Review
Chemistry, Multidisciplinary
Zheng-Li Hu, Ming-Zhu Huo, Yi-Lun Ying, Yi-Tao Long
Summary: Proteins play a crucial role in disease occurrence and treatment, making protein sequencing a game changer for proteomics and clinical diagnostics. While the biological nanopore approach has shown success in single-molecule DNA sequencing, challenges remain in sequentially identifying each amino acid of single proteins.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Juan Zhou, Qing Lan, Wang Li, Li-Na Ji, Kang Wang, Xing-Hua Xia
Summary: Obtaining sequential and conformational information on proteins is important for understanding their functions. This study combines surface enhanced Raman scattering (SERS) with a nanopore to observe the unfolding and multistep sequential translocation of single molecule (SM) cytochrome c (cyt c). The high bias voltage unfolds the SM protein, slowing down the translocation and allowing specific SERS traces of different SM cyt c segments to be recorded. This research provides insight into protein segments and accelerates the development of nanopore-based SM protein sequencing.
Article
Chemistry, Analytical
Hong Sun, Chuan Yao, Kaibo You, Can Chen, Shuoshuo Liu, Zhihong Xu
Summary: In this study, a dynamic monitoring approach based on nanopore single-molecule biosensor was developed to detect the folding and unfolding transitions of proteins. By gradually increasing the concentration of denaturant guanidine hydrochloride (GdmCl), sensitive responses were observed with lysozyme unfolding. The existence of a stable intermediate was experimentally confirmed, providing insights into the conformation of the intermediate and the manner of denaturant towards lysozyme.
ANALYTICA CHIMICA ACTA
(2023)
Article
Biophysics
David Rodriguez-Larrea
Summary: The study demonstrates the use of simple neural networks to identify protein mutants, with poor generalization ability. By utilizing a thermal annealing protocol and examining multiple mutants in repeated experiments, the generalizability of the neural network can be improved.
BIOSENSORS & BIOELECTRONICS
(2021)
Review
Chemistry, Multidisciplinary
Yanfang Wu, J. Justin Gooding
Summary: This review provides an overview of the concepts, fabrication, and applications of nanopore sensors, with a focus on their potential and recent developments in quantitative analysis.
CHEMICAL SOCIETY REVIEWS
(2022)
Article
Chemistry, Multidisciplinary
Shuanghong Yan, Jinyue Zhang, Yu Wang, Weiming Guo, Shanyu Zhang, Yao Liu, Jiao Cao, Yuqin Wang, Liying Wang, Fubo Ma, Panke Zhang, Hong-Yuan Chen, Shuo Huang
Summary: Proteins exhibit diverse functions due to their variable amino acid sequences, but current technology for direct protein sequence analysis remains inadequate. The development of nanopore sequencing has sparked efforts to sequence peptides in a similar manner, successfully achieving direct observation of peptide's ratcheting motion and showing potential for peptide fingerprinting.
Article
Multidisciplinary Sciences
Zhongwen Chen, Yuhong Cao, Chun-Wei Lin, Steven Alvarez, Dongmyung Oh, Peidong Yang, Jay T. Groves
Summary: This study presents a practical method for intracellular multicolor single-molecule tracking using nanopore-electroporation (NanoEP) technique, which can be easily applied to commercial microscopes. By utilizing this method, successful three-color single-molecule tracking of EGFR signaling pathways in living cells was demonstrated, providing detailed spatial localization and dynamics information of Grb2 and SOS.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Multidisciplinary
Jinyue Zhang, Yu Wang, Yuqin Wang, Panke Zhang, Hong-Yuan Chen, Shuo Huang
Summary: DNA lesions induced by alkylating agents can be directly distinguished by observing the enzymatic stalling kinetics, which is not interfered with by the sequence context.
Article
Chemistry, Multidisciplinary
Arthur Rand, Philip Zimny, Roland Nagel, Chaitra Telang, Justin Mollison, Aaron Bruns, Emily Leff, Walter W. Reisner, William B. Dunbar
Summary: In this study, an electronic mapping of a bacterial genome using solid-state nanopore technology was presented. The method involves a dual-nano-pore architecture and active control logic to produce single-molecule data and estimate distances between physical tags on double-stranded DNA. Custom analysis methods were developed to generate consensus alignments from multiple scans, and this approach was applied to map the E. coli chromosome. The results showed a significant increase in alignment length with the recapture method, and the intertag resolution was determined to be around 150-166 bp.
