Single‐Molecule Photoactivation FRET: A General and Easy‐To‐Implement Approach To Break the Concentration Barrier

Single‐molecule fluorescence resonance energy transfer (sm‐FRET) has become a widely used tool to reveal dynamic processes and molecule mechanisms hidden under ensemble measurements. However, the upper limit of fluorescent species used in sm‐FRET is still orders of magnitude lower than the association affinity of many biological processes under physiological conditions. Herein, we introduce single‐molecule photoactivation FRET (sm‐PAFRET), a general approach to break the concentration barrier by using photoactivatable fluorophores as donors. We demonstrate sm‐PAFRET by capturing transient FRET states and revealing new reaction pathways during translation using μm fluorophore labeled species, which is 2–3 orders of magnitude higher than commonly used in sm‐FRET measurements. sm‐PAFRET serves as an easy‐to‐implement tool to lift the concentration barrier and discover new molecular dynamic processes and mechanisms under physiological concentrations.     

X‐ray Excited Optical Fluorescence and Diffraction Imaging of Reactivity and Crystallinity in a Zeolite Crystal: Crystallography and Molecular Spectroscopy in One

Structure–activity relationships in heterogeneous catalysis are challenging to be measured on a single‐particle level. For the first time, one X‐ray beam is used to determine the crystallographic structure and reactivity of a single zeolite crystal. The method generates μm‐resolved X‐ray diffraction (μ‐XRD) and X‐ray excited optical fluorescence (μ‐XEOF) maps of the crystallinity and Brønsted reactivity of a zeolite crystal previously reacted with a styrene probe molecule. The local gradients in chemical reactivity (derived from μ‐XEOF) were correlated with local crystallinity and framework Al content, determined by μ‐XRD. Two distinctly different types of fluorescent species formed selectively, depending on the local zeolite crystallinity. The results illustrate the potential of this approach to resolve the crystallographic structure of a porous material and its reactivity in one experiment via X‐ray induced fluorescence of organic molecules formed at the reactive centers.     

Gold Nanorod Enhanced Fluorescence Enables Single‐Molecule Electrochemistry of Methylene Blue

Redox reactions are central to energy conversion and life metabolism. Herein we present electrochemical measurements with fluorescent readout of the redox‐sensitive dye Methylene Blue (MB), at the single‐molecule (SM) level. To overcome the low fluorescence quantum yield of MB we enhanced fluorescence by using individual gold nanorods to achieve the required sensitivity. By measuring the same molecule at different electrochemical potentials we determined the mid‐point potential of each single molecule through its redox‐induced fluorescence blinking dynamics.     

Addressing the Requirements of High‐Sensitivity Single‐Molecule Imaging of Low‐Copy‐Number Proteins in Bacteria

Single‐molecule fluorescence super‐resolution imaging and tracking provide nanometer‐scale information about subcellular protein positions and dynamics. These single‐molecule imaging experiments can be very powerful, but they are best suited to high‐copy number proteins where many measurements can be made sequentially in each cell. We describe artifacts associated with the challenge of imaging a protein expressed in only a few copies per cell. We image live Bacillus subtilis in a fluorescence microscope, and demonstrate that under standard single‐molecule imaging conditions, unlabeled B. subtilis cells display punctate red fluorescent spots indistinguishable from the few PAmCherry fluorescent protein single molecules under investigation. All Bacillus species investigated were strongly affected by this artifact, whereas we did not find a significant number of these background sources in two other species we investigated, Enterococcus faecalis and Escherichia coli. With single‐molecule resolution, we characterize the number, spatial distribution, and intensities of these impurity spots.     

Optische Einzelmolekülspektroskopie. Einblicke in den Nanokosmos

Single‐molecule fluorescence spectroscopy evolved to a variety of tools to investigate molecular dynamics in thermodynamic equilibrium and to reveal subpopulations in heterogeneous molecular distributions which usually remain hidden in bulk experiments. Applications of single‐molecule experiments range from life sciences and material sciences to photo‐physics and photo‐chemistry. Some of these research fields, like chemical catalysis, have just recently been entered. This article summarizes major principles of single‐molecule fluorescence spectroscopy and gives an overview on some important applications up to the development of novel microscopic techniques with nanometer resolution.     

SLAP: Small Labeling Pair for Single‐Molecule Super‐Resolution Imaging

Protein labeling with synthetic fluorescent probes is a key technology in chemical biology and biomedical research. A sensitive and efficient modular labeling approach (SLAP) was developed on the basis of a synthetic small‐molecule recognition unit (Ni‐trisNTA) and the genetically encoded minimal protein His_6‐10‐tag. High‐density protein tracing by SLAP was demonstrated. This technique allows super‐resolution fluorescence imaging and fulfills the necessary sampling criteria for single‐molecule localization‐based imaging techniques. It avoids masking by large probes, for example, antibodies, and supplies sensitive, precise, and robust size analysis of protein clusters (nanodomains).     

