Article
Chemistry, Physical
Yunjiao Wang, Min Cheng, Liang Wang, Daming Zhou, Shixuan He, Liyuan Liang, Feng Zhang, Chang Liu, Deqiang Wang, Jiahu Yuan
Summary: The free-standing nanocrystalline graphite (NCG) membranes were grown directly on SiNx substrates using catalyst-free chemical vapor deposition. A new type of NCG nanopore was created via controlled dielectric breakdown in KCl electrolyte, and its electrical properties, particularly the ionic conductance, were examined under different physical parameters. The impressive transport properties of NCG nanopores were utilized for DNA sensing in this study.
Review
Multidisciplinary Sciences
Simon Finn Mayer, Chan Cao, Matteo Dal Peraro
Summary: Evolution has discovered numerous ways to transport material across cell membranes. Protein assemblies are essential for the formation of channels and pores that allow molecules to enter and exit cells, contributing to the processes that sustain living organisms. These biological pores are now being utilized as molecular sensors to study biomolecules and have potential applications in life sciences and medicine.
Article
Chemistry, Multidisciplinary
Jing Yang, Juan Wang, Xuan Liu, Yiming Chen, Yuan Liang, Qi Wang, Shuoxing Jiang, Cheng Zhang
Summary: The solid-state nanopore (SS nanopore) is a sensitive tool for detecting single molecules. By using a DNA polyhedral carrier coating strategy to assist protein translocation through SS nanopores, the current signal-to-noise ratios are significantly improved, which aids the detection of proteins. This coating-assisted method offers a wide range of applications for SS nanopore detection and promotes the development of single-molecule detection.
Article
Chemistry, Multidisciplinary
Yuqing Li, Hang Gao, Zengyao Qi, Zhicheng Huang, Lingzi Ma, Juewen Liu
Summary: Unmodified DNA can achieve high conjugation efficiency under freezing conditions, and diblock DNA design containing A(5) block allows attachment of various functional DNA sequences, suitable for ultrasensitive DNA hybridization and Hg2+ detection.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Chaoming Gu, Zhoubin Yu, Xiaojie Li, Xin Zhu, Chuanhong Jin, Zhen Cao, Shurong Dong, Jikui Luo, Zhi Ye, Yang Liu
Summary: Solid-state nanopores are crucial in sensing single-biomolecules, but their ultra-short translocation time limits the acquisition of detailed information and further applications. Combining MoS2 and graphene, we fabricated sub-10 nm ultra-thin MoS2-graphene heterostructure nanopores that slowed down the passage of biomolecules. By testing dsDNA and BSA at the single-molecule level, we observed special signals indicating the shape change of BSA during the slow translocation process. These findings suggest the potential of MoS2-graphene heterostructure nanopores in slowing down translocation and acquiring more detailed information about biomolecules.
Article
Chemistry, Multidisciplinary
Christopher A. Thomas, Jonathan M. Craig, Shuichi Hoshika, Henry Brinkerhoff, Jesse R. Huang, Sarah J. Abell, Hwanhee C. Kim, Michaela C. Franzi, Jessica D. Carrasco, Hyo-Joong Kim, Drew C. Smith, Jens H. Gundlach, Steven A. Benner, Andrew H. Laszlo
Summary: Chemists have synthesized new types of DNA that can add nucleotides to the traditional four nucleotides found in standard DNA. These expanded genetic systems are used in molecular diagnostics and the study of life's early evolution. Nanopore sequencing is a promising method for sequencing DNA with nonstandard nucleotides. In this study, the researchers assessed the signal range and enzyme compatibility of an 8-letter expanded DNA alphabet, demonstrating its potential for future sequencing applications.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biophysics
Pengkun Xia, Jiawei Zuo, Pravin Paudel, Shinhyuk Choi, Xiahui Chen, Md Ashiqur Rahman Laskar, Jing Bai, Weisi Song, JongOne Im, Chao Wang
Summary: Solid-state nanopores have various applications in single-molecule biosensing and sequencing, but high capacitive noise from conventional silicon substrates limits their performance. A new approach using insulating sapphire wafers for nanopore membranes is proposed, demonstrating scalable formation of small membranes with low noise sensing capabilities.
