Single-molecule imaging at high fluorophore concentrations by local activation of dye

Embracing Heterogeneity: Challenging the Paradigm of Replisomes as Deterministic Machines

The paradigm of cellular systems as deterministic machines has long guided our understanding of biology. Advancements in technology and methodology, however, have revealed a world of stochasticity, challenging the notion of determinism. Here, we explore the stochastic behavior of multi-protein complexes, using the DNA replication system (replisome) as a prime example. The faithful and timely copying of DNA depends on the simultaneous action of a large set of enzymes and scaffolding factors. This fundamental cellular process is underpinned by dynamic protein-nucleic acid assemblies that must transition between distinct conformations and compositional states. Traditionally viewed as a well-orchestrated molecular machine, recent experimental evidence has unveiled significant variability and heterogeneity in the replication process. In this review, we discuss recent advances in single-molecule approaches and single-particle cryo-EM, which have provided insights into the dynamic processes of DNA replication. We comment on the new challenges faced by structural biologists and biophysicists as they attempt to describe the dynamic cascade of events leading to replisome assembly, activation, and progression. The fundamental principles uncovered and yet to be discovered through the study of DNA replication will inform on similar operating principles for other multi-protein complexes.

Strategies for Overcoming the Single-Molecule Concentration Barrier

Fluorescence-based single-molecule approaches have helped revolutionize our understanding of chemical and biological mechanisms. Unfortunately, these methods are only suitable at low concentrations of fluorescent molecules so that single fluorescent species of interest can be successfully resolved beyond background signal. The application of these techniques has therefore been limited to high-affinity interactions despite most biological and chemical processes occurring at much higher reactant concentrations. Fortunately, recent methodological advances have demonstrated that this concentration barrier can indeed be broken, with techniques reaching concentrations as high as 1 mM. The goal of this Review is to discuss the challenges in performing single-molecule fluorescence techniques at high-concentration, offer applications in both biology and chemistry, and highlight the major milestones that shatter the concentration barrier. We also hope to inspire the widespread use of these techniques so we can begin exploring the new physical phenomena lying beyond this barrier.

Detecting molecular interactions in live-cell single-molecule imaging with proximity-assisted photoactivation (PAPA)

Single-molecule imaging provides a powerful way to study biochemical processes in live cells, yet it remains challenging to track single molecules while simultaneously detecting their interactions. Here, we describe a novel property of rhodamine dyes, proximity-assisted photoactivation (PAPA), in which one fluorophore (the 'sender') can reactivate a second fluorophore (the 'receiver') from a dark state. PAPA requires proximity between the two fluorophores, yet it operates at a longer average intermolecular distance than Förster resonance energy transfer (FRET). We show that PAPA can be used in live cells both to detect protein-protein interactions and to highlight a subpopulation of labeled protein complexes in which two different labels are in proximity. In proof-of-concept experiments, PAPA detected the expected correlation between androgen receptor self-association and chromatin binding at the single-cell level. These results establish a new way in which a photophysical property of fluorophores can be harnessed to study molecular interactions in single-molecule imaging of live cells.

Zero-Overlap Fluorophores for Fluorescent Studies at Any Concentration

Fluorophores are powerful tools for the study of chemistry, biology, and physics. However, fluorescence is severely impaired when concentrations climb above 5 μM as a result of effects like self-absorption and chromatic shifts in the emitted light. Herein, we report the creation of a charge-transfer (CT) fluorophore and the discovery that its emission color seen at low concentrations is unchanged even at 5 mM, some 3 orders of magnitude beyond typical limits. The fluorophore is composed of a triphenylamine-substituted cyanostar macrocycle, and it exhibits a remarkable Stokes shift of 15 000 cm^-1 to generate emission at 633 nm. Crucial to the performance of this fluorophore is the observation that its emission spectrum shows near-zero overlap with the absorption band at 325 nm. We propose that reducing the spectral overlap to zero is a key to achieving full fluorescence across all concentrations. The triphenylamine donor and five cyanostilbene acceptor units of the macrocycle generate an emissive CT state. Unlike closely related donor-acceptor control compounds showing dual emission, the cyanostar framework inhibited emission from the second state to create a zero-overlap fluorophore. We demonstrated the use of emission spectroscopy for characterization of host-guest complexation at millimolar concentrations, which are typically the exclusive domain of NMR spectroscopy. The binding of the PF₆^- anion generates a 2:1 sandwich complex with blue-shifted emission. Distinct from twisted intramolecular charge-transfer (TICT) states, experiment-supported density functional theory shows a 67° twist inside an acceptor unit in the CT state instead of displaying a twist between the donor and acceptor; it is TICT-like. Inspired by the findings, we uncovered similar concentration-independent behavior from a control compound, strongly suggesting this behavior may be latent to other large Stokes-shift fluorophores. We discuss strategies capable of generating zero-overlap fluorophores to enable accurate fluorescence characterization of processes across all practical concentrations.