Article
Chemistry, Analytical
Ting Li, Xinying Li, Xiaoxue Li, Li Yang, Hailong Wang
Summary: Developing a new method for bleomycin detection using dumbbell DNA as probe on the nanopore sensor platform is described in this study, which shows a quantitative relationship between event intervals (tau(on)) and the concentration of bleomycin with high selectivity and ultra-low detection limit.
MICROCHEMICAL JOURNAL
(2021)
Article
Chemistry, Analytical
Hye-Jin Hwang, Jin-Sik Kim, Jeonghyun Lee, Jun Sik Min, Ki-Baek Jeong, Eunha Kim, Mi-Kyung Lee, Seung-Wook Chi
Summary: Nanopore sensors are a promising platform for single-molecule sensing, such as sequencing, disease diagnostics, and drug screening. In this study, the interaction between Bcl-xL and Bak-BH3 was characterized using chemically modified OmpG nanopores, and specific inhibition of Bcl-xL was achieved using a small-molecule antagonist. The results demonstrate that chemically modified OmpG nanopores can serve as a valuable sensor platform for ultrasensitive, rapid, and single-molecule-based drug screening against protein-protein interactions.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Alexandra J. Schmeltzer, Joel M. Harris, Henry S. White
Summary: A quantitative description of ionophore-mediated ion transport is important in understanding ionophore activity. We directly measured the electrical current resulting from K+ transport mediated by individual valinomycin (val) ionophores. Our studies show that approximately 30 val are present in the membrane on average with a val entering or leaving the bilayer approximately every 50 s.
Article
Chemistry, Multidisciplinary
Mirko Palla, Sukanya Punthambaker, Benjamin Stranges, Frederic Vigneault, Jeff Nivala, Daniel Wiegand, Aruna Ayer, Timothy Craig, Dmitriy Gremyachinskiy, Helen Franklin, Shaw Sun, James Pollard, Andrew Trans, Cleoma Arnold, Charles Schwab, Colin Mcgaw, Preethi Sarvabhowman, Dhruti Dalal, Eileen Thai, Evan Amato, Ilya Lederman, Meng Taing, Sara Kelley, Adam Qwan, Carl W. Fuller, Stefan Roever, George M. Church
Summary: The use of single-molecule DNA sequencing platform allows for rapid screening of polymerase variants, enabling the identification of enzymes with different features. This approach is valuable for applications requiring polymerases with altered physical properties.
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
Chemistry, Multidisciplinary
Wei Liu, Zhong-Lin Yang, Chao-Nan Yang, Yi-Lun Ying, Yi-Tao Long
Summary: The study investigated the kinetics of single-molecule reactions under nanoconfinement using an aerolysin nanopore reactor. A four-state kinetics model was proposed based on the identification of bond-forming and non-bond-forming events. The results showed that the kinetics of single-molecule reactions inside a nanopore depends on the frequency of reactant capture and the fraction of effective collision inside the confined space.
Article
Chemistry, Physical
Nicolas Arroyo, Sebastien Balme, Fabien Picaud
Summary: The study investigated the conformation of PEG inside hydrophobic and hydrophilic nanopores through molecular dynamic simulation, showing that the nanopore inner surface affects the organization of PEG and the speed of salt constituents. The pair interaction between PEG and its environment demonstrates a greater affinity for K+ cations compared to Li+ cations.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Analytical
Lucile Reynaud, Aurelie Bouchet-Spinelli, Jean-Marc Janot, Arnaud Buhot, Sebastien Balme, Camille Raillon
Summary: Solid-state nanopores are used for discriminating closely related proteins alpha-thrombin and gamma-thrombin, with aptamer functionalization enhancing discrimination. Postprocessing signals with machine learning and training algorithms, an accuracy of 98.8% is achieved using seven features and ensemble methods.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Applied
Graycyelle R. S. Cavalcanti, Francisco Rodrigues, Guanzheng Zhuang, Sebastien Balme, Jean-Marc Janot, Maria G. Fonseca, Maguy Jaber
Summary: Hybrid pigments based on carminic acid stabilized by clay minerals were prepared and characterized using various techniques. The pigments showed different stability levels, with the hydrogels covered in polyorganosilane exhibiting the highest light stability.