BIOSENSORS & BIOELECTRONICS
(2021)
Review
Biology
Ana Crnkovic, Marija Srnko, Gregor Anderluh
Summary: Nanopore-based sensing is a powerful technique that allows for the detection of diverse molecules, sequencing of nucleic acids, and analysis of enzymatic reactions. Protein-based nanopores selected from natural sources offer rapid, label-free detection and are easily produced and manipulated with standard techniques. The range of analytes can be expanded by using externally added adapter molecules.
Article
Chemistry, Analytical
Yu Dai, Yiwei Zhang, Qun Ma, Meihua Lin, Xiaojin Zhang, Fan Xia
Summary: Solid-state nanopores have advantages such as stability and easy modification, and they find applications in various fields. In addition to functional modification of the inner wall, researchers have also focused on the functional elements on the outer surface.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Masateru Taniguchi, Hiroyasu Takei, Kazuhiko Tomiyasu, Osamu Sakamoto, Norihiko Naono
Summary: This study reveals the sensing performance of artificially intelligent nanopores (AINs). By combining nanopores with machine learning methods, accurate identification of single nanoparticles within different diameter ranges is achieved, and the potential application of AINs in multiplex diagnostics is demonstrated.
JOURNAL OF PHYSICAL CHEMISTRY C
(2022)
Review
Chemistry, Analytical
Xiaojin Zhang, Meihua Lin, Yu Dai, Fan Xia
Summary: Nanoporesensing technology is a promising analysis method with various advantages such as simplicity, high sensitivity, fast output, and label-free detection. It has been widely used in protein analysis, gene sequencing, biomarker detection, and other fields. By utilizing the confined space of the nanopore, this technology enables real-time tracking of dynamic interactions and chemical reactions at the single-molecule level, providing insights into the mechanisms of these processes. This paper reviews the development of biological nanopores and solid-state nanopores/nanochannels in stochastic sensing of dynamic interactions and chemical reactions, aiming to stimulate researchers' interest and promote the advancement of this field.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Shuanghong Yan, Liying Wang, Xiaoyu Du, Shanyu Zhang, Sha Wang, Jiao Cao, Jinyue Zhang, Wendong Jia, Yuqin Wang, Panke Zhang, Hong-Yuan Chen, Shuo Huang
Summary: This study has developed an efficient and cost-effective protocol for preparing a variety of MspA mutants for nanopore insertion, sequencing, and other operations, reducing the costs and time associated with human operations.
Article
Chemistry, Multidisciplinary
Hsin-Yun Tsai, W. Russ Algar
Summary: Forster resonance energy transfer (FRET) is widely used for biological probes and sensors. Concentric FRET (cFRET) probes enable multiplexed sensing with a single vector. This study demonstrates that dendrimers labeled with a luminescent terbium complex (Tb) can be a viable alternative platform for cFRET probes. This dendrimer-based architecture shows the importance of cFRET for the development of a new generation of probes for biological sensing.
Article
Multidisciplinary Sciences
Metin Kayci, Jilin Fan, Onur Bakirman, Andreas Herrmann
Summary: In the past decade, there has been a great effort to develop new biosensor platforms for the detection of various analytes. Among these platforms, magneto-DNA assay using diamond nitrogen-vacancy quantum centers as transducers for magnetic nanotags has shown promise for high sensitive and specific detection of targets. The hydrogel-based, multiplexed magneto-DNA assay platform offers near-background-free sensing with diamond-based imaging, making it suitable for medical diagnostics, life science, and pharmaceutical drug research.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Multidisciplinary
Shulin Chen, Tzu-Li Liu, Yan Dong, Jinghua Li
Summary: A key challenge in continuous biosensing is the poor reusability of biorecognition interfaces. This study introduces a regeneratable biosensing scheme using a re-engineered pH sensitive anti-cocaine aptamer. The aptamer can regain affinity with target analytes through proton-promoted duplex-to-triplex transition in DNA configuration. The use of a Pd/PdHx electrode enables pH regulation of the local chemical environment. A flower-shaped, stretchable, and inductively coupled electronic system was also demonstrated for wireless biointegrated devices with sensing and energy harvesting capabilities. These advances have the potential to develop electronic sensing platforms with on-chip regeneration capability for continuous and real-time monitoring of chemical and biological markers.