Fluorescence microscopy for visualizing single-molecule protein dynamics

BACKGROUND

Single-molecule fluorescence imaging (smFI) has evolved into a valuable method used in biophysical and biochemical studies as it can observe the real-time behavior of individual protein molecules, enabling understanding of their detailed dynamic features. smFI is also closely related to other state-of-the-art microscopic methods, optics, and nanomaterials in that smFI and these technologies have developed synergistically.

SCOPE OF REVIEW

This paper provides an overview of the recently developed single-molecule fluorescence microscopy methods, focusing on critical techniques employed in higher-precision measurements in vitro and fluorescent nanodiamond, an emerging promising fluorophore that will improve single-molecule fluorescence microscopy.

MAJOR CONCLUSIONS

smFI will continue to improve regarding the photostability of fluorophores and will develop via combination with other techniques based on nanofabrication, single-molecule manipulation, and so on.

GENERAL SIGNIFICANCE

Quantitative, high-resolution single-molecule studies will help establish an understanding of protein dynamics and complex biomolecular systems.

Ultralow- and Low-Background Surfaces for Single-Molecule Localization Microscopy of Multistep Biointerfaces for Single-Molecule Sensing

Single-molecule localization microscopy (SMLM) has created the opportunity of pushing fluorescence microscopy from being a biological imaging tool to a surface characterization and possibly even a quantitative analytical tool. The latter could be achieved by molecular counting using pointillist SMLM data sets. However, SMLM is especially sensitive to background fluorescent signals, which influences any subsequent analysis. Therefore, fabricating sensing surfaces that resist nonspecific adsorption of proteins, even after multiple modification steps, has become paramount. Herein is reported two different ways to modify surfaces: dichlorodimethylsilane-biotinylated bovine serum albumin-Tween-20 (DbT20) and poly-l-lysine grafted polyethylene glycol (PLL-PEG) mixed with biotinylated PLL-PEG (PLL-PEG/PEGbiotin). The results show that the ability to resist nonspecific adsorption of DbT20 surfaces deteriorates with an increase in the number of modification steps required after the addition of the DbT20, which limits the applicability of this surface for SMLM. As such, a new surface for SMLM that employs PLL-PEG/PEGbiotin was developed that exhibits ultralow amounts of nonspecific protein adsorption even after many modification steps. The utility of the surface was demonstrated for human influenza hemagglutinin-tagged mEos2, which was directly pulled down from cell lysates onto the PLL-PEG/PEGbiotin surface. The results strongly indicated that the PLL-PEG/PEGbiotin surface satisfies the criteria of SMLM imaging of a negligible background signal and negligible nonspecific adsorption.

Alternative fluorophores designed for advanced molecular imaging

Fluorescent molecular imaging has advanced drastically over the past decade. With the development of high-resolution microscopy techniques and the ability to visualize intracellular molecular events, there is a growing need for new fluorophores to accompany these fast-developing techniques. Therefore, there has been substantial development of alternative fluorophores for single-molecule detection and molecular imaging. These rationally designed fluorophores have infinite possibilities and novel fluorophores are constantly being produced for different applications. This review focuses on the recent developments in novel fluorophores designed for molecular imaging and single-molecule detection. Here, single-molecule imaging, smart fluorescent probes, two-photon microscopy, Förster resonance energy transfer (FRET) and super-resolution microscopy are discussed in detail.

