Power-law-distributed dark states are the main pathway for photobleaching of single organic molecules

Symmetry-Breaking Charge Separation Mediated Triplet Population in a Perylenediimide Trimer at the Single-Molecule Level

Herein, we demonstrate triplet excited-state population in a conformationally rigid perylenediimide trimer (PDI-T) via intramolecular symmetry-breaking charge separation (SB-CS) at the single-molecule level. The single-molecule fluorescence intensity trajectories of PDI-T in nonpolar polystyrene matrix (ε = 2.60) exhibit prolonged fluorescence with infrequent dark states, representing the triplet and/or the charge transfer states. In contrast, in a poly(vinyl alcohol) matrix (ε = 7.80), erratic blinking dynamics resulting in low photon counts were observed, corroborating the feasibility of charge separation in a polar environment. In agreement with the single-molecule measurements, transient absorption spectroscopy of PDI-T reveals ultrafast SB-CS (τCS < 5 ps) in polar tetrahydrofuran (ε = 7.58) and acetone (ε = 20.70), with the population of the triplet excited-state through charge recombination. The current investigation shows the utility of rigid and weakly coupled molecular constructs in controlling triplet generation and SB-CS for potential applications in optoelectronic devices.

Insights into protein structure using cryogenic light microscopy

Fluorescence microscopy has witnessed many clever innovations in the last two decades, leading to new methods such as structured illumination and super-resolution microscopies. The attainable resolution in biological samples is, however, ultimately limited by residual motion within the sample or in the microscope setup. Thus, such experiments are typically performed on chemically fixed samples. Cryogenic light microscopy (Cryo-LM) has been investigated as an alternative, drawing on various preservation techniques developed for cryogenic electron microscopy (Cryo-EM). Moreover, this approach offers a powerful platform for correlative microscopy. Another key advantage of Cryo-LM is the strong reduction in photobleaching at low temperatures, facilitating the collection of orders of magnitude more photons from a single fluorophore. This results in much higher localization precision, leading to Angstrom resolution. In this review, we discuss the general development and progress of Cryo-LM with an emphasis on its application in harnessing structural information on proteins and protein complexes.

Symmetry-Breaking Charge Separation in a Chiral Bis(perylenediimide) Probed at Ensemble and Single-Molecule Levels

Chiral molecular assemblies exhibiting symmetry-breaking charge separation (SB-CS) are potential candidates for the development of chiral organic semiconductors. Herein, we explore the excited-state dynamics of a helically chiral perylenediimide bichromophore (Cy-PDI2) exhibiting SB-CS at the ensemble and single-molecule levels. Solvent polarity-tunable interchromophoric excitonic coupling in chiral Cy-PDI2 facilitates the interplay of SB-CS and excimer formation in the ensemble domain. Analogous to the excited-state dynamics of Cy-PDI2 at the ensemble level, single-molecule fluorescence lifetime traces of Cy-PDI2 depicted long-lived off-states characteristic of the radical ion pair-mediated dark states. The discrete electron transfer and charge separation dynamics in Cy-PDI2 at the single-molecule level are governed by the distinct influence of the local environment. The present study aims at understanding the fundamental excited-state dynamics in chiral organic bichromophores for designing efficient chiral organic semiconductors and applications toward charge transport materials.

Photostable fluorescent molecules on layered hexagonal boron nitride: Ideal single-photon sources at room temperature

Photoblinking and photobleaching are commonly encountered problems for single-photon sources. Numerous methods have been devised to suppress these two impediments; however, either the preparation procedures or the operating conditions are relatively harsh, making them difficult to apply to practical applications. Here, we reported giant suppression of both photoblinking and photobleaching of a single fluorescent molecule, terrylene, via the utilization of hexagonal boron nitride (h-BN) flakes as substrates. Experimentally, a much-prolonged survival time of terrylene has been determined, which can have a photostable emission over 2 h at room temperature under ambient atmospheres. Compared with single molecules on a SiO₂/Si substrate or glass coverslip, a more than 100-fold increase in the total number of photons collected from each terrylene on h-BN flakes has been demonstrated. We also proved that the photostability of terrylene molecules can be well maintained for more than 6 months even under ambient conditions without any further protection. Our results demonstrate that the utilization of h-BN flakes to suppress photoblinking and photobleaching of fluorescent molecules has promising applications in the production of high-quality single-photon sources at room temperature.