FRET Enhancement in Aluminum Zero‐Mode Waveguides

Zero‐mode waveguides (ZMWs) can confine light into attoliter volumes, which enables single molecule fluorescence experiments at physiological micromolar concentrations. Of the fluorescence spectroscopy techniques that can be enhanced by ZMWs, Förster resonance energy transfer (FRET) is one of the most widely used in life sciences. Combining zero‐mode waveguides with FRET provides new opportunities to investigate biochemical structures or follow interaction dynamics at micromolar concentrations with single‐molecule resolution. However, prior to any quantitative FRET analysis on biological samples, it is crucial to establish first the influence of the ZMW on the FRET process. Here, we quantify the FRET rates and efficiencies between individual donor–acceptor fluorophore pairs that diffuse into aluminum zero‐mode waveguides. Aluminum ZMWs are important structures thanks to their commercial availability and the large amount of literature that describe their use for single‐molecule fluorescence spectroscopy. We also compared the results between ZMWs milled in gold and aluminum, and found that although gold has a stronger influence on the decay rates, the lower losses of aluminum in the green spectral region provide larger fluorescence brightness enhancement factors. For both aluminum and gold ZMWs, we observed that the FRET rate scales linearly with the isolated donor decay rate and the local density of optical states. Detailed information about FRET in ZMWs unlocks their application as new devices for enhanced single‐molecule FRET at physiological concentrations.     

Single-Molecule Photoactivation FRET: A General and Easy-To-Implement Approach To Break the Concentration Barrier

Single-molecule fluorescence resonance energy transfer (sm-FRET) has become a widely used tool to reveal dynamic processes and molecule mechanisms hidden under ensemble measurements. However, the upper limit of fluorescent species used in sm-FRET is still orders of magnitude lower than the association affinity of many biological processes under physiological conditions. Herein, we introduce single-molecule photoactivation FRET (sm-PAFRET), a general approach to break the concentration barrier by using photoactivatable fluorophores as donors. We demonstrate sm-PAFRET by capturing transient FRET states and revealing new reaction pathways during translation using μm fluorophore labeled species, which is 2–3 orders of magnitude higher than commonly used in sm-FRET measurements. sm-PAFRET serves as an easy-to-implement tool to lift the concentration barrier and discover new molecular dynamic processes and mechanisms under physiological concentrations.     

Temperature-cycle single-molecule FRET microscopy on polyprolines

Accessing the microsecond dynamics of a single fluorescent molecule in real time is difficult because molecular fluorescence rates usually limit the time resolution to milliseconds. We propose to apply single-molecule temperature-cycle microscopy to probe molecular dynamics at microsecond timescales. Here, we follow donor and acceptor signals of single FRET-labeled polyprolines in glycerol to investigate their conformational dynamics. We observe a steady-state FRET efficiency distribution which differs from theoretical distributions for isotropically orientated fluorescent labels. This may indicate that the orientation of fluorescent labels in glycerol is not isotropic and may reflect the influence of the dye linkers. With proper temperature-cycle parameters, we observed large FRET changes in long series of cycles of the same molecule. We attribute the main conformational changes to reorientations of the fluorescent labels with respect to the oligopeptide chain, which take place in less than a few microseconds at the highest temperature of the cycle (250 K). We were able to follow the FRET efficiency of a particular construct for more than 2000 cycles. This trajectory displays switching between two conformations, which give rise to maxima in the FRET efficiency histogram. Our experiments open the possibility to study biomolecular dynamics at a time scale of a few microseconds at the single-molecule level.     

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.     

Electrochemical Signal‐triggered Release of Biomolecules Functionalized with His‐tag Units

His‐tagged molecular species, a ferrocene derivative and Protein A, were immobilized on electrode surfaces (Au and graphite) through formation of a chelated complex in the presence of Cu²⁺ cations used as bridging units. The complex was cleaved and the attached molecules were released from the electrode surface by applying reductive potential to the electrodes resulting in Cu²⁺ reduction, thus decomposing the chelate complex. The molecule release process was followed by cyclic voltammetry in case of the ferrocene derivative. His‐tagged Protein A was additionally labeled with a fluorescent tag and its release was followed by fluorescence measurements in the solution and by impedance spectroscopy at the electrode. The studied release of the His‐tagged redox species and biomolecules was considered as a new generic approach to the signal‐controlled molecule release applicable in various biotechnological and biomedical applications.     

