterizing the spatial fluorophore distribution using convex hull and related properties of localization clusters can be used for diagnostic purposes, as a parameter for cluster selection, or as a tool to determine localization precision.
Article
Biology
Adrien C. Descloux, Kristin S. Grussmayer, Aleksandra Radenovic
Summary: Descloux et al. introduce a parameter-free modified histogram rendering method for resolution estimation in localization microscopy datasets, accurately conveying localization information and depending on precision and density of localizations. Localization microscopy is a super-resolution imaging technique that relies on spatial and temporal separation of blinking fluorescent emitters, achieving sub-diffraction precision bounded by photon emission and sensor noise. The proposed bilinear histogram rendering pipeline avoids biases from Gaussian or standard rendering, demonstrating resolution estimation dependence on localization density and precision.
COMMUNICATIONS BIOLOGY
(2021)
Review
Chemistry, Multidisciplinary
Weijie Chi, Davin Tan, Qinglong Qiao, Zhaochao Xu, Xiaogang Liu
Summary: Single-molecule localization microscopy (SMLM) has been widely used in biology and chemistry. Fluorophores, as an essential component of SMLM, play a crucial role in obtaining super-resolution fluorescence images. Recent research on spontaneously blinking fluorophores simplifies experimental setups and extends the imaging duration of SMLM. This review provides an overview of the development of spontaneously blinking rhodamines from 2014 to 2023 and the key mechanistic aspects of intramolecular spirocyclization reactions, aiming to accelerate the advancement of super-resolution imaging technologies.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Selma E. Anton, Charlotte Kayser, Isabella Maiellaro, Katarina Nemec, Jan Moeller, Andreas Koschinski, Manuela Zaccolo, Paolo Annibale, Martin Falcke, Martin J. Lohse, Andreas Bock
Summary: Cells use independent cAMP nanodomains to send different signals, which form self-sufficient cell signaling units. Each nanodomain contains a highly localized cAMP pool that is protected from other receptors and cell compartments. The gradients of local cAMP concentrations define the size of each individual nanodomain. The coexistence of many such nanodomains allows a single cell to operate multiple independent cellular signals simultaneously.
Article
Chemistry, Multidisciplinary
Zhenyu Wang, Mukesh Tripathi, Zahra Golsanamlou, Poonam Kumari, Giuseppe Lovarelli, Fabrizio Mazziotti, Demetrio Logoteta, Gianluca Fiori, Luca Sementa, Guilherme Migliato Marega, Hyun Goo Ji, Yanfei Zhao, Aleksandra Radenovic, Giuseppe Iannaccone, Alessandro Fortunelli, Andras Kis
Summary: In this study, high-quality NbS2-MoS2 lateral heterostructures were synthesized by one-step metal-organic chemical vapor deposition (MOCVD) with Nb substitutionally doped monolayer MoS2, showing p-type doped behavior. The heterojunction exhibited p-type transfer characteristic with a high on/off current ratio of approximately 10^4, surpassing previous reports. The band structure of the NbS2-MoS2 heterojunction was investigated using density functional theory (DFT) and quantum transport simulations. This research provides a scalable approach to synthesize doped TMDC materials and offers insight into the interface between 2D metals and semiconductors in lateral heterostructures, which is crucial for the development of next-generation nanoelectronics and highly integrated devices.
ADVANCED MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Andrey Chernev, Yunfei Teng, Mukeshchand Thakur, Victor Boureau, Lucie Navratilova, Nianduo Cai, Tzu-Heng Chen, Liping Wen, Vasily Artemov, Aleksandra Radenovic
Summary: Nature provides a wide range of self-assembled structures, and this study presents a fast, nature-inspired method for growing stalactite nanopores using heterogeneous atomic deposition. The stalactite nanostructures combine the advantages of reduced sensing region typically for 2D material nanopores with the asymmetric geometry of capillaries, resulting in ionic selectivity, stability, and scalability. The proposed growing method provides an adaptable nanopore platform for basic and applied nanofluidic research.
