Article
Biology
Dominique Bourgeois
Summary: Single Molecule Imaging Simulator (SMIS) is a simulation software that models the photophysical behavior of fluorophores in single-molecule localization experiments. It can simulate a widefield microscope and incorporate fluorophores with their spectral and photophysical properties. SMIS allows the evaluation of advanced fluorophore characteristics, imaging conditions, and environmental parameters, facilitating the design of real experiments and their interpretation.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Boris I. Godoy, Nicholas A. Vickers, Sean B. Andersson
Summary: Single Particle Tracking (SPT) is a powerful method for studying biomolecular dynamics in living cells, revealing trajectories of individual particles and motion model parameters. However, existing algorithms assume constant parameters, while this study proposes an estimation algorithm to determine time-varying parameters in systems that switch between different linear models of motion.
Review
Biochemistry & Molecular Biology
Nitesh Kumar Podh, Sheetal Paliwal, Partha Dey, Ayan Das, Shruti Morjaria, Gunjan Mehta
Summary: Single-molecule imaging in live yeast cells has become a powerful tool for researchers to quantitatively measure cellular activities in real time, with significant progress made in recent years to provide important references for studying biological processes. Different labs have tailored imaging setups and data analysis pipelines to estimate biophysical parameters for various biological processes, reflecting a rich variety of experimental experiences.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biology
Thomas G. W. Graham, John Joseph Ferrie, Gina M. Dailey, Robert Tjian, Xavier Darzacq
Summary: Single-molecule imaging is a powerful tool for studying biochemical processes in live cells, but tracking single molecules and detecting their interactions simultaneously remains challenging. This study describes a novel property of rhodamine dyes, proximity-assisted photoactivation (PAPA), which allows the detection of protein-protein interactions in live cells using two different labeled protein complexes in proximity.
Article
Chemistry, Multidisciplinary
Yan Zhang, Chen Wang, Xiaoran Zou, Xiaorui Tian, Juan Hu, Chun-Yang Zhang
Summary: This enzyme-free single-molecule/particle detection method enables simultaneous detection of multiple lncRNAs in cancer cells with dual-targetability, good selectivity, and high sensitivity, even in single cancer cells. It has the ability to discriminate cancer cells from normal cells, features simple sequence design and enzyme-free, holding great potential in living cell imaging and early clinical diagnosis.
Article
Multidisciplinary Sciences
Esley Torres-Garcia, Raul Pinto-Camara, Alejandro Linares, Damian Martinez, Victor Abonza, Eduardo Brito-Alarcon, Carlos Calcines-Cruz, Gustavo Valdes-Galindo, David Torres, Martina Jablonski, Hector H. Torres-Martinez, Jose L. Martinez, Haydee O. Hernandez, Jose P. Ocelotl-Oviedo, Yasel Garces, Marco Barchi, Rocco D'Antuono, Ana Boskovic, Joseph G. Dubrovsky, Alberto Darszon, Mariano G. Buffone, Roberto Rodriguez Morales, Juan Manuel Rendon-Mancha, Christopher D. Wood, Armando Hernandez-Garcia, Diego Krapf, Alvaro H. Crevenna, Adan Guerrero
Summary: This study presents a new super-resolution microscopy algorithm called Mean-Shift Super Resolution (MSSR), which extends the spatial resolution of single fluorescence images beyond the diffraction limit. MSSR works on various fluorophore densities and optical setups, and has denoising capabilities.
NATURE COMMUNICATIONS
(2022)
Review
Chemistry, Multidisciplinary
Wei Chen, Xiaoying Zhao, Nanyang Yang, Xing Li
Summary: Messenger RNA (mRNA) serves as the fundamental information transfer system in cells. Tracking single mRNA from transcription to degradation using fluorescent probes provides spatiotemporal information about how genetic information is transferred from DNA to proteins. RNA aptamers: small-molecule fluorophores (SFs) systems, as exciting alternatives for single mRNA imaging, offer advantages such as fluorogenic ability and minimal perturbation. This review summarizes the five reported RNA aptamers: SFs systems for single mRNA imaging in living cells so far, discusses challenges, and provides prospects for single mRNA imaging applications.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Nanoscience & Nanotechnology
Danni Chen, Heng Li, Bin Yu, Junle Qu
Summary: This study proposes a method for researching dynamic events in living cells by simultaneously monitoring spatial positions and changes in local environment related to fluorescence lifetime. The feasibility of the method is verified through experiments, and intracellular endocytosis in a living cell is successfully observed.
