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
Biochemistry & Molecular Biology
Mashari Alangari, Busra Demir, Caglanaz Akin Gultakti, Ersin Emre Oren, Joshua Hihath
Summary: DNA has unique electronic properties that are sensitive to its sequence and structure, making it an attractive material for electronic DNA biosensors. This study investigates the origin of multiple conductance peaks in single-molecule break-junction measurements on DNA and demonstrates that these peaks come from different DNA conformations, such as double-stranded B-form DNA and G-quadruplex structures. By using various techniques and controls, the study shows that specific conductance values correspond to specific DNA conformations and that the occurrence of these conductance peaks can be controlled by the local environment.
Article
Chemistry, Multidisciplinary
Samuel Naudi-Fabra, Maud Tengo, Malene Ringkjobing Jensen, Martin Blackledge, Sigrid Milles
Summary: Studying the conformational landscape of intrinsically disordered and partially folded proteins is challenging and requires an integrated approach using multiple techniques to accurately describe the conformational ensembles of these proteins. This integrated approach has been successfully tested and validated, providing new insights into the conformational landscape of viral proteins and demonstrating its potential for integrative dynamic structural biology.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biochemistry & Molecular Biology
Arpan Dey, Vicky Vishvakarma, Anirban Das, Mamata Kallianpur, Simli Dey, Roshni Joseph, Sudipta Maiti
Summary: The text describes a method for measuring the degree of surface exposure of protein molecules through photobleaching and fluorescence quenching techniques. By analyzing the increase in step length, the accessibility of fluorophores to solvents is determined, revealing different species with varying levels of exposure. This approach provides a simple way to probe the conformational states of membrane proteins at a single molecule level.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Review
Chemistry, Multidisciplinary
Ruiqin Sun, Jieyao Lv, Xinyi Xue, Shiyong Yu, Zhibing Tan
Summary: Driven by the digitization and informatization of contemporary society, electrical sensors are developing toward minimal structure, intelligent function, and high detection resolution. Single-molecule electrical measurement techniques have been proven to be capable of label-free molecular recognition and detection, which opens a new strategy for the design of efficient single-molecule detection sensors. This review outlines the main advances and potentials of single-molecule electronics for qualitative identification and recognition assays at the single-molecule level, with a focus on the detection of ions, small molecules, oligomers, genetic materials, and proteins. It also summarizes the remaining challenges in the current development of single-molecule electrical sensing and presents some potential perspectives for this field.
CHEMISTRY-AN ASIAN JOURNAL
(2023)
Article
Biochemical Research Methods
Artur Speiser, Lucas-Raphael Mueller, Philipp Hoess, Ulf Matti, Christopher J. Obara, Wesley R. Legant, Anna Kreshuk, Jakob H. Macke, Jonas Ries, Srinivas C. Turaga
Summary: DECODE is a computational tool that uses deep learning to localize single emitters in high-density two-dimensional and three-dimensional single-molecule localization microscopy data. It outperforms available methods and enables fast live-cell SMLM of dynamic processes.
Article
Optics
Jessica A. Arnold, Aimable Kalume, Hairou Yu, Christopher L. Wirth, Gorden Videen, Yong-Le Pan
Summary: This study demonstrates a method for recording 2D forward-scattering patterns of optically trapped single airborne particles at different angles. The measurements include particles with various morphologies and are compared with calculated diffraction patterns. The study has the potential to assist in characterizing airborne aerosol particles based on morphological information.
JOURNAL OF QUANTITATIVE SPECTROSCOPY & RADIATIVE TRANSFER
(2022)
Review
Chemistry, Multidisciplinary
Yuki Komoto, Jiho Ryu, Masateru Taniguchi
Summary: Single-molecule measurements of single-molecule conductance between metal nanogap electrodes have been actively investigated for various applications. The advantage of rapid data acquisition through repeated breaking and forming of junctions outweighs the disadvantage of fluctuating and unreliable conductance. Machine learning-based analysis has greatly improved the analysis of single-molecule measurements, enabling detection and identification at the single-molecule level.
CHEMICAL COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Magdalena C. Schneider, Roger Telschow, Gwenael Mercier, Montserrat Lopez-Martinez, Otmar Scherzer, Gerhard J. Schuetz
Summary: Single molecule localization microscopy (SMLM) has the potential to resolve subcellular structures below the diffraction limit, with high localization precision. Sample fixation is necessary to prevent molecular motion during recording, but can affect the sample's ultrastructure. Performing SMLM at low temperatures can improve localization precision and enable reliable assignment of dye molecules.
Article
Multidisciplinary Sciences
Mark A. Hilton, Harris W. Manning, Ireneusz Gorniak, Sonia K. Brady, Madeline M. Johnson, Jochen Zimmer, Matthew J. Lang
Summary: Cellulose biosynthesis in bacterial colonies depends on the membrane-integrated bacterial cellulose synthase AB complex. The synthesis process is influenced by various substances and the complex has a strong gripping ability. Stretching experiments revealed the formation of cellulose microstructure during synthesis and the impact of cellohexaose on enzyme activity and polymer mechanical properties.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Chemistry, Medicinal
Pathum Chandika, Pipuni Tennakoon, Tae-Hee Kim, Se-Chang Kim, Jae-Young Je, Jae-Il Kim, Bonggi Lee, BoMi Ryu, Hyun Wook Kang, Hyun-Woo Kim, Young-Mog Kim, Chang Su Kim, Il-Whan Choi, Won Sun Park, Myunggi Yi, Won-Kyo Jung
Summary: Coagulation is a defense mechanism that prevents bleeding, but excessive clot formation can lead to serious diseases. The use of anticoagulants like heparin is limited, so there is interest in studying natural anticoagulants from marine sources.
Article
Multidisciplinary Sciences
Yi Wang, Zhuodong Tang, Hong-Yuan Chen, Wei Wang, Nongjian Tao, Hui Wang
Summary: A nanoparticle-based technique has been developed to probe the energetic contributions of single-molecule binding events, introducing a single-molecule calorimeter that uncovers the complexity of molecular interactions and provides a comprehensive thermodynamic profile.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Junrong Li, Alain Wuethrich, Abu A. I. Sina, Han-Hao Cheng, Yuling Wang, Andreas Behren, Paul N. Mainwaring, Matt Trau
Summary: The study develops a digital nanopillar SERS platform for real-time single cytokine counting and dynamic tracking of immune toxicities in cancer patients receiving immune checkpoint inhibitor treatment. By predicting cytokine concentrations, the platform demonstrates capability to identify patients at higher risk for developing severe immune toxicities.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Yevgeni Nogin, Tahir Detinis Zur, Sapir Margalit, Ilana Barzilai, Onit Alalouf, Yuval Ebenstein, Yoav Shechtman
Summary: A new computational method called DeepOM, which utilizes deep learning, is presented for efficient retrieval of genomic information from a single microscopic image of intact DNA molecules. The method employs a convolutional neural network trained on simulated images of labeled DNA molecules to improve the alignment success rate of DNA images to genomic references.
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)
