DNA Microenvironment Monitored by Controlling Redox Blinking

Single-Molecule Study of Redox Reaction Kinetics by Observing Fluorescence Blinking

Recent advances in fluorescence microscopy allow us to track chemical reactions at the single-molecule level. Single-molecule measurements make it possible to minimize the amount of sample needed for analysis and diagnosis. Signal amplification is often applied to ultralow-level biomarker detection. Polymerase chain reaction (PCR) is used to detect DNA/RNA, and enzyme-linked immunosorbent assay (ELISA) can sensitively probe antigen-antibody interactions. While these techniques are brilliant and will continue to be used in the future, single-molecule-level measurements would allow us to reduce the time and cost needed to amplify signals.The kinetics of chemical reactions have been studied mainly using ensemble-averaged methods. However, they can hardly distinguish time-dependent fluctuations and static heterogeneity of the kinetics. The information hidden in ensemble-averaged measurements would be extractable from a single-molecule experiment. Thus, single-molecule measurement would provide unique opportunities to investigate unrevealed phenomena and to elucidate the questions in chemistry, physics, and life sciences. Redox reaction, which is triggered by electron transfer, is among the most fundamental and ubiquitous chemical reactions. The redox reaction of a fluorescent molecule results in the formation of radical ions, which are normally nonemissive. In single-molecule-level measurements, the redox reaction causes the fluctuation of fluorescence signals between the bright ON-state and the dark OFF-state, in a phenomenon called blinking. The duration of the OFF-state (τ_OFF) corresponds to the lifetime of the radical ion state, and its reaction kinetics can be measured as 1/τ_OFF. Thus, the kinetics of redox reactions of fluorescent molecules can be accessed at the single-molecule level by monitoring fluorescence blinking. One of the key aspects of single-molecule analysis based on blinking is its robustness. A blinking signal with a certain regular pattern enables single fluorescent molecules to be distinguished and resolved from the random background signal.In this Account, we summarize the recent studies on the single-molecule measurement of redox reaction kinetics, with a focus on our group's recent progress. We first introduce the control of redox blinking to increase the photostability of fluorescent molecules. We then demonstrate the control of redox blinking, which allows us to detect target DNA by monitoring the function of a molecular beacon-type probe, and we investigate antigen-antibody interactions at the single-molecule level. By tracing the time-dependent changes in blinking patterns, redox blinking is shown to be adaptable to tracking the structural switching dynamics of RNA, the preQ₁ riboswitch. This Account ends with a discussion of our ongoing work on the control of fluorescent blinking. We also discuss the development of devices that allow single-molecule-level analysis in a high-throughput fashion.

Redefining the photo-stability of common fluorophores with triplet state quenchers: mechanistic insights and recent updates

Light microscopy can offer certain advantages over electron microscopy in terms of acquiring detailed insights into the biological/intra-cellular milieu. In recent years, with the development of new fluorescence imaging technologies, it has become extremely important to assess the role of designing appropriate fluorophores in acquiring desired biological information without encountering any untoward hitches. Over the years, external fluorophores have been prevalently used in fluorescence microscopy and single-molecule fluorescence microscopy-based studies. Photostable fluorogenic probes with high extinction coefficients and quantum yields, exhibiting minimum autofluorescence and photobleaching properties, are preferred in single-molecule microscopy as they can tolerate long-term laser exposure. Therefore, the development of triplet state quenchers and/or any other suitable new strategy to ensure the photo-stability of the fluorophores during long-term live cell imaging exercises is highly anticipated. In this feature article, various strategies for stabilizing fluorophores, including the mechanisms of TSQ-induced stabilization, have been thoroughly reviewed considering contemporary literature reports and applications.

Fluorescence-based monitoring of electronic state and ion exchange kinetics with FCS and related techniques: from T-jump measurements to fluorescence fluctuations

In this review, we give a historical view of how our research in the development and use of fluorescence correlation spectroscopy (FCS) and related techniques has its roots and how it originally evolved from the pioneering work of Manfred Eigen, his colleagues, and coworkers. Work on temperature-jump (T-jump) experiments, conducted almost 50 years ago, led on to the development of the FCS technique. The pioneering work in the 1970s, introducing and demonstrating the concept for FCS, in turn formed the basis for the breakthrough use of FCS more than 15 years later. FCS can be used for monitoring reaction kinetics, based on fluctuations at thermodynamic equilibrium, rather than on relaxation measurements following perturbations. In this review, we more specifically discuss FCS measurements on photodynamic, electronic state transitions in fluorophore molecules, and on proton exchange dynamics in solution and on biomembranes. In the latter case, FCS measurements have proven capable of casting new light on the mechanisms of proton exchange at biological membranes, of central importance to bioenergetics and signal transduction. Finally, we describe the transient-state (TRAST) spectroscopy/imaging technique, sharing features with both relaxation (T-jump) and equilibrium fluctuation (FCS) techniques. TRAST is broadly applicable for cellular and molecular studies, and we briefly outline how TRAST can provide unique information from fluorophore blinking kinetics, reflecting e.g., cellular metabolism, rare molecular encounters, and molecular stoichiometries.

Single-Molecule Monitoring of the Structural Switching Dynamics of Nucleic Acids through Controlling Fluorescence Blinking

Single-molecule fluorescence resonance energy transfer (smFRET) is a powerful tool to investigate the dynamics of biomolecular events in real time. However, it requires two fluorophores and can be applied only to dynamics that accompany large changes in distance between the molecules. Herein, we introduce a method for kinetic analysis based on control of fluorescence blinking (KACB), a general approach to investigate the dynamics of biomolecules by using a single fluorophore. By controlling the kinetics of the redox reaction the blinking kinetics or pattern can be controlled to be affected by microenvironmental changes around a fluorophore (rKACB), thereby enabling real-time single-molecule measurement of the structure-changing dynamics of nucleic acids.