Article
Nanoscience & Nanotechnology
Pablo Martin-Baniandres, Wei-Hsuan Lan, Stephanie Board, Mercedes Romero-Ruiz, Sergi Garcia-Manyes, Yujia Qing, Hagan Bayley
Summary: Electro-osmosis in an anion-selective alpha-hemolysin nanopore is utilized for capturing, unfolding, and transporting polypeptides with more than 1,200 residues. By monitoring the ionic current at a single-molecule resolution, this method enables the mapping of post-translational modifications in polypeptide chains. The application of nanopore technology holds potential for identifying full-length proteoforms.
NATURE NANOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jonathan M. Craig, Maria Mills, Hwanhee C. Kim, Jesse R. Huang, Sarah J. Abell, Jonathan W. Mount, Jens H. Gundlach, Keir C. Neuman, Andrew H. Laszlo
Summary: Nanopore Tweezers are used to observe the translocation and unwinding processes of Escherichia coli RecQ helicases on DNA at ultra-high spatiotemporal resolution, revealing the mechanochemical coupling and asymmetric energy landscape that drive helicase motion.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biology
Martin Rieu, Jessica Valle-Orero, Bertrand Ducos, Jean-Francois Allemand, Vincent Croquette
Summary: The researchers introduced a single-molecule manipulation method called kinetic locking based on magnetic tweezers, which enables direct detection of biomolecular binding without the use of fluorescent probes. By measuring the dynamic interactions of E. coli RecQ helicase with its DNA substrate, they demonstrated the potential of this method for studying DNA-DNA and DNA-protein interactions while avoiding the need for labeling. This fluorescence-free micro-manipulation technique allows functional characterization of DNA/RNA processing proteins, without interference from labels.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemical Research Methods
Xiaoyu Guan, Zhongnian Li, Yueying Zhou, Wei Shao, Daoqiang Zhang
Summary: Nanopore sequencing, as a high-throughput sequencing technology for DNA, RNA, and proteins, faces the challenge of high labeling costs for the enormous generated data. This study introduces active learning to select samples that need to be labeled, reducing the labeling costs significantly. Experimental results demonstrate that active learning can greatly reduce the labeling amount while achieving the best baseline performance for nanopore data analysis.
Article
Chemistry, Analytical
Y. M. Nuwan D. Y. Bandara, Jugal Saharia, Buddini Karawdeniya, Patrick Kluth, Min Jun Kim
Summary: This study introduces an analysis platform with four baseline fitting methods adaptable to various nanopore traces for extracting events effectively. The performance was tested with stable and fluctuating current profiles, showing that event count increased significantly with increasing fitting robustness for fluctuating profiles. Event turning points were clustered using the dbscan method, with subsequent segmentation and iterative refinement to deduce final event levels.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Xiaoyi Wang, Tina-Marie Thomas, Ren Ren, Yu Zhou, Peng Zhang, Jingjing Li, Shenglin Cai, Kai Liu, Aleksandar P. Ivanov, Andreas Herrmann, Joshua B. Edel
Summary: The analysis of proteins and their interactions at the single-molecule level has important implications for understanding biological processes and diseases, especially for proteins found in low copy numbers in biological samples. Nanopore sensing is a label-free detection technique that is well-suited for applications such as studying protein-protein interactions, biomarker screening, drug discovery, and protein sequencing. However, current limitations in protein nanopore sensing pose challenges in controlling protein translocation and relating protein structures and functions to nanopore readouts.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Review
Chemistry, Analytical
Jiajun Wang, Yi-Lun Ying, Cheng-Bing Zhong, Li-Min Zhang, Feng Yan, Yi-Tao Long
Summary: Nanopore electrochemistry, a promising tool for single molecule sensing, requires appropriate nanopore sensing interface, advanced instrumentation, and multi-disciplinary collaboration for high resolution and throughput. Recent improvements in the nanopore sensing interface, nanopore arrays, and intelligent data analysis methods have enhanced the potential for widespread application in single-molecule research.