Pyrene-Benzimidazole Derivatives as Novel Blue Emitters for OLEDs

Three novel small organic heterocyclic compounds: 2-(1,2-diphenyl)-1H-benzimidazole-7-tert-butylpyrene (compound A), 1,3-di(1,2-diphenyl)-1H-benzimidazole-7-tert-butylpyrene (compound B), and 1,3,6,8-tetra(1,2-diphenyl)-1H-benzimidazolepyrene (compound C) were synthesized and characterized for possible applications as blue OLED emitters. The specific molecular design targeted decreasing intermolecular aggregation and disrupting crystallinity in the solid-state, in order to reduce dye aggregation, and thus obtain efficient pure blue photo- and electroluminescence. Accordingly, the new compounds displayed reasonably high spectral purity in both solution- and solid-states with average CIE coordinates of (0.160 ± 0.005, 0.029 ± 0.009) in solution and (0.152 ± 0.007, 0.126 ± 0.005) in solid-state. These compounds showed a systematic decrease in degree of crystallinity and intermolecular aggregation due to increasing steric hindrance, as revealed using powder X-ray diffraction analysis and spectroscopic studies. An organic light-emitting diode (OLED) prototype fabricated using compound B as the non-doped emissive layer displayed an external quantum efficiency (EQE) of 0.35 (±0.04)% and luminance 100 (±6) cd m⁻² at 5.5 V with an essentially pure blue electroluminescence corresponding to CIE coordinates of (0.1482, 0.1300). The highest EQE observed from this OLED prototype was 4.3 (±0.3)% at 3.5 V, and the highest luminance of 290 (±10) cd m⁻² at 7.5 V. These values were found comparable to characteristics of the best pure blue OLED devices based on simple fluorescent small-molecule organic chromophores.

Molecular layer deposition of photoactive metal-naphthalene hybrid thin films

We here report on photoactive organic-inorganic hybrid thin films prepared by the molecular layer deposition (MLD) method. The new series of hybrid films deposited using 2,6-naphthalenedicarboxylic acid (2,6-NDC) and either hafnium chloride (HfCl₄), yttrium tetramethylheptanedionate (Y(thd)₃) or titanium chloride (TiCl₄) were compared with the known zirconium chloride (ZrCl₄) based system. All metal-naphthalene films are amorphous as-deposited and show self-saturating growth as expected for an ideal MLD process with varied growth rates depending on the choice of metal precursor. The growth was studied in situ using quartz crystal microbalance (QCM) and the films were further characterised using spectroscopic ellipsometry (SE), Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), and UV-Vis and photoluminescence (PL) spectroscopy to obtain information on their physicochemical properties. The hybrid thin films display intense blue photoluminescence, except for the Ti-organic complex in which titanium clusters were found to be an effective PL quencher for the organic linker. We demonstrate how the optical properties of the films depend on the choice of metal component to make a foundation for further studies on these types of organic-inorganic hybrid materials for applications as photoactive agents.

Pyrenylpyridines: Sky-Blue Emitters for Organic Light-Emitting Diodes

A novel sky-blue-emitting tripyrenylpyridine derivative, 2,4,6-tri(1-pyrenyl)pyridine (2,4,6-TPP), has been synthesized using a Suzuki coupling reaction and compared with three previously reported isomeric dipyrenylpyridine (DPP) analogues (2,4-di(1-pyrenyl)pyridine (2,4-DPP), 2,6-di(1-pyrenyl)pyridine (2,6-DPP), and 3,5-di(1-pyrenyl)pyridine (3,5-DPP)). As revealed by single-crystal X-ray analysis and computational simulations, all compounds possess highly twisted conformations in the solid state with interpyrene torsional angles of 42.3°-57.2°. These solid-state conformations and packing variations of pyrenylpyridines could be correlated to observed variations in physical characteristics such as photo/thermal stability and spectral properties, but showed only marginal influence on electrochemical properties. The novel derivative, 2,4,6-TPP, exhibited the lowest degree of crystallinity as revealed by powder X-ray diffraction analysis and formed amorphous thin films as verified using grazing-incidence wide-angle X-ray scattering. This compound also showed high thermal/photo stability relative to its disubstituted analogues (DPPs). Thus, a nondoped organic light-emitting diode (OLED) prototype was fabricated using 2,4,6-TPP as the emissive layer, which displayed a sky-blue electroluminescence with Commission Internationale de L'Eclairage (CIE) coordinates of (0.18, 0.34). This OLED prototype achieved a maximum external quantum efficiency of 6.0 ± 1.2% at 5 V. The relatively high efficiency for this simple-architecture device reflects a good balance of electron and hole transporting ability of 2,4,6-TPP along with efficient exciton formation in this material and indicates its promise as an emitting material for design of blue OLED devices.

