Protocol for live-cell super-resolution imaging of transport of pre-ribosomal subunits through the nuclear pore complex

Here, we present a protocol for single-molecule super-resolution imaging of the nuclear export of pre-ribosomal subunits pre-40S and pre-60S through nuclear pore complexes. We describe steps for plating cells and co-transfecting cells. We then detail steps for using single-point edge-excitation sub-diffraction microscopy, allowing visualization of real-time dynamics of the pre-ribosomal subunits. For complete details on the use and execution of this protocol, please refer to Junod et al. (2023).1.

Protocol for single-molecule labeling and tracking of bacterial cell division proteins

Here, we present a protocol for labeling and tracking individual molecules, particularly cell division proteins in live bacterial cells. The protocol encompasses strain construction, single-molecule imaging, trajectory segmentation, and motion property analysis. The protocol enables the identification of distinctive motion states associated with different cell division proteins. Subsequent assessments of the dynamic behaviors of these proteins provide insights into their activities and interactions at the septum during cell division. For complete details on the use and execution of this protocol, please refer to Yang et al. (2021),1 Lyu et al. (2022),2 and Mahone et al. (2024).3.

Protocol for single-molecule pull-down of fluorescently tagged oligomers from cell lysates

Mutations in intrinsically disordered proteins drive the irreversible formation of pathological aggregates, a hallmark of neurodegenerative diseases. Here, we present a protocol to pull down fluorescently tagged proteins to characterize their basal oligomeric states. We describe steps for transfection and cell lysis, single-molecule slide preparation and pull-down, and oligomer dissolution. This protocol enables visualization of protein oligomers with single-molecule resolution. In addition, differences in oligomerization may provide insight on condensation or aggregation propensity in differing mutated or cell stress conditions. For complete details on the use and execution of this protocol, please refer to Djaja et al.1.

Protocol to prepare doubly labeled fluorescent nucleosomes for single-molecule fluorescence microscopy

Single-molecule fluorescence microscopy (SMFM) has been shown to be informative in understanding the interaction of chromatin-associated factors with nucleosomes, the basic building unit of chromatin. Here, we present a protocol for preparing doubly labeled fluorescent nucleosomes for SMFM. We describe steps for over-expression in E. coli and purification of recombinant human core histones. We then detail fluorescent labeling of histones and nucleosomal double-stranded DNA followed by octamer refolding and nucleosome reconstitution.

Using single-molecule fluorescence in situ hybridization and immunohistochemistry to count RNA molecules in single cells in zebrafish embryos

Taming gene expression variability is critical for robust pattern formation during embryonic development. Here, we describe an optimized protocol for single-molecule fluorescence in situ hybridization and immunohistochemistry in zebrafish embryos. We detail how to count segmentation clock RNAs and calculate their variability among neighboring cells. This approach is easily adaptable to count RNA numbers of any gene and calculate transcriptional variability among neighboring cells in diverse biological settings. For complete details on the use and execution of this protocol, please refer to Keskin et al. (2018),1 Zinani et al. (2021),2 and Zinani et al. (2022).3.

Single-molecule tracking for studying protein dynamics and target-search mechanism in live cells of S. cerevisiae

Single-molecule tracking (SMT) is a powerful approach to quantify the biophysical parameters of protein dynamics in live cells. Here, we describe a protocol for SMT in live cells of the budding yeast Saccharomyces cerevisiae. We detail how to genetically engineer yeast strains for SMT, how to set up image acquisition parameters, and how different software programs can be used to quantify a variety of biophysical parameters such as diffusion coefficient, residence time, bound fraction, jump angles, and target-search parameters. For complete details on the use and execution of this protocol, please refer to Mehta et al. ¹ and Ball et al..².

Non-invasive chimeric HaloTag labeling to study clustering and diffusion of membrane proteins

As live imaging plays an increasingly critical role in cell biology research, the desire to label and track individual protein molecules in vivo has been growing. To address this, in this protocol we describe steps for sparse labeling using two different HaloTag ligand dyes in C. elegans. This labeling approach is simple, is non-invasive, and preserves the view of the bulk protein population. We further describe how to carry out single-particle tracking experiments and extract information about particle diffusion behavior. For complete details on the use and execution of this protocol, please refer to Chang and Dickinson (2022).¹.