Article
Multidisciplinary Sciences
Fushi Wang, Chunxiao Zhao, Pinlong Zhao, Fanfan Chen, Dan Qiao, Jiandong Feng
Summary: This study reports the direct identification of single amino acids in MoS2 nanopores, as well as the discrimination of amino acid isomers and phosphorylation. This is a significant breakthrough for protein sequencing.
NATURE COMMUNICATIONS
(2023)
Article
Physics, Multidisciplinary
Antonio Suma, Vincenzo Carnevale, Cristian Micheletti
Summary: Using theory and simulations, the authors studied DNA unzipping via nanopore translocation and found three dynamical regimes depending on the applied force. They showed that the normal regime can be modeled as a one-dimensional stochastic process and used the theory of stochastic processes to recover the free-energy landscape. This approach can be applied to other single-molecule systems with periodic potentials to obtain detailed free-energy landscapes from out-of-equilibrium trajectories.
PHYSICAL REVIEW LETTERS
(2023)
Review
Biochemical Research Methods
Mahmudur Rahman, Mohammad Julker Neyen Sampad, Aaron Hawkins, Holger Schmidt
Summary: The advent of single-molecule probing techniques has led to the development of a new class of labs-on-chip based on powerful biosensors, with nanopores being one of the most recent and promising paradigms for single molecule sensing. Nanopores offer highly sensitive, label-free, amplification-free, and high-throughput real-time detection of biomolecules, with potential for integration with other technologies for more complex tasks. Integrated nanopore platforms have shown breakthrough results and are expected to see further advancements as they remain a focus of innovative research and commercial instrument development.
Article
Chemistry, Multidisciplinary
Y. M. Nuwan D. Y. Bandara, Nasim Farajpour, Kevin J. Freedman
Summary: This study presents a thorough investigation of protein sensing under low electrolyte conditions. The unfolding of proteins was found to be correlated with their isoelectric point and sensitive to the applied voltage and pH. The different forces acting on the protein movement also play a critical role.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Physical
Wei Si, Runyi Yuan, Gensheng Wu, Yajing Kan, Jingjie Sha, Yunfei Chen, Yin Zhang, Yang Shen
Summary: A heterostructural platform was theoretically designed to control the capture and linear movement of proteins in nanopore protein sequencing by utilizing the different binding affinities of proteins to two isomorphic materials. By strategically driving the peptide along a designed path to the target nanopore using real-time switching of the applied electric field, different ionic current blockades were observed when the peptide compositions were changed, indicating the potential for differentiating different peptides using this platform.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Youbin Mo, Mounir Fizari, Kristina Koharchik, Douglas E. Smith
Summary: This study demonstrates a more robust method for calibrating biophysical force and displacement measurements using DNA molecules, especially in the high force range. It shows how small variations in microsphere sizes can affect DNA length measurements and provides methods for correcting these errors. Additionally, it showcases how these measurements can be used to check the assumed linearities of system responses and assess trap compliance and positioning by combining microsphere imaging with DNA stretching.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Yaohong Zhou, Haidong Wang
Summary: Recent years have seen the emergence of nanopore sensing technology as a reliable option for the characterization and identification of single biomolecules. By modifying the structure of nanopores, the translocation speed of carbon chains can be regulated, which in turn impacts the detection of ionic current signals and improves the accuracy of DNA sequencing.
Review
Chemistry, Multidisciplinary
Jasper P. Fried, Jacob L. Swett, Binoy Paulose Nadappuram, Jan A. Mol, Joshua B. Edel, Aleksandar P. Ivanov, James R. Yates
Summary: Solid-state nanopore fabrication techniques have advanced significantly, allowing for the rapid and simple creation of nanopores with diameters down to a few nanometres in electrolyte environments, enabling applications in DNA sequencing, protein analysis, and more.
CHEMICAL SOCIETY REVIEWS
(2021)
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)
Article
Chemistry, Physical
Michal Macha, Mukeshchand Thakur, Aleksandra Radenovic, Sanjin Marion
Summary: Applying hydrostatic pressure to suspended 2D material thin membranes allows probing the effects of lateral strain on ion and fluid transport through nanopores. The study demonstrates that pressure and potential differences can induce permanent and temporary delamination of 2D materials, resulting in a strong mechanosensitive modulation of ion transport.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)