Direct monitoring of formation and dissociation of individual metal complexes by single-molecule fluorescence spectroscopy

Fluorescent organometallic dyads and triads: establishing spatial relationships

FRET pairs involving up to three different Bodipy dyes are utilized to provide information on the assembly/disassembly of organometallic complexes. Azolium salts tagged with chemically robust and photostable blue or green or red fluorescent Bodipy, respectively, were synthesized and the azolium salts used to prepare metal complexes [(NHC_blue)ML], [(NHC_green)ML] and [(NHC_red)ML] (ML = Pd(allyl)Cl, IrCl(cod), RhCl(cod), AuCl, Au(NTf₂), CuBr). The blue and the green Bodipy and the green and the red Bodipy, respectively, were designed to allow the formation of efficient FRET pairs with minimal cross-talk. Organometallic dyads formed from two subunits enable the transfer of excitation energy from the donor dye to the acceptor dye. The blue, green and red emission provide three information channels on the formation of complexes, which is demonstrated for alkyne or sulfur bridged digold species and for ion pairing of a red fluorescent cation and a green fluorescent anion. This approach is extended to probe an assembly of three different subunits. In such a triad, each component is tagged with either a blue, a green or a red Bodipy and the energy transfer blue →green → red proves the formation of the triad. The tagging of molecular components with robust fluorophores can be a general strategy in (organometallic) chemistry to establish connectivities for binuclear catalyst resting states and binuclear catalyst decomposition products in homogeneous catalysis.

A dark intermediate in the fluorogenic reaction between tetrazine fluorophores and trans-cyclooctene

Fluorogenic labeling via bioorthogonal tetrazine chemistry has proven to be highly successful in fluorescence microscopy of living cells. To date, trans-cyclooctene (TCO) and bicyclonyne have been found to be the most useful substrates for live-cell labeling owing to their fast labeling kinetics, high biocompatibility, and bioorthogonality. Recent kinetic studies of fluorogenic click reactions with TCO derivatives showed a transient fluorogenic effect but could not explain the reaction sequence and the contributions of different intermediates. More recently, fluorescence quenching by potential intermediates has been investigated, suggesting their occurrence in the reaction sequence. However, in situ studies of the click reaction that directly relate these observations to the known reaction sequence are still missing. In this study, we developed a single-molecule fluorescence detection framework to investigate fluorogenic click reactions. In combination with data from ultra-performance liquid chromatography-tandem mass spectrometry, this explains the transient intensity increase by relating fluorescent intermediates to the known reaction sequence of TCO with fluorogenic tetrazine dyes. More specifically, we confirm that the reaction of TCO with tetrazine rapidly forms a fluorescent 4,5-dihydropyridazine species that slowly tautomerizes to a weakly fluorescent 1,4-dihydropyridazine, explaining the observed drop in fluorescence intensity. On a much slower timescale of hours/days, the fluorescence intensity may be recovered by oxidation of the intermediate to a pyridazine. Our findings are of importance for quantitative applications in fluorescence microscopy and spectroscopy as the achieved peak intensity with TCO depends on the specific experimental settings. They clearly indicate the requirement for more robust benchmarking of click reactions with tetrazine dyes and the need for alternative dienophiles with fast reaction kinetics and stable fluorescence emission to further applications in advanced fluorescence microscopy.

Linker Molecules Convert Commercial Fluorophores into Tailored Functional Probes during Biolabelling

Many life‐science techniques and assays rely on selective labeling of biological target structures with commercial fluorophores that have specific yet invariant properties. Consequently, a fluorophore (or dye) is only useful for a limited range of applications, e.g., as a label for cellular compartments, super‐resolution imaging, DNA sequencing or for a specific biomedical assay. Modifications of fluorophores with the goal to alter their bioconjugation chemistry, photophysical or functional properties typically require complex synthesis schemes. We here introduce a general strategy that allows to customize these properties during biolabelling with the goal to introduce the fluorophore in the last step of biolabelling. For this, we present the design and synthesis of ‘linker’ compounds, that bridge biotarget, fluorophore and a functional moiety via well‐established labeling protocols. Linker molecules were synthesized via the Ugi four‐component reaction (Ugi‐4CR) which facilitates a modular design of linkers with diverse functional properties and bioconjugation‐ and fluorophore attachment moieties. To demonstrate the possibilities of different linkers experimentally, we characterized the ability of commercial fluorophores from the classes of cyanines, rhodamines, carbopyronines and silicon‐rhodamines to become functional labels on different biological targets in vitro and in vivo via thiol‐maleimide chemistry. With our strategy, we showed that the same commercial dye can become a photostable self‐healing dye or a sensor for bivalent ions subject to the linker used. Finally, we quantified the photophysical performance of different self‐healing linker–fluorophore conjugates and demonstrated their applications in super‐resolution imaging and single‐molecule spectroscopy.

