Article
Chemistry, Multidisciplinary
Aurimas Kopustas, Sarune Ivanovaite, Tomas Rakickas, Ernesta Pocevicitue, Juste Paksaite, Tautvydas Karvelis, Mindaugas Zaremba, Elena Manakova, Marijonas Tutkus
Summary: Over the past 20 years, single-molecule methods in combination with new nanotechnological platforms have become extremely important for biophysical studies, facilitating experimental design and faster data acquisition. Utilizing a nanotechnological platform called DNA Curtains, which involves a flow-stretch of immobilized DNA molecules, allowed for stable immobilization and orientation of DNA molecules using a protein template-directed assembly. This method improves immobilization stability and enables the study of protein-DNA interactions under more controllable conditions, demonstrating potential applications in nucleic acid-interacting protein binding assays.
Article
Chemistry, Analytical
Hyunbum Park, Doory Kim
Summary: In this study, a new single-molecule sensing approach was developed to examine the local hydrogen bonding characters with surrounding molecules. By observing the single-molecule fluorescence spectrum of a hydrogen-bonding sensor dye, the hydrogen-bonding characteristics can be differentiated at the single-molecule level.
SENSORS AND ACTUATORS B-CHEMICAL
(2022)
Article
Chemistry, Multidisciplinary
Zhenyu Zou, Jialun Liang, Qian Jia, Di Bai, Wei Xie, Wenqiang Wu, Chuang Tan, Jie Ma
Summary: “The flow-cell system, developed in this work, combines gas-pumped calibration and fluorescence imaging to enable simultaneous single-molecule force measurement and visualization. It offers high force stability and tuning accuracy, allowing for precise force application and measurement. The system also facilitates real-time tracking of protein motors and monitoring of biomolecular conformational changes under controlled forces. The findings from this work lay down a valuable foundation for the flow-cell to be utilized as a versatile, quantitative, and high-throughput tool for single-molecule manipulation and visualization.”
Review
Biochemistry & Molecular Biology
Shunsuke Takahashi, Masahiko Oshige, Shinji Katsura
Summary: DNA replication, repair, and recombination in cells regulate genetic information transfer. Single-molecule imaging provides new insights into the dynamic behaviors of individual biomolecules, helping analyze the interaction between DNA and proteins.
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.
Article
Multidisciplinary Sciences
Jibin Abraham Punnoose, Kevin J. Thomas, Arun Richard Chandrasekaran, Javier Vilcapoma, Andrew Hayden, Kacey Kilpatrick, Sweta Vangaveti, Alan Chen, Thomas Banco, Ken Halvorsen
Summary: Stacking interactions between adjacent bases in DNA and RNA are important for biological processes and biotechnology applications. In this study, the authors used a centrifuge force microscope to measure stacking energies between individual bases. They found that stacking energies are strongest between purines (G|A) and weakest between pyrimidines (C|T). Phosphorylated, methylated, and RNA nucleotides had no effect on stacking energies, but a fluorophore modification reduced stacking energy.
NATURE COMMUNICATIONS
(2023)
Review
Physics, Multidisciplinary
Jongjin Cha, Ja Yil Lee
Summary: The DNA curtain technique is a high-throughput system that visualizes protein-DNA interactions at the single-molecule level and is used for probing various DNA transactions.
JOURNAL OF THE KOREAN PHYSICAL SOCIETY
(2021)
Article
Chemistry, Physical
Cecilia Zaza, German Chiarelli, Ludovit P. Zweifel, Mauricio Pilo-Pais, Evangelos Sisamakis, Fabio Barachati, Fernando D. Stefani, Guillermo P. Acuna
Summary: Fluorescence Resonance Energy Transfer (FRET)-based approaches are unique tools for sensing the immediate surroundings and interactions of (bio)molecules. FRET imaging and Fluorescence Lifetime Imaging Microscopy (FLIM) enable the visualization of the spatial distribution of molecular interactions and functional states. However, conventional FLIM and FRET imaging provide average information over an ensemble of molecules within a diffraction-limited volume, which limits the spatial information, accuracy, and dynamic range of the observed signals. Here, an approach to obtain super-resolved FRET imaging based on single-molecule localization microscopy using an early prototype of a commercial time-resolved confocal microscope is demonstrated. DNA Points Accumulation for Imaging in Nanoscale Topography with fluorogenic probes provides a suitable combination of background reduction and binding kinetics compatible with the scanning speed of usual confocal microscopes. A single laser is used to excite the donor, a broad detection band is employed to retrieve both donor and acceptor emission, and FRET events are detected from lifetime information.
