Live-cell single-molecule fluorescence imaging has become a powerful analytical tool to investigate cellular processes that are not accessible to conventional biochemical approaches. This has greatly enriched our understanding of the behaviors of single biomolecules in their native environments and their roles in cellular events. Here, we review recent advances in fluorescence-based single-molecule bioimaging of proteins in living cells. We begin with practical considerations of the design of single-molecule fluorescence imaging experiments such as the choice of imaging modalities, fluorescent probes, and labeling methods. We then describe analytical observables from single-molecule data and the associated molecular parameters along with examples of live-cell single-molecule studies. Lastly, we discuss computational algorithms developed for single-molecule data analysis.
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http://dx.doi.org/10.1146/annurev-anchem-091619-094308 | DOI Listing |
Bioinformatics
January 2025
Rudolf Virchow Center for Integrative and Translational Bioimaging, Julius-Maximilians-University Würzburg (JMU), Würzburg, Germany.
Summary: We introduce software for reading, writing and processing fluorescence single-molecule and image spectroscopy data and developing analysis pipelines to unify various spectroscopic analysis tools. Our software can be used for processing multiple experiment types, e.g.
View Article and Find Full Text PDFNat Methods
January 2025
Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea.
Organic dyes play a crucial role in live-cell imaging because of their advantageous properties, such as photostability and high brightness. Here we introduce a super-photostable and bright organic dye, Phoenix Fluor 555 (PF555), which exhibits an order-of-magnitude longer photobleaching lifetime than conventional organic dyes without the requirement of any anti-photobleaching additives. PF555 is an asymmetric cyanine structure in which, on one side, the indole in the conventional Cyanine-3 is substituted with 3-oxo-quinoline.
View Article and Find Full Text PDFHeliyon
January 2025
School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
Cellular forces regulate an untold spectrum of living processes, such as cell migration, gene expression, and ion conduction. However, a quantitative description of mechanical control remains elusive due to the lack of general, live-cell tools to measure discrete forces between biomolecules. Here we introduce a computational pipeline for force measurement that leverages well-defined, tunable release of a mechanically activated small molecule fluorophore.
View Article and Find Full Text PDFAngew Chem Int Ed Engl
January 2025
Emory University, Chemistry, 1515 Dickey Dr., 30322, Atlanta, UNITED STATES OF AMERICA.
Genetically encoded tension sensors (GETSs) allow for quantifying forces experienced by intracellular proteins involved in mechanotransduction. The vast majority of GETSs are comprised of a FRET pair flanking an elastic "spring-like" domain that gradually extends in response to force. Because of ensemble averaging, the FRET signal generated by such analog sensors conceals forces that deviate from the average, and hence it is unknown if a subset of proteins experience greater magnitudes of force.
View Article and Find Full Text PDFElife
January 2025
Department of Molecular and Cell Biology, Berkeley, United States.
Type II nuclear receptors (T2NRs) require heterodimerization with a common partner, the retinoid X receptor (RXR), to bind cognate DNA recognition sites in chromatin. Based on previous biochemical and overexpression studies, binding of T2NRs to chromatin is proposed to be regulated by competition for a limiting pool of the core RXR subunit. However, this mechanism has not yet been tested for endogenous proteins in live cells.
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