Metallation-Induced Heterogeneous Dynamics of DNA Revealed by Single-Molecule FRET

The metallation of nucleic acids is key to wide-ranging applications, from anticancer medicine to nanomaterials, yet there is a lack of understanding of the molecular-level effects of metallation. Here, we apply single-molecule fluorescence methods to study the reaction of an organo-osmium anticancer complex and DNA. Individual metallated DNA hairpins are characterised using Förster resonance energy transfer (FRET). Although ensemble measurements suggest a simple two-state system, single-molecule experiments reveal an underlying heterogeneity in the oligonucleotide dynamics, attributable to different degrees of metallation of the GC-rich hairpin stem. Metallated hairpins display fast two-state transitions with a two-fold increase in the opening rate to ≈2 s^-1 , relative to the unmodified hairpin, and relatively static conformations with long-lived open (and closed) states of 5 to ≥50 s. These studies show that a single-molecule approach can provide new insight into metallation-induced changes in DNA structure and dynamics.

Organic and Organometallic Chemistry at the Single-Molecule, -Particle, and -Molecular-Catalyst-Turnover Level by Fluorescence Microscopy

Mechanistic studies have historically played a key role in the discovery and optimization of reactions in organic and organometallic chemistry. However, even apparently simple organic and organometallic transformations may have surprisingly complicated multistep mechanisms, increasing the difficulty of extracting this mechanistic information. The resulting reaction intermediates often constitute a small fraction of the total reaction mixture, for example, creating a long-term analytical challenge of detection. This challenge is particularly pronounced in cases where the positions of intermediates on the reaction energy surface mean that they do not "build up" to the quantities needed for observation by traditional ensemble analytical tools. Thus, their existence and single-step elementary reactivity cannot be studied directly. New approaches for obtaining this otherwise-missing mechanistic information are therefore needed. Single-turnover, single-molecule, single-particle, and other subensemble fluorescence microscopy techniques are ideally suited for this role because of their sensitivity and spatiotemporal resolution. Inspired by the robust development of single-molecule fluorescence microscopy tools for studying enzyme catalysis, our laboratory has developed analogous fluorescence microscopy techniques to overcome mechanistic challenges in synthetic chemistry, with sensitivity as high as the single-complex, single-turnover, and single-molecule level. These techniques free the experimenter from the previous restriction that intermediates must "build up" to quantities needed for detection by ensemble analytical tools and are suited to systems where synchronization through flash photolysis or stopped flow would be inconvenient or inaccessible. In this process, the techniques transform certain previously "unobservable" intermediates and their elementary single-step reactivities into "observable" ones through sensitive and selective spectral handles. Our program has focused on imaging reactions in small-molecule, organic, and polymer synthetic chemistry with an accent on the reactivity of molecular transition metal complexes and catalysts. Our laboratory initiated studies in this area in 2008 with the imaging of individual palladium complexes that were tagged with spectator fluorophores. To enable imaging, we started with fluorophore selection and development, overcame challenges with imaging in organic solvents, and developed strategies compatible with air-sensitive chemistry and concentrations of reagents generally used in small-molecule synthesis. These studies grew to include characterization of previously unknown organometallic intermediates in the synthesis of organozinc reagents and the direct study of their elementary-step reactivity. The ability to directly observe this behavior generated predictive power for selecting salts that accelerated organozinc reagent formation in synthesis, including salts that had not yet been reported synthetically. In 2017 we also developed the first single-turnover imaging of molecular (chemo)catalysts, which through the technique's spatiotemporal resolution revealed abruptly time-variable polymerization kinetics wherein molecular ruthenium ring-opening metathesis polymerization (ROMP) catalysts changed rates independently from other catalysts less than 1 μm away. Individual catalytic turnovers, each corresponding to one single-chain-elongation reaction arising from insertion of single ROMP or enyne monomers at individual Grubbs II molecular ruthenium catalysts, were spatiotemporally resolved as green flashes in growing polymers. In this Account, we discuss the development of this technique from idea to application, including challenges overcome and strategies created to image synthetic organic and organometallic molecular chemistry at the highest levels of detection sensitivity. We also describe challenges not yet solved and provide an outlook for this growing field at the intersection of microscopy and synthetic/molecular chemistry.