Emergence of multiple fluorophores in individual cesium lead bromide nanocrystals

Cesium-based perovskite nanocrystals (PNCs) possess alluring optical and electronic properties via compositional and structural versatility, tunable bandgap, high photoluminescence quantum yield and facile chemical synthesis. Despite the recent progress, origins of the photoluminescence emission in various types of PNCs remains unclear. Here, we study the photon emission from individual three-dimensional and zero-dimensional cesium lead bromide PNCs. Using photon antibunching and lifetime measurements, we demonstrate that emission statistics of both type of PNCs are akin to individual molecular fluorophores, rather than traditional semiconductor quantum dots. Aided by density functional modelling, we provide compelling evidence that green emission in zero-dimensional PNCs stems from exciton recombination at bromide vacancy centres within lead-halide octahedra, unrelated to external confinement. These findings provide key information about the nature of defect formation and the origin of emission in cesium lead halide perovskite materials, which foster their utilization in the emerging optoelectronic applications.

Inorganic perovskite nanocrystals attract lots of research attention but the origin of their photoluminescence remains debatable. Here Zhang et al. show that behavior of both CsPbBr₃ and Cs₄PbBr₆ nanocrystals is like individual molecular fluorophores and independent of the structural dimensionalities.

Practical Considerations in Particle and Object Tracking and Analysis

The rapid advancement of live-cell imaging technologies has enabled biologists to generate high-dimensional data to follow biological movement at the microscopic level. Yet, the "perceived" ease of use of modern microscopes has led to challenges whereby sub-optimal data are commonly generated that cannot support quantitative tracking and analysis as a result of various ill-advised decisions made during image acquisition. Even optimally acquired images often require further optimization through digital processing before they can be analyzed. In writing this article, we presume our target audience to be biologists with a foundational understanding of digital image acquisition and processing, who are seeking to understand the essential steps for particle/object tracking experiments. It is with this targeted readership in mind that we review the basic principles of image-processing techniques as well as analysis strategies commonly used for tracking experiments. We conclude this technical survey with a discussion of how movement behavior can be mathematically modeled and described. © 2019 by John Wiley & Sons, Inc.

Unraveling the Excited-State Dynamics of Eosin Y Photosensitizers Using Single-Molecule Spectroscopy

The intersystem crossing and dispersive electron-transfer dynamics of eosin Y (EY) photosensitizers are probed using single-molecule microscopy. The blinking dynamics of EY on glass are quantified by constructing cumulative distribution functions of emissive ("on") and nonemissive ("off") events. Maximum likelihood estimation (MLE) and goodness-of-fit tests based on the Kolmogorov-Smirnov (KS) statistic are used to establish the best fit to the blinking data and differentiate among competitive photophysical processes. The on-time probability distributions for EY in N₂ and air are power-law distributed after ∼1 s, with fit parameters that are significantly modified upon exposure to oxygen. By extending the statistically principled MLE/KS approach to include an onset time for log-normal behavior, we demonstrate that the off-time distribution for EY in N₂ is best fit to a combination of exponential and log-normal functions. The corresponding distribution for EY in air is best fit to a log-normal function alone. Furthermore, power law and log-normal distributions are observed for an individual molecule in air, consistent with dynamic fluctuations in the rate constant for dark-state population and depopulation. These observations support the interpretation that dispersive electron transfer (i.e., the Albery model) from the first excited singlet state (S₁) of EY to trap states on glass is predominately responsible for blinking in oxic conditions. In anoxic environment, both triplet-state blinking and dispersive electron transfer from S₁ and the excited triplet state (T₁) contribute to the excited-state dynamics of EY.

