Probing the Charge-Transfer Dynamics in DNA at the Single-Molecule Level

Polymerization-Mediated Through-Space Charge Transfer: An Emerging Strategy for Light-Emitting Materials

Through-space charge transfer (TSCT) has attracted increasing attention owing to its great potential in designing efficient light-emitting molecules and polymers. Complementary to through-bond charge transfer and Förster resonance energy transfer, TSCT offers an alternative approach for the manipulation of molecular fluorescence. Recently, the synergy between TSCT and polymer systems through polymerization-mediated charge transfer has fostered the advancements of innovative light-emitting functional materials featuring thermally activated delayed fluorescence and/or aggregation-induced emission. This perspective highlights the significant progress in tailoring emission properties through structural engineering of donor and acceptor groups within polymeric systems, leveraging the TSCT mechanism. This strategy has transcended the limitations of traditional charge transfer systems with its tolerance to extended donor-acceptor distance, paving the way for novel applications beyond organic light-emitting diodes. The discussion concludes with a forward-looking analysis of potential future research trajectories in the field of polymerization-mediated charge transfer for developing next-generation light-emitting materials.

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.

G-Tetrad-Selective Ligand Binding Kinetics in G-Quadruplex DNA Probed with Fluorescence Correlation Spectroscopy

Probing the kinetics of ligand binding to biomolecules is of paramount interest in biology and pharmacology. Measurements of such kinetic processes provide information on the rate-determining steps that control the binding affinity of ligands to biomolecules, thereby predicting the mechanism of the molecular interaction. In this context, ligand binding to G-quadruplex DNA (GqDNA) structures has attracted tremendous attention primarily because of their use in possible anticancer therapy. Although a large number of G-quadruplex-specific ligands have been proposed, probing the kinetics of G-tetrad-selective binding of (multiple) ligands within a G-quadruplex DNA (GqDNA) structure remains challenging. Most of the earlier studies focused on the thermodynamics of ligand binding; however, the kinetics of ligand association and dissociation with GqDNA, particularly binding of multiple ligands within a GqDNA structure, have not been explored. Here, we propose a simple fluorescence correlation spectroscopy-based method that measures the G-tetrad-selective association and dissociation rates of ligands within a GqDNA structure by correlating the fluorescence fluctuations of a site-specific (5' or 3' end-labeled) fluorophore (Cy3) in GqDNA due to quenching of Cy3 fluorescence, induced by the ligand binding to the G-tetrads. We show that well-known GqDNA ligands, BRACO19, TMPyP4, Hoechst 33258, and Hoechst 33342, have G-tetrad-selective association and dissociation rates, which suggest site-dependent variation of free energy barriers for binding/unbinding of the ligands with GqDNA. We also show that the measured kinetic rates depend not only on the G-tetrad site (5' vs 3' end) but also on the ligand and GqDNA structures.

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.

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.

Triple helix conformation-specific blinking of Cy3 in DNA

We report that Cy3 undergoes triple helix conformation-specific blinking in DNA. Blinking patterns were affected by the stabilization of the Hoogsteen base-pair, suggesting that not only the presence but also the fluctuating behaviour of the triple helix can be monitored by the changes in the Cy3 blinking patterns.

A two-photon "turn-on" fluorescent probe based on carbon nanodots for imaging and selective biosensing of hydrogen sulfide in live cells and tissues

Determination of hydrogen sulfide (H2S) in live cells and tissues is still a challenge for evaluating the key roles that H2S plays in physiological and pathological processes. In this work, a "turn-on" two-photon fluorescent (TPF) sensor for H2S is developed, in which carbon nanodot (C-Dot) was employed as a two-photon fluorophore due to its large two-photon absorption cross-section (σ), and AE-TPEA-Cu(2+) complex [AE-TPEA = N-(2-aminoethyl)-N,N,N'-tris(pyridin-2-ylmethyl)ethane-1,2-diamine] was first designed as a specific receptor for H2S. The fluorescence of C-Dot conjugated with AE-TPEA (C-Dot-TPEA) was quenched upon the addition of Cu(2+). Then, the fluorescence was restored after the addition of H2S, because Cu(2+) could be released from TPEA binding site when H2S interacted with the Cu(2+) ion. The designed C-Dot-TPEA-Cu(2+) fluorescent sensor exhibited high specificity for H2S over biothiols, sulfur-containing compounds, reactive oxygen species (ROS), and other biological interferences. Meanwhile, a broad linear range from 5 μM to 100 μM was obtained and the detection limit was achieved to 0.7 μM. In addition, the C-Dot-based TPF probe exhibited bright two-photon fluorescence, favourable photostability against light illumination and pH change, and low cytotoxicity. Accordingly, the nanohybridized TPF sensor with high selectivity and sensitivity, as well as the fascinating properties of C-Dot themselves, successfully provided a new way for TPF imaging and biosensing of H2S in live cells and tissues. We believe this is the first report of TPF imaging and biosensing of H2S in live cells and tissues using a specially engineered C-Dot-based nanosystem.