Article
Multidisciplinary Sciences
Mohammed F. Alawami, Filip Boskovic, Jinbo Zhu, Kaikai Chen, Sarah E. Sandler, Ulrich F. Keyser
Summary: In this study, 102 quartz glass nanopores with a diameter of 11-18 nm were fabricated using laser-assisted capillary pulling. The use cycles of the nanopores were improved by vacuum storage and minimal washing steps. The single-molecule biosensing capability of the nanopores over repeated use cycles was demonstrated through quantitative analysis of a DNA carrier.
Article
Chemistry, Multidisciplinary
Marcus Fletcher, Jinbo Zhu, Roger Rubio-Sanchez, Sarah E. Sandler, Kareem Al Nahas, Lorenzo Di Michele, Ulrich F. Keyser, Ran Tivony
Summary: Accurate measurement of ion permeability through cellular membranes has been a challenge due to the lack of suitable ion-selective probes. Researchers have used giant unilamellar vesicles (GUVs) as membrane models and a DNA-based sensor to visualize and measure ion transport. The study found that the permeability coefficients of potassium ions were at least one order of magnitude larger than previously reported values, and the presence of octanol increased the permeation rates across lipid bilayers.
Review
Chemistry, Multidisciplinary
Andrea Doricchi, Casey M. Platnich, Andreas Gimpel, Friederikee Horn, Max Earle, German Lanzavecchia, Aitziber L. Cortajarena, Luis M. Liz-Marzan, Na Liu, Reinhard Heckel, Robert N. Grass, Roman Krahne, Ulrich F. Keyser, Denis Garoli
Summary: This article discusses the latest advances in DNA-based data storage, highlighting its advantages over traditional storage methods, while also addressing current challenges and future directions for development.
Article
Chemistry, Multidisciplinary
Kaikai Chen, Adnan Choudhary, Sarah E. Sandler, Christopher Maffeo, Caterina Ducati, Aleksei Aksimentiev, Ulrich F. Keyser
Summary: High-resolution analysis of biomolecules has greatly advanced biosensing, but there are limited methods available for high-resolution analysis of unlabeled single molecules in their native states. In this work, label-free electrical sensing of single molecules with nanometer resolution is demonstrated using a narrow solid-state nanopore. The super-resolution ability is attributed to the enhancement of the electric field at the tip of the nanopore induced by nanostructures. This work presents a general approach to improve the resolution of single-molecule nanopore sensing and has implications for label-free high-resolution DNA sequence mapping and digital information storage.
ADVANCED MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Yesheng Wang, Zhentong Zhu, Chunmiao Yu, Ruiping Wu, Jinbo Zhu, Bingling Li
Summary: This article proposes a solution for improving the performance of solid-state nanopore in sensitive and label-free single molecular analysis by designing a model nucleic acid circuit reaction to produce controllable Y-shaped three-way DNA oligomers. Experimental results show that the oligomers can significantly enhance signal resolution and stability, and can be used as tags for specific identification and multiple assays.
Article
Chemistry, Multidisciplinary
Jinbo Zhu, Ran Tivony, Filip Boskovic, Joana Pereira-Dias, Sarah E. Sandler, Stephen Baker, Ulrich F. Keyser
Summary: In this study, a nanopore sensor based on DNA dumbbell nanoswitches was established for multiplexed nucleic acid detection and bacterial identification. By assembling four DNA dumbbell nanoswitches on one carrier, simultaneous detection of four different sequences of nucleic acids was achieved. The high specificity of the dumbbell nanoswitch was verified by distinguishing single base variants in DNA and RNA targets using barcoded DNA carriers in multiplexed measurements. By combining multiple dumbbell nanoswitches with barcoded DNA carriers, different bacterial species could be identified even with high sequence similarity by detecting strain specific 16S ribosomal RNA (rRNA) fragments.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Raphael P. B. Jacquat, Georg Krainer, Quentin A. E. Peter, Ali Nawaz Babar, Oliver Vanderpoorten, Catherine K. Xu, Timothy J. Welsh, Clemens F. Kaminski, Ulrich F. Keyser, Jeremy J. Baumberg, Tuomas P. J. Knowles
Summary: This paper presents an approach called nanocavity diffusional sizing (NDS) that relies on nanocavity confinement to measure the size of nanoscale particles and single biomolecules in solution. It uses particle residence times within nanofluidic cavities to determine their hydrodynamic radii. Experimental results show that the residence times scale linearly with the sizes of nanoscale colloids, protein aggregates, and single DNA oligonucleotides. NDS offers a new optofluidic approach for rapid and quantitative sizing of nanoscale particles with potential applications in nanobiotechnology, biophysics, and clinical diagnostics.