Photo-Induced Depletion of Binding Sites in DNA-PAINT Microscopy

The limited photon budget of fluorescent dyes is the main limitation for localization precision in localization-based super-resolution microscopy. Points accumulation for imaging in nanoscale topography (PAINT)-based techniques use the reversible binding of fluorophores and can sample a single binding site multiple times, thus elegantly circumventing the photon budget limitation. With DNA-based PAINT (DNA-PAINT), resolutions down to a few nanometers have been reached on DNA-origami nanostructures. However, for long acquisition times, we find a photo-induced depletion of binding sites in DNA-PAINT microscopy that ultimately limits the quality of the rendered images. Here we systematically investigate the loss of binding sites in DNA-PAINT imaging and support the observations with measurements of DNA hybridization kinetics via surface-integrated fluorescence correlation spectroscopy (SI-FCS). We do not only show that the depletion of binding sites is clearly photo-induced, but also provide evidence that it is mainly caused by dye-induced generation of reactive oxygen species (ROS). We evaluate two possible strategies to reduce the depletion of binding sites: By addition of oxygen scavenging reagents, and by the positioning of the fluorescent dye at a larger distance from the binding site.

Spectroscopic and Device Aspects of Nanocrystal Quantum Dots

The field of nanocrystal quantum dots (QDs) is already more than 30 years old, and yet continuing interest in these structures is driven by both the fascinating physics emerging from strong quantum confinement of electronic excitations, as well as a large number of prospective applications that could benefit from the tunable properties and amenability toward solution-based processing of these materials. The focus of this review is on recent advances in nanocrystal research related to applications of QD materials in lasing, light-emitting diodes (LEDs), and solar energy conversion. A specific underlying theme is innovative concepts for tuning the properties of QDs beyond what is possible via traditional size manipulation, particularly through heterostructuring. Examples of such advanced control of nanocrystal functionalities include the following: interface engineering for suppressing Auger recombination in the context of QD LEDs and lasers; Stokes-shift engineering for applications in large-area luminescent solar concentrators; and control of intraband relaxation for enhanced carrier multiplication in advanced QD photovoltaics. We examine the considerable recent progress on these multiple fronts of nanocrystal research, which has resulted in the first commercialized QD technologies. These successes explain the continuing appeal of this field to a broad community of scientists and engineers, which in turn ensures even more exciting results to come from future exploration of this fascinating class of materials.

Design and validation of a new ratiometric intracellular pH imaging probe using lanthanide-doped upconverting nanoparticles

A ratiometric probe based on upconversion nanoparticles modified with a pH sensitive moiety for the quantitative imaging of pH at the subcellular level in living cells.

Tracing Single Electrons in a Disordered Polymer Film at Room Temperature

The transport of charges lies at the heart of essentially all modern (opto-) electronic devices. Although inorganic semiconductors built the basis for current technologies, organic materials have become increasingly important in recent years. However, organic matter is often highly disordered, which directly impacts the charge carrier dynamics. To understand and optimize device performance, detailed knowledge of the transport mechanisms of charge carriers in disordered matter is therefore of crucial importance. Here we report on the observation of the motion of single electrons within a disordered polymer film at room temperature, using single organic chromophores as probe molecules. The migration of a single electron gives rise to a varying electric field in its vicinity, which is registered via a shift of the emission spectra (Stark shift) of a chromophore. The spectral shifts allow us to determine the electron mobility and reveal for each nanoenvironment a distinct number of different possible electron-transfer pathways within the rugged energy landscape of the disordered polymer matrix.

Conformational Memory of a Protein Revealed by Single-Molecule Spectroscopy

Proteins are supramolecular machines that carry out a wide range of different functions, many of which require flexibility. Up until now spontaneous conformational fluctuations of proteins have always been assumed to reflect a stochastic random process. However, if changing between different conformational states was random, then it would be difficult to understand how conformational control of protein function could have evolved. Here we demonstrate that a single protein can show conformational memory. This is exactly the process that can facilitate the evolution of control of switching between two conformational states that can then be used to regulate protein function.

Multi-Level, Multi Time-Scale Fluorescence Intermittency of Photosynthetic LH2 Complexes: A Precursor of Non-Photochemical Quenching?