Quantifying transport dynamics with three-dimensional single-particle tracking in adherent cells

Intracellular transport plays an important role in maintaining the physiological functions of cells. Here, we describe a protocol for 3D single-particle tracking within living cells. We detail the use of a two-focal imaging system and the analytical steps for quantifying 3D transport dynamics. This protocol can be used to characterize the intracellular diffusion and trafficking of macromolecules, nanoparticles, and endocytic vesicles in adherent cells. For complete details on the use and execution of this protocol, please refer to Jiang et al. (2022).

DNA fiber combing protocol using in-house reagents and coverslips to analyze replication fork dynamics in mammalian cells

DNA fiber combing is a versatile technique that provides insight into replication fork dynamics at single-molecule resolution. DNA fibers are bound to silanized coverslips and combed, which straightens and aligns the fibers along a single axis. Here, we present a DNA fiber combing protocol that does not use commercial kits; we detail the steps to prepare all materials, reagents, and silanized coverslips. We describe the use of DLD-1 cells, but the protocol is amenable to other cell types.

Characterization of human aquaporin protein-protein interactions using microscale thermophoresis (MST)

Aquaporin water channels (AQPs) are membrane proteins that maintain cellular water homeostasis. The interactions between human AQPs and other proteins play crucial roles in AQP regulation by both gating and trafficking. Here, we describe a protocol for characterizing the interaction between a human AQP and a soluble interaction partner using microscale thermophoresis (MST). MST has the advantage of low sample consumption and high detergent compatibility enabling AQP protein-protein interaction investigation with a high level of control of components and environment. For complete details on the use and execution of this protocol, please refer to Kitchen et al. (2020) and Roche et al. (2017).

Single molecule probing of disordered RNA binding proteins

Liquid-liquid phase separation of intrinsically disordered proteins is known to underlie diverse pathologies such as neurodegeneration, cancer, and aging. The nucleation step of condensate formation is of critical importance for understanding how healthy and disease-associated condensates differ. Here, we describe four orthogonal single-molecule techniques that enable molecular tracking of the RNA-protein interaction, RNA-induced oligomerization, and kinetics of nucleation. These approaches allow researchers to directly interrogate the initial steps of liquid-liquid phase separation. For complete details on the use and execution of this profile, please refer to Niaki et al. (2020), Rhine et al. (2020), and Rhine et al. (2022).

Protocol for generation and regeneration of PEG-passivated slides for single-molecule measurements

Single-molecule fluorescence detection by total internal reflection microscope requires surface passivation by polyethylene glycol (PEG) coating, which is labor intensive and is only good for one or two experiments. Here, we present an efficient and reliable protocol for generating and regenerating the PEG surface for multiple rounds of experiments (∼5–10 times) in the same channel. This protocol is very simple, robust, rapid, and versatile; i.e., multiple strategies can be implemented to regenerate different layers of surface. The regeneration strategy saves time, improves the cost effectiveness, and enhances the efficiency of single-molecule experiments.

For complete details on the use and execution of this profile, please refer to Paul et al. (2021a).

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Regeneration of PEG-passivated slide is simple, quick, and cost effective

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Multiple experiments can be performed in a single channel

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Different strategies are implemented for different level of regeneration

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Regeneration leads to highly reproducible results

Fast-dissociating but highly specific antibodies are novel tools in biology, especially useful for multiplex super-resolution microscopy

Fast-dissociating, highly specific monoclonal antibodies (FDSAs) are single-molecule imaging probes useful for many biological assays including consecutive, multiplexable super-resolution microscopy. We developed a screening assay to characterize the kinetics of antibody-antigen interactions using single-molecule microscopy and established a pipeline to identify FDSAs from thousands of monoclonal candidates. Provided here are detailed protocols to prepare multi-well glass-bottom plates necessary for our assay to identify hybridoma clones secreting FDSAs. Synthesis of fluorescently labeled Fab fragments (Fab probes) from FDSAs is also described. For complete details on the use and execution of this protocol, please refer to Miyoshi et al. (2021).