Article
Biology
Jigmi Basumatary, Neptune Baro, Prakash Joshi, Partha Pratim Mondal
Summary: Single-molecule localization microscopy (SMLM) is a powerful technique that improves spatial resolution beyond the diffraction limit and allows for the analysis of biological features at the nanoscale. This study introduces a single molecule-based scanning SMLM (scanSMLM) system that enables rapid volume imaging. By rapidly changing the aperture of an electrically-tunable lens, the system achieves selective imaging of the axial object plane, allowing for volume scanning. The technique is employed to visualize the architecture of actin-filaments, the distribution of Meos-Tom20 molecules on the mitochondrial membrane, and the clustering of Hemagglutinin (HA) protein single molecules for studying Influenza-A disease progression. The system enables 3D visualization of HA distribution, providing unprecedented insights into the disease progression at the single-molecule level.
COMMUNICATIONS BIOLOGY
(2023)
Review
Chemistry, Multidisciplinary
Bin Dong, Nourhan Mansour, Teng-Xiang Huang, Wenyu Huang, Ning Fang
Summary: Recent progress has been made in using single molecule fluorescence microscopy imaging to study nanoconfinement in porous materials, revealing static and dynamic heterogeneities between seemingly equal molecules by removing ensemble averaging effects. These studies allow for the investigation of various physicochemical processes at nanometer spatial resolution and provide the ability to quantitatively measure the inhomogeneities of nanoconfinement effects.
CHEMICAL SOCIETY REVIEWS
(2021)
Article
Multidisciplinary Sciences
Patrick Hunter, Alex L. Payne-Dwyer, Michael Shaw, Nathalie Signoret, Mark C. Leake
Summary: The ability of tumors to create a pro-tumorigenic microenvironment is an important area of study in the development of new therapeutics. CCR5, a receptor associated with pro-tumorigenic features, is being considered as a potential target for treatment. Various biophysical methods, such as super-resolution structured illumination microscopy and single molecule partially TIRF-coupled HILO microscopy, can provide valuable insights into the structure and function of onco-immunogenic receptors and other biomolecules.
Article
Multidisciplinary Sciences
Tobias F. Bartsch, Camila M. Villasante, Felicitas E. Hengel, Ahmed Toure, Daniel M. Firester, Aaron Oswald, A. J. Hudspeth
Summary: In high-speed single-molecule experiments, tethering proteins with force probes can avoid nonspecific interactions, but dissipate rapidly exerted forces through long linkers; due to the high frequency of mammalian hearing, short tethers are required for single-molecule experiments.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Qiaoqiao Ruan, Patrick J. Macdonald, Kerry M. Swift, Sergey Y. Tetin
Summary: This study demonstrates that direct single-molecule imaging can fundamentally improve the sensitivity and specificity of medically relevant assays, enhancing the screening of blood donations and diagnostic testing. Compared to traditional microparticle-based assays, single-molecule imaging increases signal-to-noise ratio and improves discrimination against nonspecific effects. This approach lowers detection sensitivity to attomolar levels and enables a wider linear detection range, shorter incubation times, simpler assay protocols, and reduced reagent consumption.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Materials Science, Multidisciplinary
Sijia Liu, Jie Rong, Rui Liu, Jonathan S. Lindsey
Summary: A recent design successfully addressed the solubilization of hydrophobic fluorophores in aqueous solution by utilizing amphiphilic polymers to encapsulate the fluorophores. By adjusting the molecular design of the polymer and the attachment of the hydrophobic fluorophores, the formation of single-chain nanoparticles bearing single fluorophores in PBS solution was achieved with high fluorescence quantum yield. This molecular design is well-suited for aqueous solubilization of hydrophobic fluorophores in life science applications.