Switchable Fluorophores for Single-Molecule Localization Microscopy

The past decade has witnessed an explosion in the use of super-resolution fluorescence microscopy methods in biology and other fields. Single-molecule localization microscopy (SMLM) is one of the most widespread of these methods and owes its success in large part to the ability to control the on-off state of fluorophores through various chemical, photochemical, or binding-unbinding mechanisms. We provide here a comprehensive overview of switchable fluorophores in SMLM including a detailed review of all major classes of SMLM fluorophores, and we also address strategies for labeling specimens, considerations for multichannel and live-cell imaging, potential pitfalls, and areas for future development.

Nanofiber-Directed Anisotropic Self-Assembly of CdSe-CdS Quantum Rods for Linearly Polarized Light Emission Evidenced by Quantum Rod Orientation Microscopy

Hybrid soft materials composed of CdSe-CdS nanorods or "quantum rods" (QRs) and the fluorescent 2,3-didecyloxyanthracene (DDOA) low molecular weight organogelator are obtained through self-assembly. Spectroscopy, microscopy, and rheology studies show that the QRs and DDOA coassemble, thereby stabilizing the organogels. Depending on the QR load and excitation wavelength, single nanofibers (NFs) of the hybrid gel display either sharp polarized red luminescence (under green excitation), or dual perpendicularly polarized blue and red emissions (under UV excitation). Transmission electron microscopy, microspectroscopy, and quantum rod orientation microscopy (QROM) reveal that QRs align along the organogel NFs with order parameters reaching 76% and 87%. This paves the way for obtaining surfaces of QR/NF assemblies yielding sharp red linearly polarized emission. In addition, this work demonstrates that QRs can be used more generally to probe nanostructured soft materials, even nonemissive ones. QROM allows to establish maps of the orientation of single QRs dispersed onto or within a gel network by measuring the polarization of the emission of the individual QRs. As occurs within this work in which QRs and NFs interact, the orientation of each QR reveals information on the underlying nanostructure (such as surface striation, bundle formation, and helicity).

Fluorescence resonance energy transfer (FRET) for the verification of dual gold catalysis

Two gold complexes with different bodipy-tagged N-heterocyclic carbene ligands, which are a potential FRET pair, were synthesized. It was shown, that the formation of dinuclear intermediates in alkyne transformations (“dual gold catalysis”) are characterized by a FRET signal.

Photon Antibunching in a Cyclic Chemical Reaction Scheme

The direct observation of chemical reactions on the single-molecule level is an ultimate goal in single-molecule chemistry, which also includes kinetic analyses. To analyze the lifetime of reaction intermediates, very sophisticated excitation schemes are often required. Here we focus on the kinetic analysis of the ground-state proton transfer within the photocycle of a photoacid. In detail, we demonstrate the determination of the bimolecular rate constant of this process with nanosecond resolution. The procedure relies on the exploration of a purely quantum-optical effect, namely, photon antibunching, and thus on evaluating interphoton arrival times to extract the reaction rate constant.

Nucleic acid-specific photoactivation of oligodeoxyribonucleotides labeled with deuterated dihydro-N,N,N',N'-tetramethylrhodamine using green light

We developed a simple protocol for high-yielding synthesis of conjugates of a deuterated dihydro-N,N,N',N'-tetramethylrhodamine (F*) with oligodeoxyribonucleotides and a 2'-OMe RNA (a representative nuclease-resistant, chemically modified oligonucleotide) using easily accessible starting materials including NaBD4 and conjugates of oligonucleotides with N,N,N',N'-tetramethylrhodamine (F). These compounds were found to be stable in air and insensitive to light at 525, 635 and 650 nm, whereas slow activation occurs upon their exposure to 470 nm light. However, at the conditions of the templated reaction, in the presence of a target nucleic acid and a photocatalyst based on the eosin structure, the F* is oxidized forming fluorescent F. This reaction is >30-fold faster than the background reaction in the absence of the template. Moreover, the presence of a single mismatch in the target nucleic acid slows down the templated reaction by eightfold. These activatable dyes can potentially find applications as nucleic acid-specific probes for super-resolution imaging in live cells.