ADVANCED MATERIALS
(2023)
Article
Chemistry, Physical
Vasily Artemov, Laura Frank, Roman Doronin, Philipp Staerk, Alexander Schlaich, Anton Andreev, Thomas Leisner, Aleksandra Radenovic, Alexei Kiselev
Summary: The surface charge of an open water surface is determined by electrostatic effects in the contact line vicinity of three phases. The contact potential difference between two aqueous interfaces created by charge redistribution is shown to be pH-dependent. This discovery provides insights into solvation phenomena and interfacial processes in aqueous systems and has implications for various experimental environments.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Nanoscience & Nanotechnology
S. M. Leitao, V. Navikas, H. Miljkovic, B. Drake, S. Marion, G. Pistoletti Blanchet, K. Chen, S. F. Mayer, U. F. Keyser, A. Kuhn, G. E. Fantner, A. Radenovic
Summary: In current nanopore-based label-free single-molecule sensing technologies, stochastic processes make it challenging to control the selection, rate, and velocity of single-molecule translocations. This study proposes a method that uses a glass nanopore mounted on a three-dimensional nanopositioner to spatially select and deterministically translocate molecules tethered on a glass surface. By controlling the distance between the nanopore and glass surface, the region of interest on the molecule can be actively selected and scanned at a controlled number of times and velocity. The method demonstrates versatility in assessing DNA-protein complexes, DNA rulers, and DNA gaps, enabling single-nucleotide gap detection.
NATURE NANOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Alexey M. Romshin, Vadim Zeeb, Evgenii Glushkov, Aleksandra Radenovic, Andrey G. Sinogeikin, Igor I. Vlasov
Summary: We present a novel approach to manipulate the temperature of individual living cells and their compartments using a polycrystalline diamond particle containing silicon-vacancy color centers. This particle acts as both a heater and a thermometer, allowing for precise control and measurement of local temperature changes. By heating the vicinity of HeLa cells and isolated mouse hippocampal neurons, we observe alterations in the intracellular distribution of free calcium ions, indicating the importance of temperature in cellular processes.
SCIENTIFIC REPORTS
(2023)
Article
Nanoscience & Nanotechnology
Mukeshchand Thakur, Nianduo Cai, Miao Zhang, Yunfei Teng, Andrey Chernev, Mukesh Tripathi, Yanfei Zhao, Michal Macha, Farida Elharouni, Martina Lihter, Liping Wen, Andras Kis, Aleksandra Radenovic
Summary: Nanopores in 2D membranes, especially in single-layer MoS2, have great potential in various applications. However, the stability of these nanopores remains a challenge. This study identifies chemical oxidation and delamination of monolayers as the main reasons for instability and proposes surface modification and reducing oxygen to improve nanopore stability. Understanding nanopore growth and stability can lead to controlled pore size and shape and enable durable nanopore devices with high signal-to-noise ratio.
NPJ 2D MATERIALS AND APPLICATIONS
(2023)
Article
Biology
Arielle Louise Planchette, Cedric Schmidt, Olivier Burri, Mercedes Gomez de Agueero, Aleksandra Radenovic, Alessio Mylonas, Jerome Extermann
Summary: Optical projection tomography (OPT) enables the observation and understanding of tissue-wide networks in three dimensions. A multi-modal workflow for characterizing the mouse small intestine is presented, demonstrating its applicability for imaging the intestinal immune compartment and mucosal structures.