Single Probe for Imaging and Biosensing of pH, Cu(2+) Ions, and pH/Cu(2+) in Live Cells with Ratiometric Fluorescence Signals

It is very essential to disentangle the complicated inter-relationship between pH and Cu in the signal transduction and homeostasis. To this end, reporters that can display distinct signals to pH and Cu are highly valuable. Unfortunately, there is still no report on the development of biosensors that can simultaneously respond to pH and Cu(2+), to the best of our knowledge. In this work, we developed a single fluorescent probe, AuNC@FITC@DEAC (AuNC, gold cluster; FITC, fluorescein isothiocyanate; DEAC, 7-diethylaminocoumarin-3-carboxylic acid), for biosensing of pH, Cu(2+), and pH/Cu(2+) with different ratiometric fluorescent signals. First, 2,2',2″-(2,2',2″-nitrilotris(ethane-2,1-diyl)tris((pyridin-2-yl-methyl)azanediyl))triethanethiol (TPAASH) was designed for specific recognition of Cu(2+), as well as for organic ligand to synthesize fluorescent AuNCs. Then, pH-sensitive molecule, FITC emitting at 518 nm, and inner reference molecule, DEAC with emission peak at 472 nm, were simultaneously conjugated on the surface of AuNCs emitting at 722 nm, thus, constructing a single fluorescent probe, AuNC@FITC@DEAC, to sensing pH, Cu(2+), and pH/Cu(2+) excited by 405 nm light. The developed probe exhibited high selectivity and accuracy for independent determination of pH and Cu(2+) against reactive oxygen species (ROS), other metal ions, amino acids, and even copper-containing proteins. The AuNC-based inorganic-organic probe with good cell-permeability and high biocompatibility was eventually applied in monitoring both pH and Cu(2+) and in understanding the interplaying roles of Cu(2+) and pH in live cells by ratiometric multicolor fluorescent imaging.

Blinking triggered by the change in the solvent accessibility of a fluorescent molecule

The more a fluorescent molecule is exposed to a solvent, the faster its triplet excited state is quenched by molecular oxygen.

Detection of single-nucleotide variations by monitoring the blinking of fluorescence induced by charge transfer in DNA

Charge transfer dynamics in DNA: Photo-induced charge separation and charge-recombination dynamics in DNA was assessed by monitoring the blinking of fluorescence. Single nucleotide variations, mismatch and one base deletion, were differentiated based on the length of the off-time of the blinking, which corresponds to the lifetime of the charge-separated state.

Dynamics in cytoplasm, nucleus, and lipid droplet of a live CHO cell: time-resolved confocal microscopy

Different regions of a single live Chinese hamster ovary (CHO) cell are probed by time-resolved confocal microscopy. We used coumarin 153 (C153) as a probe. The dye localizes in the cytoplasm, nucleus, and lipid droplets, as is clearly revealed by the image. The fluorescence correlation spectroscopy (FCS) data shows that the microviscosity of lipid droplets is ~34 ± 3 cP. The microviscosities of nucleus and cytoplasm are found to be 13 ± 1 and 14.5 ± 1 cP, respectively. The average solvation time (<τs>) in the lipid droplets (3600 ± 50 ps) is slower than that in the nucleus (<τs> = 750 ± 50 ps) and cytoplasm (<τs> = 1100 ± 50 ps). From the position of emission maxima of C153, the polarity of the nucleus is estimated to be similar to that of a mixture containing 26% DMSO in triacetin (η ~ 11.2 cP, ε ~ 26.2). The cytoplasm resembles a mixture of 18% DMSO in triacetin (η ∼ 12.6 cP, ε ∼ 21.9). The polarity of lipid droplets is less than that of pure triacetin (η ~ 21.7 cP, ε ~ 7.11).

Ultrafast fluorescence quenching dynamics of Atto655 in the presence of N-acetyltyrosine and N-acetyltryptophan in aqueous solution: proton-coupled electron transfer versus electron transfer

We studied the ultrafast fluorescence quenching dynamics of Atto655 in the presence of N-acetyltyrosine (AcTyr) and N-acetyltryptophan (AcTrp) in aqueous solution with femtosecond transient absorption spectroscopy. We found that the charge-transfer rate between Atto655 and AcTyr is about 240 times smaller than that between Atto655 and AcTrp. The pH value and D2O dependences of the excited-state decay kinetics of Atto655 in the presence of AcTyr and AcTrp reveal that the quenching of Atto655 fluorescence by AcTyr in aqueous solution is via a proton-coupled electron-transfer (PCET) process and that the quenching of Atto655 fluorescence by AcTrp in aqueous solution is via an electron-transfer process. With the version of the semiclassical Marcus ET theory, we derived that the electronic coupling constant for the PCET reaction between Atto655 and AcTyr in aqueous solution is 8.3 cm(-1), indicating that the PCET reaction between Atto655 and AcTyr in aqueous solution is nonadiabatic.

