Kinetics of Photoinduced Reactions at the Single‐Molecule Level: The KACB Method

Trans-cis isomerization kinetics of cyanine dyes reports on the folding states of exogeneous RNA G-quadruplexes in live cells

Guanine (G)-rich nucleic acids are prone to assemble into four-stranded structures, so-called G-quadruplexes. Abnormal GGGGCC repeat elongations, and in particular their folding states, are associated with amyotrophic lateral sclerosis and frontotemporal dementia. Due to methodological constraints however, most studies of G quadruplex structures are restricted to in vitro conditions. Evidence of how GGGGCC repeats form into G-quadruplexes in vivo is sparse. We devised a readout strategy, exploiting the sensitivity of trans-cis isomerization of cyanine dyes to local viscosity and sterical constraints. Thereby, folding states of cyanine-labeled RNA, and in particular G-quadruplexes, can be identified in a sensitive manner. The isomerization kinetics, monitored via fluorescence blinking generated upon transitions between a fluorescent trans isomer and a non-fluorescent cis isomer, was first characterized for RNA with GGGGCC repeats in aqueous solution using fluorescence correlation spectroscopy and transient state (TRAST) monitoring. With TRAST, monitoring the isomerization kinetics from how the average fluorescence intensity varies with laser excitation modulation characteristics, we could then detect folding states of fluorescently tagged RNA introduced into live cells.

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 Peptide Identification Using Fluorescence Blinking Fingerprints

The ability to identify peptides with single-molecule sensitivity would lead to next-generation proteomics methods for basic research and clinical applications. Existing single-molecule peptide sequencing methods can read some amino acid sequences, but they are limited in their ability to distinguish between similar amino acids or post-translational modifications. Here, we demonstrate that the fluorescence intermittency of a peptide labeled with a spontaneously blinking fluorophore contains information about the structure of the peptide. Using a deep learning algorithm, this single-molecule blinking pattern can be used to identify the peptide. This method can distinguish between peptides with different sequences, peptides with the same sequence but different phosphorylation patterns, and even peptides that differ only by the presence of epimerized residues. This study builds the foundation for a targeted proteomics method with single-molecule sensitivity.

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.