Fluorescence Redox Blinking Adaptable to Structural Analysis of Nucleic Acids

Programmed Control of Fluorescence Blinking Patterns based on Electron Transfer in DNA

Fluorescence imaging uses changes in the fluorescence intensity and emission wavelength to analyze multiple targets simultaneously. To increase the number of targets that can be identified simultaneously, fluorescence blinking can be used as an additional parameter. To understand and eventually control blinking, we used DNA as a platform to elucidate the processes of electron transfer (ET) leading to blinking, down to the rate constants. With a fixed ET distance, various blinking patterns were observed depending on the DNA sequence between the donor and acceptor units of the DNA platform. The blinking pattern was successfully described with a combination of ET rate constants. Therefore, molecules with various blinking patterns can be developed by tuning ET. It is expected that the number of targets that can be analyzed simultaneously will increase by the power of the number of blinking patterns.

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.