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
Biochemistry & Molecular Biology
Sophie L. Williams, Corella S. Casas-Delucchi, Federica Raguseo, Dilek Guneri, Yunxuan Li, Masashi Minamino, Emma E. Fletcher, Joseph T. P. Yeeles, Ulrich F. Keyser, Zoe A. E. Waller, Marco Di Antonio, Gideon Coster
Summary: This study investigates the effects of physiological quadruplex secondary structures on genome stability by reconstituting eukaryotic DNA replication in vitro. G-quadruplexes (G4s) and intercalated Motifs (iMs) are found to form during replication and thereby induce replisome stalling, leading to helicase-polymerase uncoupling and nascent DNA breakage. A single physiological G4 or iM structure stalls the eukaryotic replisome by inhibiting leading strand synthesis. Helicase-polymerase uncoupling occurs following replication stalling at G4s. iMs can induce breakage on nascent DNA. Stalled forks at G4s or iMs can be rescued by the accessory helicase Pif1. In vitro reconstitution shows that a single physiological G4 or iM secondary structure stalls the eukaryotic replisome by inhibiting leading strand synthesis.
Article
Chemistry, Multidisciplinary
Yunxuan Li, Sarah E. Sandler, Ulrich F. Keyser, Jinbo Zhu
Summary: Nanopores are powerful single-molecule sensors for identifying and characterizing small polymers like DNA. In this study, a programmable DNA carrier platform was introduced to capture specific DNA nanostructures, and controlled translocation experiments through glass nanopores were conducted to understand the relationship between nanopore signals and DNA physical properties. The results show that the volume and flexibility of DNA nanostructures in the nanopore primarily determine the ionic current drop. Additionally, this understanding of DNA topology allowed discrimination between circular single-stranded DNA molecules and linear ones with the same number of nucleotides using the nanopore signal.
Article
Chemistry, Multidisciplinary
Sara Rocchetti, Alexander Ohmann, Rohit Chikkaraddy, Gyeongwon Kang, Ulrich F. Keyser, Jeremy J. Baumberg
Summary: Developing highly enhanced plasmonic nanocavities allows direct observation of light-matter interactions at the nanoscale. With DNA origami, precise nanopositioning of single-quantum emitters in ultranarrow plasmonic gaps enables detailed study of their modified light emission. By developing nanoparticle-on-mirror constructs with DNA nanostructures as reliable and customizable spacers for nanoparticle binding, it is revealed that the traditional understanding of Purcell-enhanced molecular dye emission is misleading, and the enhanced dipolar dye polarizability greatly amplifies optical forces acting on the facet Au atoms, causing their rapid destabilization. Different dyes exhibit emission spectra dominated by inelastic (Raman) scattering rather than fluorescence, challenging the conventional theories in the field of quantum optics using plasmonics.
Article
Chemistry, Multidisciplinary
Jeffrey Mc Hugh, Stanislaw Makarchuk, Daria Mozheiko, Ana Fernandez-Villegas, Gabriele S. Kaminski Schierle, Clemens F. Kaminski, Ulrich F. Keyser, David Holcman, Nathalie Rouach
Summary: Dendrites and dendritic spines play crucial roles in neuronal communication by conveying information through voltage signals. Using nanopipettes, researchers were able to access and record voltage dynamics in fine dendrites, revealing diverse patterns such as spontaneous transients, bursting events, and oscillations. These voltage patterns were found to be more dependent on synaptic activity than on action potentials, and long-time recordings showed complex dynamics that may contribute to dendritic computations.
Article
Multidisciplinary Sciences
Eva Kreysing, Jeffrey Mc Hugh, Sarah K. Foster, Kurt Andresen, Ryan D. Greenhalgh, Eva K. Pillai, Andrea Dimitracopoulos, Ulrich F. Keyser, Kristian Franze