Article
Chemistry, Multidisciplinary
Nathan Meyer, Nicolas Arroyo, Jean-Marc Janot, Mathilde Lepoitevin, Anna Stevenson, Imad Abrao Nemeir, Veronique Perrier, Daisy Bougard, Maxime Belondrade, Didier Cot, Jeremy Bentin, Fabien Picaud, Joan Torrent, Sebastien Balme
Summary: This study investigates the impact of nanoscale geometry and molecular crowding on Aβ fibril sensing using nanopore technology. It was found that a conical nanopore functionalized with PEG 5 kDa can discriminate fibril size, while a bullet-like-shaped nanopore enhances current amplitude and dwell time. However, a nanopore crowded with PEG 20 kDa increases relative current blockade without improving fibril discrimination compared to the bullet-shaped nanopore.
Review
Chemistry, Physical
Nathan Meyer, Imad Abrao-Nemeir, Jean-Marc Janot, Joan Torrent, Mathilde Lepoitevin, Sebastien Balme
Summary: In the past two decades, solid state and polymer nanopores have emerged as attractive methods for protein sensing, offering high specificity and sensitivity. This review focuses on the technique of protein detection using resistive pulse and ionic diodes, discussing significant achievements in detecting peptides and proteins, as well as strategies for improving nanopore resolution and accuracy. Challenges such as protein adsorption and nanopore lifetime are also highlighted.
ADVANCES IN COLLOID AND INTERFACE SCIENCE
(2021)
Article
Engineering, Chemical
Imad Abrao-Nemeir, Oumaima Zaki, Nathan Meyer, Mathilde Lepoitevin, Joan Torrent, Jean-Marc Janot, Sebastien Balme
Summary: In this study, two strategies based on single nanopore sensing and multipore membrane were combined to separate, detect, and identify antibodies. The ability to detect antibodies specifically in a single nanopore was demonstrated, and a multipore membrane was also designed to extract antibodies effectively.
JOURNAL OF MEMBRANE SCIENCE
(2022)
Article
Environmental Sciences
Nathan Meyer, Nicolas Arroyo, Matteo Baldelli, Nicolas Coquart, Jean Marc Janot, Veronique Perrier, Mauro Chinappi, Fabien Picaud, Joan Torrent, Sebastien Balme
Summary: This study analyzed the interaction between pyrimethanil and A beta (1-42) using conical track-etched nanopore and found that pyrimethanil promotes the aggregation of A beta (1-42). The study also revealed the mechanism of pyrimethanil-induced aggregation of A beta (1-42) involving two steps including reorganization and elongation phase prior to aggregation.
Article
Chemistry, Multidisciplinary
Nathan Meyer, Jean-Marc Janot, Joan Torrent, Sebastien Balme
Summary: In this study, a proof of concept real-time fast amyloid seeding and translocation (RT-FAST) method based on a nanopipette was presented. It combines a reaction vessel and a nanopore sensor in one system to detect α-synuclein assemblies. The method allows rapid and accurate detection of α-synuclein seeds in a sample within 90 minutes, and it has the potential for quantitative analysis of seed concentration.
ACS CENTRAL SCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Imad Abrao-Nemeir, Jeremy Bentin, Nathan Meyer, Jean-Marc Janot, Joan Torrent, Fabien Picaud, Sebastien Balme
Summary: Solid-state nanopores are a promising technology for high-throughput, label-free analysis of protein aggregation. In this study, we coated the surface of a silicon nitride nanopore with levodopamine to reduce nonspecific adsorption, and investigated its application in characterizing the aggregation of amyloid-beta and alpha-synuclein.
CHEMISTRY-AN ASIAN JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Pelagie Kamgang-Syapnjeu, Dayirou Njoya, Elie Kamseu, Sebastien Balme, Mikhael Bechelany, Laurence Soussan
Summary: This study investigates the characteristics and performance of bio-based ceramic membranes made from kaolinite clays, coconut husks, and eggshells for the removal of E. coli bacteria in drinking water. The membranes were characterized using TGA, DSC, mercury porosimetry, and SEM. Water flux density, bacterial removal, and biofouling were evaluated. The results show that the best membrane, S3, achieved 100% bacterial removal with a water flux density of 2123 +/- 72 L/h/m(2) at an initial pressure of 0.2 bar. The production protocol for this membrane is simple, fast, and does not require chemical additives.
Editorial Material
Chemistry, Multidisciplinary
Sebastien Balme
ACS CENTRAL SCIENCE
(2023)