The light harvesting complex LH2 is a chromoprotein that is an ideal system for studying protein dynamics via the spectral fluctuations of the emission of its intrinsic chromophores. We have immobilized these complexes in a polymer film and studied the fluctuations of the fluorescence intensity from individual complexes over 9 orders of magnitude in time. Combining time-tagged detection of single photons with a change-point analysis has allowed the unambigeous identification of the various intensity levels due to the huge statistical basis of the data set. We propose that the observed intensity level fluctuations reflect conformational changes of the protein backbone that might be a precursor of the mechanism from which nonphotochemical quenching of higher plants has evolved.

In Search for the Best Environment for Single Molecule Studies: Photostability of Single Terrylenediimide Molecules in Various Polymer Matrices

Photobleaching is the main limiting factor in single molecule studies by optical techniques. We investigated the dependence of photostability of terrylene diimide (TDI) derivative on its environment using confocal fluorescence microscopy. Seven different polymers were tested. Depending on the matrix, photobleaching quantum yields vary by 2 orders of magnitude. Their values correlate with parameters characterizing oxygen mobility in polymers: diffusion coefficient and permeability. Poly(vinyl chloride) (PVC) and poly(methyl methacrylate) (PMMA) exhibit the lowest photodestruction quantum yields. Additional enhancement of photostability can be achieved by aging of PVC or by flushing the sample with nitrogen, which confirms the involvement of oxygen in photodestruction. Different character of the time traces of the intensity of emission from single TDI molecules is observed for different polymer matrices, ranging from intense blinking in the least stable polycarbonate, to practically no blinking in the most stable PVC. These results suggest a photodegradation mechanism involving self-sensitized photooxidation in oxygen complexes of TDI.

Role of photophysics processes in thermal lens spectroscopy of fluids: a theoretical study

Photophysics processes are ubiquitous in nature and difficult to be quantitatively characterized by conventional spectroscopy. Alternatively, pump-probe methods have been widely applied to study these complex processes. In this context, the thermal lens technique is a precise spectroscopic tool for material characterization and presents a wide range of applications in chemical analysis. Here, we present an all numerical approach to analyze the dynamics of photophysics processes and to identify the role of individual contributions of photoreaction and mass diffusion in the thermal lens experiments. The results are essential for a proper understanding of the dominant physical mechanisms in laser-induced photodegradation, which allow precise data analysis of the effects in photosensitive fluids.

Stepwise decrease of fluorescence versus sequential photobleaching in a single multichromophoric system

For individual molecules from the newly synthesized calix[4]arene tethered perylene bisimide (PBI) trimer, we studied the emitted fluorescence intensity as a function of time. Owing to the zigzag arrangement of PBI dyes in these trimers, the polarization state of the emission provides directly information about the emitting subunit within the trimer. Interestingly, we observed emission from all neutral subunits within a trimer rather than exclusively from the subunit with the lowest site energy. This can be understood in terms of thermally activated uphill energy transfer that repopulates the higher energetic chromophores. Together with the simultaneously recorded polarization-resolved emission spectra, this reveals that the emission from a multichromophoric system is governed by a complex interplay between the temporal variations of the photophysical parameters of the subunits, bidirectional hopping processes within the trimer, and unavoidable photobleaching. Moreover, it is demonstrated that the typically observed stepwise decrease of the signal from a multichromophoric system does not necessarily reflect sequential bleaching of the individual chromophores within the macromolecule.

Heterogeneity in Single-Molecule Observables in the Study of Supercooled Liquids

Bulk approaches to studying heterogeneous systems obscure important details, as they report average behavior rather than the distribution of behaviors in such environments. Small-molecule and polymeric supercooled liquids, which display heterogeneity in their dynamics without an underlying structural heterogeneity that sets those dynamics, are important constituents of this category of condensed matter systems. A variety of approaches have been devised to unravel ensemble averaging in supercooled liquids. This review focuses on the ultimate subensemble approach, single-molecule measurements, as they have been applied to the study of supercooled liquids. We detail how three key experimental observables (single-molecule probe rotation, translation, and fluorescence lifetime) have been employed to provide detail on dynamic heterogeneity in supercooled liquids. Special attention is given to the potential for, but also the challenges in, discriminating spatial and temporal heterogeneity and detailing the length scales and timescales of heterogeneity in these systems.