Article
Chemistry, Physical
Boogeon Choi, Gyouil Jeong, Hyun-Hang Shin, Zee Hwan Kim
Summary: The demand for visualizing the spatial distribution of chemical species based on vibrational spectra is rapidly increasing. Two vibrational nano-imaging techniques, scattering-type scanning near-field optical microscopy and tip-enhanced Raman scattering, face key challenges and recent breakthroughs. This Perspective highlights the current gap between general needs and achievable results.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Review
Biotechnology & Applied Microbiology
Yujin Kang, Soyeong An, Duyoung Min, Ja Yil Lee
Summary: Advances in single-molecule techniques, specifically single-molecule fluorescence imaging, have revolutionized our understanding of biological processes, particularly in DNA repair. These techniques enable real-time visualization of biomolecular interactions and have provided convincing evidence for the importance of DNA repair in maintaining genomic integrity. Additionally, live-cell imaging at the single-molecule level has contributed to our understanding of DNA repair processes inside cells.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Elliot J. Fuller, David S. Ashby, Celia Polop, Elena Salagre, Bhuvsmita Bhargava, Yueming Song, Enrique Vasco, Joshua D. Sugar, Paul Albertus, Tevfik Onur Mentes, Andrea Locatel, Pilar Segovia, Miguel Angel Gonzalez-Barrio, Arantzazu Mascaraque, Enrique G. Michel, A. Alec Talin
Summary: In this study, isolated LiCoO2 islands were subjected to electrochemical cycling and the spatial distribution of conductive and insulating phases was observed using conductive atomic force microscopy (c-AFM). The research findings show that smaller LCO islands have a higher conductive fraction and surface energy can dominate in smaller islands. Additionally, significant shifts in current flow were observed when force was applied to strain the islands, and the underlying mechanisms for this behavior were discussed. Comparison with photoemission electron microscopy images indicated that strain and morphology become more critical to electrochemical performance as particles approach nanometer dimensions.
Review
Biochemical Research Methods
Jonathan Jeffet, Sapir Margalit, Yael Michaeli, Yuval Ebenstein
Summary: The human genome contains multiple layers of information that go beyond the genetic sequence, leading to differences in phenotype even with identical genetics. Genetic and epigenetic patterns work together to maintain specific cell functions in health and disease. Single-molecule optical genome mapping allows for the study of genetic and epigenetic patterns on a single-molecule level, providing insights inaccessible by sequencing technologies.
BIOCHEMISTRY: ONE MOLECULE AT A TIME
(2021)
Article
Chemistry, Multidisciplinary
Michael Darcy, Kyle Crocker, Yuchen Wang, Jenny Le, Golbarg Mohammadiroozbahani, Mahmoud A. S. Abdelhamid, Timothy D. Craggs, Carlos E. Castro, Ralf Bundschuh, Michael G. Poirier
Summary: The ability to apply and measure high forces on the nanometer scale is crucial for the development of nanomedicine, molecular robotics, and understanding biological processes. Current force spectroscopy techniques have limitations in applying forces in constrained geometries. DNA-based molecular calipers have shown promise as an alternative, but their force application capabilities are currently limited. This study implemented DNA origami nanocalipers with tunable mechanical properties to demonstrate the ability to apply forces of at least 20 piconewtons with a nanometer-scale dynamic range.
Review
Chemistry, Analytical
Shengnan Fu, Tengfang Zhang, Huanling Jiang, Yan Xu, Jing Chen, Linghao Zhang, Xin Su
Summary: Single-molecule tools, with the application of DNA nanotechnology, not only improve sensitivity and specificity, but also provide molecular receptors and rulers, helping to address the challenges hindering the development of single-molecule sensing and imaging.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2021)
Article
Optics
Aleksandr Barulin, Inki Kim
Summary: Hyperlenses offer the potential for bioimaging beyond the diffraction limit. Researchers demonstrate the feasibility of sub-diffraction fluorescence correlation spectroscopy using a spherical gold/silicon multilayered hyperlens. The hyperlens can effectively distinguish nanoscale transient trapping sites in simulated 2D lipid diffusion in cell membranes.