ACS APPLIED POLYMER MATERIALS
(2021)
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
Zoology
Claudia A. Grillo, Mande Holford, Nils G. Walter
Summary: This article proposes using agent-based models to define general rules for interactions across biological systems and evolutionary time, and speculates on the possibility of simulating self-organizing systems and deciphering universal principles that govern biological interactions. It aims to explore further advancements in biosciences in the 21st century.
INTEGRATIVE AND COMPARATIVE BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Rajeev Yadav, Julia R. Widom, Adrien Chauvier, Nils G. Walter
Summary: This study used single molecule fluorescence technology to reveal three dynamically interconverting conformations of the fluoride riboswitch. Specifically, the fluoride ion snap-locks the conformation through its interaction with magnesium-induced RNA, and a long-range base pair plays a crucial role in the process. Additionally, the proximally paused RNA polymerase further promotes riboswitch docking. Finally, the study found that fluoride binding at short RNA lengths is an early step towards folding into the docked conformation.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Zi Li, Molly McNeely, Erin Sandford, Muneesh Tewari, Alexander Johnson-Buck, Nils G. Walter
Summary: From traditional enzyme-linked immunosorbent assay (ELISA) to modern next-generation sequencing, many sensitive and specific biomarker detection assays require capturing analytes at a surface. However, surface-based assays have limited capture efficiency from dilute solutions, resulting in detection sensitivity in the femtomolar-to-nanomolar range. To address this challenge, we use an aqueous two-phase system (ATPS) to concentrate target molecules near the assay surface, improving capture efficiency and achieving subfemtomolar detection limits without amplification. This approach enhances the sensitivity of surface-based assays by approximately 300-fold.
Article
Chemistry, Multidisciplinary
Aaron T. Blanchard, Zi Li, Elizabeth C. Duran, Catherine E. Scull, J. Damon Hoff, Keenan R. Wright, Victor Pan, Nils G. Walter
Summary: DNA-based FluoroCubes were developed as a solution to photobleaching in fluorescence microscopy. These compact FluoroCubes, coupled with up to 6 fluorescent dyes, exhibit enhanced photostability up to 50 times and emit a higher number of photons up to 40 times compared to single dyes. The study addresses the mechanism behind the improved photostability and confirms the compatibility of FluoroCubes with FRET and dark quenching applications.
Article
Biochemistry & Molecular Biology
Sujay Ray, Shiba S. Dandpat, Surajit Chatterjee, Nils G. Walter
Summary: The noncoding, structured 5'-untranslated regions (5'-UTRs) of bacterial mRNAs can regulate translation efficiency through the formation of structures that interact with the ribosome. This study investigates how the binding of a small ligand controls the recruitment and dissociation of the bacterial ribosome to the Shine-Dalgarno sequence. It is found that ligand binding stabilizes the riboswitch structure, which both inhibits ribosome recruitment and accelerates ribosome dissociation. The proximity of the 5'-UTR and the stability of the SD:anti-SD interaction play important roles in modulating the initial ribosome-mRNA interaction.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biophysics
Tanmay Chatterjee, Alexander Johnson-Buck, Nils G. Walter
Summary: Sensitive assays of protein biomarkers play a critical role in clinical diagnostics and biomedical research. Nucleic acid aptamers generated by SELEX have shown promise as an alternative to immunoreagents for detection, offering advantages in synthesis and reproducibility. SiMREPS, a single molecule recognition platform, allows for high sensitivity detection of biomarkers without requiring high-affinity probes. This study demonstrates the applicability of aptamers as detection probes in SiMREPS for two clinically relevant biomarkers, VEGF165 and IL-8, with detection limits in the low femtomolar range.