Opportunities and challenges in single-molecule and single-particle fluorescence microscopy for mechanistic studies of chemical reactions

In recent years, single-molecule and single-particle fluorescence microscopy has emerged as a tool to investigate chemical systems. After an initial lag of over a decade with respect to biophysical studies, this powerful imaging technique is now revealing mechanisms of 'classical' organic reactions, spatial distribution of chemical reactivity on surfaces and the phase of active catalysts. The recent advance into commercial imaging systems obviates the need for home-built laser systems and thus opens this technique to traditionally trained synthetic chemists. We discuss the requisite photophysical and chemical properties of fluorescent reporters and highlight the main challenges in applying single-molecule techniques to chemical questions. The goal of this Perspective is to provide a snapshot of an emerging multidisciplinary field and to encourage broader use of this young experimental approach that aids the observation of chemical reactions as depicted in many textbooks: molecule by molecule.

Monitoring hydroquinone–quinone redox cycling by single molecule fluorescence spectroscopy

Current research in the field of single-molecule chemistry is increasingly focused on the development of reliable experimental approaches for investigating chemical processes on a molecular level using single-molecule fluorescence spectroscopy (SMFS).

Single-molecule dynamics and mechanisms of metalloregulators and metallochaperones

Understanding how cells regulate and transport metal ions is an important goal in the field of bioinorganic chemistry, a frontier research area that resides at the interface of chemistry and biology. This Current Topic reviews recent advances from the authors' group in using single-molecule fluorescence imaging techniques to identify the mechanisms of metal homeostatic proteins, including metalloregulators and metallochaperones. It emphasizes the novel mechanistic insights into how dynamic protein-DNA and protein-protein interactions offer efficient pathways via which MerR-family metalloregulators and copper chaperones can fulfill their functions. This work also summarizes other related single-molecule studies of bioinorganic systems and provides an outlook toward single-molecule imaging of metalloprotein functions in living cells.

Ensemble and single-molecule studies on fluorescence quenching in transition metal bipyridine-complexes

Beyond their use in analytical chemistry fluorescent probes continuously gain importance because of recent applications of single-molecule fluorescence spectroscopy to monitor elementary reaction steps. In this context, we characterized quenching of a fluorescent probe by different metal ions with fluorescence spectroscopy in the bulk and at the single-molecule level. We apply a quantitative model to explain deviations from existing standard models for fluorescence quenching. The model is based on a reversible transition from a bright to a dim state upon binding of the metal ion. We use the model to estimate the stability constants of complexes with different metal ions and the change of the relative quantum yield of different reporter dye labels. We found ensemble data to agree widely with results from single-molecule experiments. Our data indicates a mechanism involving close molecular contact of dye and quenching moiety which we also found in molecular dynamics simulations. We close the manuscript with a discussion of possible mechanisms based on Förster distances and electrochemical potentials which renders photo-induced electron transfer to be more likely than Förster resonance energy transfer.

Characterization of dark quencher chromophores as nonfluorescent acceptors for single-molecule FRET

Dark quenchers are chromophores that primarily relax from the excited state to the ground state nonradiatively (i.e., are dark). As a result, they can serve as acceptors for Förster resonance energy transfer experiments without contributing significantly to background in the donor-emission channel, even at high concentrations. Although the advantages of dark quenchers have been exploited for ensemble bioassays, no systematic single-molecule study of dark quenchers has been performed, and little is known about their photophysical properties. Here, we present the first systematic single-molecule study of dark quenchers in conjunction with fluorophores and demonstrate the use of dark quenchers for monitoring multiple interactions and distances in multichromophore systems. Specifically, using double-stranded DNA standards labeled with two fluorophores and a dark quencher (either QSY7 or QSY21), we show that the proximity of a fluorophore and dark quencher can be monitored using the stoichiometry ratio available from alternating laser excitation spectroscopy experiments, either for single molecules diffusing in solution (using a confocal fluorescence) or immobilized on surfaces (using total-internal-reflection fluorescence). The latter experiments allowed characterization of the dark-quencher photophysical properties at the single-molecule level. We also use dark-quenchers to study the affinity and kinetics of binding of DNA Polymerase I (Klenow fragment) to DNA. The measured properties are in excellent agreement with the results of ensemble assays, validating the use of dark quenchers. Because dark-quencher-labeled biomolecules can be used in total-internal-reflection fluorescence experiments at concentrations of 1 μM or more without introducing a significant background, the use of dark quenchers should permit single-molecule Förster resonance energy transfer measurements for the large number of biomolecules that participate in interactions of moderate-to-low affinity.