Plasmonic coupling and long-range transfer of an excitation along a DNA nanowire

We demonstrate an excitation transfer along a fluorescently labeled dsDNA nanowire over a length of several micrometers. Launching of the excitation is done by exciting a localized surface plasmon mode of a 40 nm silver nanoparticle by 800 nm femtosecond laser pulses via two-photon absorption. The plasmonic mode is subsequently coupled or transformed to excitation in the nanowire in contact with the particle and propagated along it, inducing bleaching of the dyes on its way. In situ as well as ex situ fluorescence microscopy is utilized to observe the phenomenon. In addition, transfer of the excitation along the nanowire to another nanoparticle over a separation of 5.7 μm was clearly observed. The nature of the excitation coupling and transfer could not be fully resolved here, but injection of an electron into the DNA from the excited nanoparticle and subsequent coupled transfer of charge (Dexter) and delocalized exciton (Frenkel) is the most probable mechanism. However, a direct plasmonic or optical coupling and energy transfer along the nanowire cannot be totally ruled out either. By further studies the observed phenomenon could be utilized in novel molecular systems, providing a long-needed communication method between molecular devices.

Nucleic acid fluorescent probes for biological sensing

Nucleic acid fluorescent probes are playing increasingly important roles in biological sensing in recent years. In addition to the conventional functions of single-stranded DNA/RNA to hybridize with their complementary strands, affinity nucleic acids (aptamers) with specific target binding properties have also been developed, which has greatly broadened the application of nucleic acid fluorescent probes to the detection of a large variety of analytes, including small molecules, proteins, ions, and even whole cells. Another chemical property of nucleic acids is to act as substrates for various nucleic acid enzymes. This property can be utilized not only to detect those enzymes and screen their inhibitors, but also employed to develop effective signal amplification systems, which implies extensive applications. This review mainly covers the biosensing methods based on the above three types of nucleic acid fluorescent probes. The most widely used intensity-based biosensing assays are covered first, including nucleic acid probe-based signal amplification methods. Then fluorescence lifetime, fluorescence anisotropy, and fluorescence correlation spectroscopy assays are introduced, respectively. As a rapidly developing field, fluorescence imaging approaches are also briefly summarized.

Solution, surface, and single molecule platforms for the study of DNA-mediated charge transport

The structural core of DNA, a continuous stack of aromatic heterocycles, the base pairs, which extends down the helical axis, gives rise to the fascinating electronic properties of this molecule that is so critical for life. Our laboratory and others have developed diverse experimental platforms to investigate the capacity of DNA to conduct charge, termed DNA-mediated charge transport (DNA CT). Here, we present an overview of DNA CT experiments in solution, on surfaces, and with single molecules that collectively provide a broad and consistent perspective on the essential characteristics of this chemistry. DNA CT can proceed over long molecular distances but is remarkably sensitive to perturbations in base pair stacking. We discuss how this foundation, built with data from diverse platforms, can be used both to inform a mechanistic description of DNA CT and to inspire the next platforms for its study: living organisms and molecular electronics.

Photoluminescence intermittency from single quantum dots to organic molecules: emerging themes

Recent experimental and theoretical studies of photoluminescence intermittency (PI) or “blinking” exhibited by single core/shell quantum dots and single organic luminophores are reviewed. For quantum dots, a discussion of early models describing the origin of PI in these materials and recent challenges to these models are presented. For organic luminophores the role of electron transfer, proton transfer and other photophysical processes in PI are discussed. Finally, new experimental and data analysis methods are outlined that promise to be instrumental in future discoveries regarding the origin(s) of PI exhibited by single emitters.

HOMO energy gap dependence of hole-transfer kinetics in DNA

DNA consists of two type of base-pairs, G-C and A-T, in which the highest occupied molecular orbital (HOMO) localizes on the purine bases G and A. While the hole transfer through consecutive Gs or As occurs faster than 10(9) s(-1), a significant drop in the hole transfer rate was observed for G-C and A-T mixed random sequences. In this study, by using various natural and artificial nucleobases having different HOMO levels, the effect of the HOMO-energy gap between bases (Δ(HOMO)) on the hole-transfer kinetics in DNA was investigated. The results demonstrated that the hole transfer rate can be increased by decreasing the Δ(HOMO) and can be finely tuned over 3 orders of magnitude by varying the Δ(HOMO).