Quantifying the global binding and target-search dynamics of epigenetic regulatory factors using live-cell single-molecule tracking

This protocol provides instructions to track the global dynamics of single epigenetic regulatory factors in live cells. We describe an approach to generate cell lines that stably express HaloTag-fused proteins. We then use live-cell single-molecule tracking to obtain kinetic populations and residence times. The kinetic parameters obtained can be used to determine important aspects of transcriptional regulation such as target-search time, 3D free diffusion time, and number of non-specific sites sampled before reaching a specific site and compare behaviors across different nuclear environments.

For complete details on the use and execution of this protocol, please refer to Kent et al. (2020).

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Generate cell lines stably expressing HaloTag fusion genes

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Quantify global binding and target-search kinetics of epigenetic factors

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Map binding dynamics of epigenetic factors within transcriptional condensates

Co-immunoprecipitation and semi-quantitative immunoblotting for the analysis of protein-protein interactions

Co-immunoprecipitation (co-IP) of protein complexes from cell lysates is widely used to study protein-protein interactions. However, establishing robust co-IP assays often involves considerable optimization. Moreover, co-IP results are frequently presented in non-quantitative ways. This protocol presents an optimized co-IP workflow with an analysis based on semi-quantitative immunoblot densitometry to increase reliability and reproducibility. For complete details on the use and execution of this protocol, please refer to Burckhardt et al. (2021).

Live and fixed imaging of translation sites at single mRNA resolution in the Drosophila embryo

Significant regulation of gene expression is mediated at the translation level. Here, we describe protocols for imaging and analysis of translation at single mRNA resolution in both fixed and living Drosophila embryos. These protocols use the SunTag system, in which the protein of interest is visualized by inserting a peptide array that is recognized by a single chain antibody. Simultaneous detection of individual mRNAs using the MS2/MCP system or by smFISH allows translation sites to be identified and quantified.

For complete information on the generation and use of this protocol, please refer to Vinter et al. (2021).

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Visualization of translation of single mRNAs in Drosophila using SunTag labeling

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Fixed embryo analysis reveals the mRNA translation efficiency in each expressing cell

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Live SunTag confocal imaging uncovers mRNA translation dynamics

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Image analysis pipelines allow quantitative and temporal information to be extracted

Assessing reversible and irreversible binding effects of kinase covalent inhibitors through ADP-Glo assays

Typical enzymatic inhibition assays often demonstrate improved potency for kinase covalent inhibitors compared to reversible inhibitors. This can primarily be attributed to the irreversible mode of action and could affect the evaluations of the ATP-competitive nature of covalent inhibitors, hindering optimization of these compounds. Here, we describe a version of ADP-Glo assay, in which modification of inhibitor incubation time in the presence or absence of ATP enables a quick assessment of relative reversible and irreversible effects of kinase covalent inhibitors.

For complete details on the use and execution of this protocol, please refer to Schröder et al. (2020).

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Simple enzymatic assays for quick assessment of kinase covalent inhibitors

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Modification of incubation time allows probing ATP-competitive nature of inhibitors

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The assays enable the evaluation of relative reversible and irreversible effects

Generation of versatile ss-dsDNA hybrid substrates for single-molecule analysis

Here, we describe a rapid and versatile protocol to generate gapped DNA substrates for single-molecule (SM) analysis using optical tweezers via site-specific Cas9 nicking and force-induced melting. We provide examples of single-stranded (ss) DNA gaps of different length and position. We outline protocols to visualize these substrates by replication protein A-enhanced Green Fluorescent Protein (RPA-eGFP) and SYTOX Orange staining using commercially available optical tweezers (C-TRAP). Finally, we demonstrate the utility of these substrates for SM analysis of bidirectional growth of RAD-51-ssDNA filaments. For complete details on the use and execution of this protocol, please refer to Belan et al. (2021).