Caging and Photoactivation in Single-Molecule Förster Resonance Energy Transfer Experiments

Caged organic fluorophores are established tools for localization-based super-resolution imaging. Their use relies on reversible deactivation of standard organic fluorophores by chemical reduction or commercially available caged dyes with ON switching of the fluorescent signal by ultraviolet (UV) light. Here, we establish caging of cyanine fluorophores and caged rhodamine dyes, i.e., chemical deactivation of fluorescence, for single-molecule Förster resonance energy transfer (smFRET) experiments with freely diffusing molecules. They allow temporal separation and sorting of multiple intramolecular donor–acceptor pairs during solution-based smFRET. We use this “caged FRET” methodology for the study of complex biochemical species such as multisubunit proteins or nucleic acids containing more than two fluorescent labels. Proof-of-principle experiments and a characterization of the uncaging process in the confocal volume are presented. These reveal that chemical caging and UV reactivation allow temporal uncoupling of convoluted fluorescence signals from, e.g., multiple spectrally similar donor or acceptor molecules on nucleic acids. We also use caging without UV reactivation to remove unwanted overlabeled species in experiments with the homotrimeric membrane transporter BetP. We finally outline further possible applications of the caged FRET methodology, such as the study of weak biochemical interactions, which are otherwise impossible with diffusion-based smFRET techniques because of the required low concentrations of fluorescently labeled biomolecules.

Single-Molecule Analysis of Bacterial DNA Repair and Mutagenesis

Ubiquitous conserved processes that repair DNA damage are essential for the maintenance and propagation of genomes over generations. Then again, inaccuracies in DNA transactions and failures to remove mutagenic lesions cause heritable genome changes. Building on decades of research using genetics and biochemistry, unprecedented quantitative insight into DNA repair mechanisms has come from the new-found ability to measure single proteins in vitro and inside individual living cells. This has brought together biologists, chemists, engineers, physicists, and mathematicians to solve long-standing questions about the way in which repair enzymes search for DNA lesions and form protein complexes that act in DNA repair pathways. Furthermore, unexpected discoveries have resulted from capabilities to resolve molecular heterogeneity and cell subpopulations, provoking new questions about the role of stochastic processes in DNA repair and mutagenesis. These studies are leading to new technologies that will find widespread use in basic research, biotechnology, and medicine.

Watching cellular machinery in action, one molecule at a time

Monachino et al. review recent developments in single-molecule biophysical approaches and the cell biological advances they allow.

Single-molecule manipulation and imaging techniques have become important elements of the biologist’s toolkit to gain mechanistic insights into cellular processes. By removing ensemble averaging, single-molecule methods provide unique access to the dynamic behavior of biomolecules. Recently, the use of these approaches has expanded to the study of complex multiprotein systems and has enabled detailed characterization of the behavior of individual molecules inside living cells. In this review, we provide an overview of the various force- and fluorescence-based single-molecule methods with applications both in vitro and in vivo, highlighting these advances by describing their applications in studies on cytoskeletal motors and DNA replication. We also discuss how single-molecule approaches have increased our understanding of the dynamic behavior of complex multiprotein systems. These methods have shown that the behavior of multicomponent protein complexes is highly stochastic and less linear and deterministic than previously thought. Further development of single-molecule tools will help to elucidate the molecular dynamics of these complex systems both inside the cell and in solutions with purified components.

Dense small molecule labeling enables activator-dependent STORM by proximity mapping

Stochastic optical reconstruction microscopy (STORM) enables high-resolution imaging, but multi-channel 3D imaging is problematic because of chromatic aberrations and alignment errors. The use of activator-dependent STORM in which spectrally distinct activators can be coupled with a single reporter can circumvent such issues. However, the standard approach of linking activators and reporters to a single antibody molecule is hampered by low labeling density and the large size of the antibody. We proposed that small molecule labels might enable activator-dependent STORM if the reporter or activator were linked to separate small molecules that bound within 3.5 nm of each other. This would greatly increase the labeling density and therefore improve resolution. We tested various mixtures of phalloidin- or mCling-conjugated fluorophore to demonstrate this feasibility. The specific activation was dependent on the choice of activator, its density, a matching activating laser and its power. In addition to providing an effective means of multi-channel 3D STORM imaging, this method also provides information about the local proximity between labels, potentially enabling super-resolved mapping of the conformation of the labeled structures.