BIOSENSORS & BIOELECTRONICS
(2022)
Correction
Chemistry, Multidisciplinary
Aaron T. Blanchard, Zi Li, Elizabeth C. Duran, Catherine E. Scull, J. Damon Hoff, Keenan R. Wright, Victor Pan, Nils G. Walter
Article
Biochemistry & Molecular Biology
Adrien Chauvier, Jason C. C. Porta, Indrajit Deb, Emily Ellinger, Katarina Meze, Aaron T. T. Frank, Melanie D. D. Ohi, Nils G. G. Walter
Summary: This study investigates the interaction between RNA polymerase and nascent transcripts during transcription. It is found that the transcription process of a preQ(1) riboswitch can be modulated by the RNA polymerase and the conformation of the nascent RNA. Ligand binding to the riboswitch leads to the release of RNA polymerase pause and the continuation of transcription. The mechanism by which riboswitch folding modulates pausing is revealed through cryo-electron microscopy reconstructions.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Cell Biology
Elizabeth Duran, Andreas Schmidt, Robb Welty, Ameya P. Jalihal, Sethuramasundaram Pitchiaya, Nils G. Walter
Summary: Cellular machineries that drive gene expression and regulate it rely on the assembly and interactions of proteins and RNA called ribonucleoprotein complexes (RNPs). Recreating these cellular machines and understanding their mechanisms is challenging. Single molecule fluorescence microscopy studies within crude or recombinantly supplemented cell extracts can provide insights into the behavior of specific biomolecules within RNPs in native cellular environments. This review discusses the methods and strategies used in dissecting RNP-driven processes, with a focus on pre-mRNA splicing and transcription regulation.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2023)
Article
Pharmacology & Pharmacy
Emily Ellinger, Adrien Chauvier, Rosa A. Romero, Yichen Liu, Sujay Ray, Nils G. Walter
Summary: This review examines the potential of riboswitches as novel antibacterial drug targets. The limited mechanisms of action of currently available antibiotics are summarized, followed by a delineation of the functional mechanisms of riboswitches. The potential for developing novel approaches that target paradigmatic riboswitches in the context of their bacterial gene expression machinery is discussed.
EXPERT OPINION ON THERAPEUTIC TARGETS
(2023)
Article
Chemistry, Physical
Guoming Gao, Nils G. Walter
Summary: Biomolecular condensates are membraneless cellular compartments formed by phase separation, which play crucial roles in regulating cellular functions. Live-cell single particle tracking has revealed the mesoscopic organization and biological functions of condensates. However, there is a lack of quantitative benchmarking and objective comparison of boundary detection methods for condensates. In this study, synthetic data with defined ground truth is used to evaluate the most commonly used methods for condensate boundary detection, providing guidance for selecting optimal methods in imaging-based studies of condensates.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Nanoscience & Nanotechnology
Mathias Centola, Erik Poppleton, Sujay Ray, Martin Centola, Robb Welty, Julian Valero, Nils G. Walter, Petr Sulc, Michael Famulok
Summary: Molecular engineering aims to design nanoassemblies for complex tasks, but efficient chemical-fuel-driven nanoscale driver-follower systems have not been realized. In this study, a DNA nanomachine driven by the chemical energy of DNA-templated RNA-transcription-consuming nucleoside triphosphates was developed, generating rhythmic pulsating motion and successfully coupling with a passive follower.
NATURE NANOTECHNOLOGY
(2023)
Review
Urology & Nephrology
Guoming Gao, Emily S. Sumrall, Sethuramasundaram Pitchiaya, Markus Bitzer, Simon Alberti, Nils G. Walter
Summary: The regulation of solute microenvironments is crucial for cellular homeostasis. In the kidney, biomolecular condensates formed through hyperosmotic phase separation play important roles in kidney physiology and disease.
NATURE REVIEWS NEPHROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Qian Hou, Surajit Chatterjee, Paul E. Lund, Krishna C. Suddala, Nils G. Walter
Summary: This study investigates the thermodynamic and kinetic folding properties of two riboswitches from different bacteria and the effects of urea and trimethylamine N-oxide (TMAO) on their folding. The results show that the riboswitch from a thermophilic bacterium is more thermotolerant and that urea destabilizes their folded structure while TMAO counteracts urea denaturation. These findings shed light on how subtle sequence adaptations in a thermophilic bacterium can stabilize a common RNA structure.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Rebecca T. Perelman, Andreas Schmidt, Umar Khan, Nils G. Walter
Summary: This study investigates the spatial localization and diffusion of mRNA in cellular ribonucleoprotein (RNP) granules. The results show that mRNA molecules are often localized at the boundaries of these granules, potentially due to intermolecular interactions.