Photophysics of fluorescent probes for single-molecule biophysics and super-resolution imaging

Single-molecule fluorescence spectroscopy and super-resolution microscopy are important elements of the ongoing technical revolution to reveal biochemical and cellular processes in unprecedented clarity and precision. Demands placed on the photophysical properties of the fluorophores are stringent and drive the choice of appropriate probes. Such fluorophores are not simple light bulbs of a certain color and brightness but instead have their own "personalities" regarding spectroscopic parameters, redox properties, size, water solubility, photostability, and several other factors. Here, we review the photophysics of fluorescent probes, both organic fluorophores and fluorescent proteins, used in applications such as particle tracking, single-molecule FRET, stoichiometry determination, and super-resolution imaging. Of particular interest is the thiol-induced blinking of Cy5, a curse for single-molecule biophysical studies that was later overcome using Trolox through a reducing/oxidizing system but a boon for super-resolution imaging owing to the controllable photoswitching. Understanding photophysics is critical in the design and interpretation of single-molecule experiments.

Quantitative photo activated localization microscopy: unraveling the effects of photoblinking

In this work we discuss how to use photophysical information for improved quantitative measurements using Photo Activated Localization Microscopy (PALM) imaging. We introduce a method that reliably estimates the number of photoblinking molecules present in a biological sample and gives a robust way to quantify proteins at the single-cell level from PALM images. We apply this method to determine the amount of β2 adrenergic receptor, a prototypical G Protein Coupled Receptor, expressed on the plasma membrane of HeLa cells.

Photounbinding of calmodulin from a family of CaM binding peptides

Background

Recent studies have shown that fluorescently labeled antibodies can be dissociated from their antigen by illumination with laser light. The mechanism responsible for the photounbinding effect, however, remains elusive. Here, we give important insights into the mechanism of photounbinding and show that the effect is not restricted to antibody/antigen binding.

Methodology/Principal Findings

We present studies of the photounbinding of labeled calmodulin (CaM) from a set of CaM-binding peptides with different affinities to CaM after one- and two-photon excitation. We found that the photounbinding effect becomes stronger with increasing binding affinity. Our observation that photounbinding can be influenced by using free radical scavengers, that it does not occur with either unlabeled protein or non-fluorescent quencher dyes, and that it becomes evident shortly after or with photobleaching suggest that photounbinding and photobleaching are closely linked.

Conclusions/Significance

The experimental results exclude surface effects, or heating by laser irradiation as potential causes of photounbinding. Our data suggest that free radicals formed through photobleaching may cause a conformational change of the CaM which lowers their binding affinity with the peptide or its respective binding partner.

Observation and control of blinking nitrogen-vacancy centres in discrete nanodiamonds

Nitrogen-vacancy colour centres in diamond can undergo strong, spin-sensitive optical transitions under ambient conditions, which makes them attractive for applications in quantum optics, nanoscale magnetometry and biolabelling. Although nitrogen-vacancy centres have been observed in aggregated detonation nanodiamonds and milled nanodiamonds, they have not been observed in very small isolated nanodiamonds. Here, we report the first direct observation of nitrogen-vacancy centres in discrete 5-nm nanodiamonds at room temperature, including evidence for intermittency in the luminescence (blinking) from the nanodiamonds. We also show that it is possible to control this blinking by modifying the surface of the nanodiamonds.

Strong field line shapes and photon statistics from a single molecule under anomalous noise

We revisit the line-shape theory of a single molecule with anomalous stochastic spectral diffusion. Waiting time profiles for bath induced spectral jumps in the ground and excited states become different when a molecule, probed by continuous-wave laser field, reaches the steady state. This effect is studied for the stationary dichotomic continuous-time-random-walk spectral diffusion of a single two-level chromophore with power-law distributions of waiting times. Correlated waiting time distributions, line shapes, two-point fluorescence correlation function, and Mandel Q parameter are calculated for arbitrary magnitude of laser field. We extended previous weak field results and examined the breakdown of the central limit theorem in photon statistics, indicated by asymptotic power-law growth of Mandel Q parameter. Frequency profile of the Mandel Q parameter identifies the peaks of spectrum, which are related to anomalous spectral diffusion dynamics.