Towards artificial metallonucleases for gene therapy: recent advances and new perspectives

The process of DNA targeting or repair of mutated genes within the cell, induced by specifically positioned double-strand cleavage of DNA near the mutated sequence, can be applied for gene therapy of monogenic diseases. For this purpose, highly specific artificial metallonucleases are developed. They are expected to be important future tools of modern genetics. The present state of art and strategies of research are summarized, including protein engineering and artificial ‘chemical’ nucleases. From the results, we learn about the basic role of the metal ions and the various ligands, and about the DNA binding and cleavage mechanism. The results collected provide useful guidance for engineering highly controlled enzymes for use in gene therapy.

Experimental approach to extend the range for counting fluorescent molecules based on photon-antibunching

In single-molecule fluorescence spectroscopy photon-antibunching is frequently used to prove the occurrence of single fluorophores. Furthermore, the relative frequency of coincident photon pairs was also used to determine the number of fluorophores in the diffraction limited observation volume of a confocal microscope. However, the ability to count fluorophores is so far limited to approximately 3 molecules due to saturation of the calibration curve with increasing number of fluorophores. Recently, we introduced a novel theoretical framework for counting the number of emitting molecules by analyzing photon-distributions acquired with a confocal microscope using four single-photon detectors. Here, we present the experimental realization of the proposed scheme in a confocal setup using novel multi-channel photon-counting electronics and DNA constructs that were labelled with five fluorophores. Our experimental results give a clear correlation between the number of estimated fluorophores and the number of bleaching steps for DNA probes conjugated with five ATTO647N labels with an error of approximately 20%. Moreover, we could acquire experimental data for up to 15 fluorophores indicating the simultaneous occurrence of three DNA probes. Our experiments put into perspective that the analysis of photon-distributions acquired with four detection channels is suited to count the number of fluorescently labelled molecules in larger aggregates or clusters with potential for applications in molecular and cell biology and for time-resolved analysis of multi-chromophoric compounds in material sciences.

Fluorescent probes and delivery methods for single-molecule experiments

The recent explosion in papers utilising single-molecule experiments pushes the envelope further for increased spatial and temporal resolution. In order to achieve this, a combination of novel fluorescent probes and spectroscopy techniques are required. Herein, we provide an overview on our contribution to developments in the field of fluorescent probes along with a palette of alternative delivery methods for introducing the probes into living cells. We discuss probe requirements arising from the use of single-molecule spectroscopy methods and the customisation of probes that depends on the target molecule, the chemical state of the molecule as well as the distance and the type of interaction between sensor and ligand. We explain how Förster resonance energy transfer (FRET) and photon-induced electron transfer (PET) can increase the probe customisation. We also discuss additional requirements that arise when performing experiments in living cells like toxicity and cell permeability. Regarding the latter, we devote a special paragraph on the different ways to introduce the desired probe into the cell and how the different properties of each probe and cell type may require different delivery methods. We offer insights based on our experience working with a variety of single-molecule methods, fluorescent probes and delivery systems. Overall, we encompass the latest developments on probe design and delivery and illustrate that the wealth of information provided by single-molecule studies goes along with increased complexity.

Analysis of single-molecule fluorescence spectroscopic data with a Markov-modulated Poisson process

We present a photon-by-photon analysis framework for the evaluation of data from single-molecule fluorescence spectroscopy (SMFS) experiments using a Markov-modulated Poisson process (MMPP). A MMPP combines a discrete (and hidden) Markov process with an additional Poisson process reflecting the observation of individual photons. The algorithmic framework is used to automatically analyze the dynamics of the complex formation and dissociation of Cu2+ ions with the bidentate ligand 2,2'-bipyridine-4,4'dicarboxylic acid in aqueous media. The process of association and dissociation of Cu2+ ions is monitored with SMFS. The dcbpy-DNA conjugate can exist in two or more distinct states which influence the photon emission rates. The advantage of a photon-by-photon analysis is that no information is lost in preprocessing steps. Different model complexities are investigated in order to best describe the recorded data and to determine transition rates on a photon-by-photon basis. The main strength of the method is that it allows to detect intermittent phenomena which are masked by binning and that are difficult to find using correlation techniques when they are short-lived.

A fluorescent redox sensor with tuneable oxidation potential

A fluorescent redox sensor was prepared by attachment of hydroquinones to the fluorophore rhodamine B; fluorescence is reversibly modulated by hydroquinone-centered chemical redox reactions, and oxidation potential of the sensor is tuneable by variation of hydroquinone structure.