Make them Blink: Probes for Super‐Resolution Microscopy

In recent years, a number of approaches have emerged that enable far‐field fluorescence imaging beyond the diffraction limit of light, namely super‐resolution microscopy. These techniques are beginning to profoundly alter our abilities to look at biological structures and dynamics and are bound to spread into conventional biological laboratories. Nowadays these approaches can be divided into two categories, one based on targeted switching and readout, and the other based on stochastic switching and readout of the fluorescence information. The main prerequisite for a successful implementation of both categories is the ability to prepare the fluorescent emitters in two distinct states, a bright and a dark state. Herein, we provide an overview of recent developments in super‐resolution microscopy techniques and outline the special requirements for the fluorescent probes used. In combination with the advances in understanding the photophysics and photochemistry of single fluorophores, we demonstrate how essentially any single‐molecule compatible fluorophore can be used for super‐resolution microscopy. We present examples for super‐resolution microscopy with standard organic fluorophores, discuss factors that influence resolution and present approaches for calibration samples for super‐resolution microscopes including AFM‐based single‐molecule assembly and DNA origami.     

Bleaching-resistant,Near-continuous Single-molecule Fluorescence and FRET Based on Fluorogenic and Transient DNA Binding

Photobleaching of fluorescent probes limits the observation span of typical single-molecule fluorescence measurements and hinders observation of dynamics at long timescales. Here, we present a general strategy to circumvent photobleaching by replenishing fluorescent probes via transient binding of fluorogenic DNAs to complementary DNA strands attached to a target molecule. Our strategy allows observation of near-continuous single-molecule fluorescence for more than an hour, a timescale two orders of magnitude longer than the typical photobleaching time of single fluorophores under our conditions. Using two orthogonal sequences, we show that our method is adaptable to Förster Resonance Energy Transfer (FRET) and that can be used to study the conformational dynamics of dynamic structures, such as DNA Holliday junctions, for extended periods. By adjusting the temporal resolution and observation span, our approach enables capturing the conformational dynamics of proteins and nucleic acids over a wide range of timescales.     

Elastic Organic Crystals of a Fluorescent π‐Conjugated Molecule

An elastic organic crystal of a π‐conjugated molecule has been fabricated. A large fluorescent single crystal of 1,4‐bis[2‐(4‐methylthienyl)]‐2,3,5,6‐tetrafluorobenzene (over 1 cm long) exhibited a fibril lamella morphology based on slip‐stacked molecular wires, and it was found to be a remarkably elastic crystalline material. The straight crystal was capable of bending more than 180° under applied stress and then quickly reverted to its original shape upon relaxation. In addition, the fluorescence quantum yield of the crystal was about twice that of the compound in THF solution. Mechanical bending–relaxation resulted in reversible change of the morphology and fluorescence. This research offers a more general approach to flexible crystals as a promising new family of organic semiconducting materials.     

The effect of irradiation by ultraviolet light on ureido‐pyrimidinone based biomaterials

Supramolecular polymers based on ureido‐pyrimidinone (UPy) represent a promising class of biocompatible materials for medical applications. Here, the chemical modification effect of UV irradiation, used to sterilize these materials, is studied. Besides anticipated crosslinking effects, UV irradiation causes telechelic UPy‐polymers to become fluorescent. UPy‐model compounds confirm a relation between UV‐induced changes and the UPy‐moiety. UV‐induced fluorescence and IR‐spectral changes are (partially) reversible by heat and/or solvent treatment. The results indicate the presence of at least two distinct UV‐induced molecular species. UPy‐model compounds with specific tautomeric forms directly relate fluorescence to UPy‐enol tautomers. Photo‐enolization is hypothesized to occur via an excited‐state intermolecular double proton transfer. Changes in UPy‐tautomeric equilibrium and crosslinking are factors that influence the dynamics of UPy‐based materials. Identification and understanding of such factors will aid in the successful application of these materials, for example as biomaterial in tissue engineering applications. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 81–90     

Single‐Molecule Fluorescence Detection of a Synthetic Heparan Sulfate Disaccharide

The first single‐molecule fluorescence detection of a structurally‐defined synthetic carbohydrate is reported: a heparan sulfate (HS) disaccharide fragment labeled with Alexa488. Single molecules have been measured whilst freely diffusing in solution and controlled encapsulation in surface‐tethered lipid vesicles has allowed extended observations of carbohydrate molecules down to the single‐molecule level. The diverse and dynamic nature of HS–protein interactions means that new tools to investigate pure HS fragments at the molecular level would significantly enhance our understanding of HS. This work is a proof‐of‐principle demonstration of the feasibility of single‐molecule studies of synthetic carbohydrates which offers a new approach to the study of pure glycosaminoglycan (GAG) fragments.     