Structural basis for the phototoxicity of the fluorescent protein KillerRed

The red fluorescent protein KillerRed, engineered from the hydrozoan chromoprotein anm2CP, has been reported to induce strong cytotoxicity through the chromophore assisted light inactivation (CALI) effect. Here, we present the X-ray structures of KillerRed in its native and bleached states. A long water-filled channel is revealed, connecting the methylene bridge of the chromophore to the solvent. This channel facilitates the transit of oxygen and of reactive oxygen species (ROS) formed by reaction with the excited chromophore. The functional roles of key mutations used to produce KillerRed are discussed, strong chromophore distortions in the bleached state are revealed, and mechanisms for ROS production and self protection are proposed. The presence of a partially mature, photo-resistant, green-emitting state is characterized, which accounts for enhanced CALI by "pre-bleached" KillerRed.

Optically modulated fluorophores for selective fluorescence signal recovery

Fluorescence imaging in biological sciences is hindered by significant depth-dependent signal attenuation and highly fluorescent backgrounds. We have developed optically modulated near-IR-emitting few-atom Ag nanodots that are selectively and dynamically photobrightened upon simultaneous excitation with a secondary laser, enabling high-sensitivity image extraction to reveal only the demodulated fluorophores. Image demodulation is demonstrated in high-background environments to extract weak signals from completely obscuring background emission.

Single-molecule photophysics of oxazines on DNA and its application in a FRET switch

The role and interplay of triplet states and radical ion states in single-molecule fluorescence spectroscopy has recently been elaborated providing us with new insights into the photophysics and photobleaching pathways of fluorescent dyes. Adjustment of fluorophore redox properties in combination with specific redox properties of the environment, i.e. addition of reducing and oxidizing agents, allows control of the emission properties: it has become possible to suppress blinking and to also induce blinking in single-molecule fluorescence transient by selectively opening and closing specific excited state pathways. Induced blinking is, for example, of interest for super-resolution fluorescence microscopy based on the subsequent localization of single fluorophores. For oxazines this control even allowed the separation of the influence of reducing and oxidizing agents, enabling switching the fluorescence of single fluorophores. Here, we study the factors that contribute to the kinetics of the photophysical pathways more closely with a focus on the photophysics of the oxazine ATTO655 labeled to DNA. Our data show that the oxazine ATTO655 interacts with DNA, shielding it efficiently from reagents in solution. Besides redox reactions, the pH also influences the blinking kinetics and especially the off-times. Moreover, we present the extension of ATTO655 as a single-molecule redox sensor to a ratiometric fluorescence-resonance-energy-transfer based sensor. Therefore, we designed FRET probes that showed the highest possible contrast of FRET changes and demonstrate reversible FRET-switching of Cy3B-ATTO655 DNA constructs.

Power spectra for both interrupted and perennial aging processes

We study the power spectrum of a random telegraphic noise with the distribution density of waiting times tau given by psi(tau) proportional to 1tau(mu), with mu approximately 2. The condition mu<2 violates the ergodic hypothesis, and in this case the adoption of Wiener-Khintchine (WK) theorem for the spectrum evaluation requires some caution. We study this problem theoretically and numerically and we prove that the power spectrum obeys the prescription S(f)=Kf(eta), with eta=3-mu, namely, the 1f noise lives at border between the ergodic mu>2 and nonergodic mu<2 condition. We study sequences with the finite length L. In the case mu<2 the adoption of WK theorem is made legitimate by two different kinds of truncation effects: the physical and observation-induced effect. In the former case psi(tau) is truncated at tau approximately T(max) and L>>T(max) ensures the condition of interrupted aging. In this case, we find that K is a number independent of L. The latter case, L<<T(max), is more challenging. It was already solved by Margolin and Barkai, who used time asymptotic arguments based on the ergodicity breakdown and obtained K proportional to 1L(2-mu), proving that the out-of-equilibrium nature of the condition mu<2 is signaled by the decrease of K with the increase of L. We use a generalized version of the Onsager principle that leads us to the same conclusion from a somewhat more extended view valid also for the transient out-of-equilibrium case of mu>2. We do not limit our treatment to the time asymptotic case, thereby producing a prediction that accounts for the transition from the 1f(eta) to the 1f(2) regime, recently observed in an experiment on blinking quantum dots. Our theoretical approach allows us to discuss some other recent experiments on molecular intermittent fluorescence and affords indications that should help to assess whether the spectrum is determined by the L<<T(max) or by the L>>T(max) condition.