COMMUNICATIONS BIOLOGY
(2023)
Article
Nanoscience & Nanotechnology
Jakub Sitek, Karolina Czerniak-Losiewicz, Arkadiusz P. Gertych, Malgorzata Giza, Pawel Dabrowski, Maciej Rogala, Konrad Wilczynski, Anna Kaleta, Slawomir Kret, Ben R. Conran, Xiaochen Wang, Clifford McAleese, Michal Macha, Aleksandra Radenovic, Mariusz Zdrojek, Iwona Pasternak, Wlodek Strupinski
Summary: Researchers have achieved the selective fabrication of van der Waals heterostructures (vdWHSs) using chemical vapor deposition by electron-beam irradiation. They have identified two growth modes, positive (P) mode on graphene and tungsten disulfide (WS2) substrates, and negative (N) mode on the graphene substrate. The growth mode can be controlled by limiting the air exposure and the time between irradiation and growth. The selective growth mechanism is explained by the competition of three effects: EB-induced defects, adsorption of carbon species, and electrostatic interaction. This study is a critical step towards industry-scale fabrication of 2D-materials-based devices.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Chemistry, Physical
Svetlana Melnik, Alexander Ryzhov, Alexei Kiselev, Aleksandra Radenovic, Tanja Weil, Keith J. Stevenson, Vasily G. Artemov
Summary: The electrodynamics properties of nanoconfined water have been significantly changed compared to bulk water, providing opportunities for safe electrochemical systems. We present a nanofluidic water-only battery that exploits the unusually high electrolytic properties of pure water under strict confinement. The device, composed of carbon-based nanomaterials, creates interconnected nanochannels filled with water between the separator and electrodes. The efficiency of the battery shows a maximum energy density at 3 nm, challenging the current metal-ion batteries. Our findings establish the electrodynamic fundamentals of nanoconfined water and pave the way for low-cost and inherently safe energy storage solutions needed in the renewable energy sector.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Nanoscience & Nanotechnology
Guilherme Migliato Marega, Zhenyu Wang, Yanfei Zhao, Hyun Goo Ji, Asmund Ottesen, Mukesh Tripathi, Aleksandra Radenovic, Andras Kis
Summary: Memory devices have gained attention again due to the increasing interest in using in-memory computing architectures. Flash memories based on monolayer MoS2 show promise as the ideal elements for this technology, but achieving large-area ultra-fast operation remains a challenge.
IEEE NANOTECHNOLOGY MAGAZINE
(2023)
Meeting Abstract
Biophysics
Jenny Sulzle, Wayne Yang, Yuta Shimoda, Eveline S. Mayner, Michal Macha, Nathan Ronceray, Aleksandra Radenovic, Suliana Manley
BIOPHYSICAL JOURNAL
(2023)
Meeting Abstract
Biophysics
Wayne Yang, Jenny Sulzle, Yuta Shimoda, Eveline Mayner, Michal Macha, Nathan Ronceray, Suliana Manley, Aleksandra Radenovic
BIOPHYSICAL JOURNAL
(2023)
Article
Engineering, Electrical & Electronic
Guilherme Migliato Marega, Hyun Goo Ji, Zhenyu Wang, Gabriele Pasquale, Mukesh Tripathi, Aleksandra Radenovic, Andras Kis
Summary: Data-driven algorithms are needed to process the massive amounts of data being produced, but the traditional von Neumann architecture limits processing capabilities, leading to the development of in-memory computing. This research presents an integrated 32x32 vector-matrix multiplier using floating-gate field-effect transistors with monolayer molybdenum disulfide as the channel material. Wafer-scale fabrication achieves high yield and low variability, and statistical analysis reveals the potential for multilevel and analogue storage. Reliable parallel signal processing is also demonstrated. In-memory computing chips for vector-matrix multiplication and signal processing can be fabricated using these transistors.
NATURE ELECTRONICS
(2023)
Article
Chemistry, Multidisciplinary
Michal Macha, Hyun Goo Ji, Mukesh Tripathi, Yanfei Zhao, Mukeshchand Thakur, Jing Zhang, Andras Kis, Aleksandra Radenovic
Summary: By adapting efficient monolayer growth methodologies from tube-furnace systems to vertical-showerhead geometries, and combining gas-phase precursor supply with unique tube-furnace approaches, we have achieved large-area, high-quality thin film synthesis.
NANOSCALE ADVANCES
(2022)