Variable Temperature Single‐Molecule Dynamics of MEH‐PPV

Herein, we continue our investigation of the single‐molecule spectroscopy of the conjugated polymer poly[2‐methoxy,5‐(2′‐ethylhexyloxy)‐p‐phenylene‐vinylene] (MEH‐PPV) at cryogenic temperatures. First, the low temperature microsecond dynamics of single MEH‐PPV conjugated polymer molecules are compared to the dynamics at room temperature revealing no detectible temperature dependence. The lack of temperature dependence is consistent with the previous assignment of the dynamics to a mechanism that involves intersystem crossing and triplet–triplet annihilation. Second, the fluorescence spectra of single MEH‐PPV molecules at low temperature are studied as a function of excitation wavelength (i.e. 488, 543, and 568 nm). These results exhibit nearly identical fluorescence spectra for different excitation wavelengths. This strongly suggests that electronic energy transfer occurs efficiently to a small number of low‐energy sites in the multichromophoric MEH‐PPV chains.     

Effect of the Side‐Chain‐Distribution Density on the Single‐Conjugated‐Polymer‐Chain Conformation

The spatial arrangement of the side chains of conjugated polymer backbones has critical effects on the morphology and electronic and photophysical properties of the corresponding bulk films. The effect of the side‐chain‐distribution density on the conformation at the isolated single‐polymer‐chain level was investigated with regiorandom (rra‐) poly(3‐hexylthiophene) (P3HT) and poly(3‐hexyl‐2,5‐thienylene vinylene) (P3HTV). Although pure P3HTV films are known to have low fluorescence quantum efficiencies, we observed a considerable increase in fluorescence intensity by dispersing P3HTV in poly(methyl methacrylate) (PMMA), which enabled a single‐molecule spectroscopy investigation. With single‐molecule fluorescence excitation polarization spectroscopy, we found that rra‐P3HTV single molecules form highly ordered conformations. In contrast, rra‐P3HT single molecules, display a wide variety of different conformations from isotropic to highly ordered, were observed. The experimental results are supported by extensive molecular dynamics simulations, which reveal that the reduced side‐chain‐distribution density, that is, the spaced‐out side‐chain substitution pattern, in rra‐P3HTV favors more ordered conformations compared to rra‐P3HT. Our results demonstrate that the distribution of side chains strongly affects the polymer‐chain conformation, even at the single‐molecule level, an aspect that has important implications when interpreting the macroscopic interchain packing structure exhibited by bulk polymer films.     

A Novel Pyrene‐Based Fluorescing Amphiphile with Unusual Bulk and Interfacial Properties

We have synthesised a new, pyrene‐based, low‐molecular‐mass, amphiphilic molecule that displays a wealth of properties of potential interest for aggregation and interfacial applications. In order to elucidate some of the key properties of this molecule, which consists of a pyrene‐containing hydrophobic head and a short PEG‐based hydrophilic tail, we investigate herein some aspects of its concentration‐dependent behaviour in aqueous solutions. We show that the inclusion of the hydrophobic pyrene group not only provides the molecule with intriguing bulk and interfacial properties down to low concentrations, but also with various means of assessing its aggregation behaviour by means of its well‐characterised fluorescence properties. Combining a range of fluorescence techniques with microscopic imaging (optical and Cryo‐TEM), interfacial tension measurements and foaming studies, we have been able to identify and characterise three concentration‐dependant regimes. At low concentrations, the molecule is dissolved in monomeric form. At intermediate concentrations, labile aggregates are formed, which, at higher concentrations, give way to aggregates containing pre‐associated pyrenes. Our measurements strongly imply that the latter aggregates are hexagonally close‐packed tubular micelles. In this latter regime we also find a range of micron‐sized precipitates. Additionally, the molecule displays strong interfacial activity, yet a surprisingly slow dynamics of interfacial adsorption. Finally, we demonstrate the possibility of using it to visualize interfaces and also create reasonably stable (1 hour) and fluorescing foams.     

具有大斯托克位移的荧光探针分子

用荧光法来监视多个生理参数时,需要几个不同的荧光探针分子.这些探针分子要被同一波长激发,但是具有明显分离的、不同的发射波长.目前,大多数荧光探针只有小的斯托克位移(50-90 nm),从而限制了它们在多个物质同时检测上的应用.在这项工作中,我们提出了一个新的分子探针设计:受体-荧光分子1-间隔-荧光分子2(简称RFSF...