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.     

Donor-acceptor interactions in red-emitting thienylbenzene-branched dendrimers with benzothiadiazole core

Synthesis and characterization of dendrimers containing thienylbenzene repeating units, red-emitting benzothiadiazole core, and triarylamine peripheries that bear naphthyl units are reported. The relevant dendrimers of different generations are classified as G(nb) (n=1-3), while the tert-butyl dendrimers G(na) with the acceptor alone were also synthesized to serve as control chromophores that avoid donor-acceptor interactions. The resulting dendrimers are capable of harvesting photon energy through efficient energy transfer among donor-acceptor moieties, so that highly luminescent red fluorophores result. Transient fluorescence studies suggest that the energy transfer and its efficiency are approximately unity in all G(a) dendrimers, whereas the rate of energy transfer for the G(b) dendrimers is suppressed, that is, charge transfer from the core to the periphery is a significant quenching pathway. These dendrimers are amorphous in nature with high glass transition temperatures (176-201 degrees C). Electroluminescent devices were fabricated by using the dendrimers as hole-transporting emitters, and the devices exhibit promising red emission parameters.     

Preparation of Fluorescence Tunable Polymer Nanoparticles by One-step Mini-emulsion

Fluorescence tunable polymer nanoparticles were prepared by incorporating two hydrophobic fluorescent dyes (9, 10-diphenylanthracene: DPA and nitrobenzoxadiazolyl: NBD) into polymethylmethacrylate (PMMA) nanoparticles via one-step mini-emulsion polymerization method. The prepared fluorescent nanoparticles exhibit the spectral properties of both DPA and NBD dye, indicating that the two fluorophores have been incorporated into the nanoparticles. The nanoparticles greatly enhance the fluorescence emission of the two hydrophobic dyes in aqueous media probably by providing good protection of the dye molecules in the polymer nanoparticles matrix. Moreover, by varying the doping ratio of the two hydrophobic dyes, the polymer nanoparticles exhibit tunable and distinguishable emission characteristics under a single wavelength excitation via occuring fluorescence resonance energy transfer (FRET).     

Readily Accessible and Predictable Naphthalene‐Based Two‐Photon Fluorophore with Full Visible‐Color Coverage

Herein we report 22 acedan‐derived, two‐photon fluorophores with synthetic feasibility and full coverage of visible wavelength emission. The emission wavelengths were predicted by computational analysis, which enabled us to visualize multicolor images by two‐photon excitation with single wavelength, and to design a turn‐on, two‐photon fluorescence sensor for endogenous H₂O₂ in Raw 264.7 macrophage and rat brain hippocampus ex vivo.     

Quantifying heterogeneity and conformational dynamics from single molecule FRET of diffusing molecules: recurrence analysis of single particles (RASP)

Single molecule F?rster resonance energy transfer (FRET) experiments are a versatile method for investigating the conformational distributions and dynamics of biological macromolecules. In a common type of experiment, the fluorescence bursts from individual molecules freely diffusing in solution are detected as they pass through the observation volume of a confocal microscope. Correlation analysis of the fluorescence bursts shows that under typical experimental conditions, for time scales up to several tens of milliseconds, the probability for a molecule to return to the confocal volume is greater than the probability of a new molecule being detected. Here we present RASP (recurrence analysis of single particles), a method that is based on this recurrence behavior and allows us to significantly extend the information that can be extracted from single molecule FRET experiments. The number and peak shapes of subpopulations within the sample can be identified essentially in a model-free way by constructing recurrence FRET efficiency histograms. These are obtained by first selecting photon bursts from a small transfer efficiency range (initial bursts), and then building the FRET efficiency histogram only from bursts detected within a short time (the recurrence interval) after the initial bursts. Systematic variation of the recurrence interval allows the kinetics of interconversion between subpopulations to be determined on time scales from ~50 μs up to ~100 ms from equilibrium measurements. We demonstrate the applicability of the method on measurements of several peptides and proteins with different degrees of conformational heterogeneity and folding dynamics. The concepts presented here can be extended to other observables available from single molecule fluorescence experiments.     

Fluorescence and Sensing Applications of Graphene Oxide and Graphene Quantum Dots: A Review

Graphene oxide and graphene quantum dots are attractive fluorophores that are inexpensive, nontoxic, photostable, water‐soluble, biocompatible, and environmentally friendly. They find extensive applications in fluorescent biosensors and chemosensors, in which they serve as either fluorophores or quenchers. As fluorophores, they display tunable photoluminescence emission and the “giant red‐edge effect”. As quenchers, they exhibit a remarkable quenching efficiency through either electron transfer or Förster resonance energy transfer (FRET) process. In this review, the origin of fluorescence and the mechanism of excitation wavelength‐dependent fluorescence of graphene oxide and graphene quantum dots are discussed. Sensor design strategies based on graphene oxide and graphene quantum dots are presented. The applications of these sensors in health care, the environment, agriculture, and food safety are highlighted.     

Origin of simultaneous donor-acceptor emission in single molecules of peryleneimide-terrylenediimide labeled polyphenylene dendrimers

F?rster type resonance energy transfer (FRET) in donor-acceptor peryleneimide-terrylenediimide dendrimers has been examined at the single molecule level. Very efficient energy transfer between the donor and the acceptor prevent the detection of donor emission before photobleaching of the acceptor. Indeed, in solution, on exciting the donor, only acceptor emission is detected. However, at the single molecule level, an important fraction of the investigated individual molecules (about 10-15%) show simultaneous emission from both donor and acceptor chromophores. The effect becomes apparent mostly after photobleaching of the majority of donors. Single molecule photon flux correlation measurements in combination with computer simulations and a variety of excitation conditions were used to determine the contribution of an exciton blockade to this two-color emission. Two-color defocused wide-field imaging showed that the two-color emission goes hand in hand with an unfavorable orientation between one of the donors and the acceptor chromophore.     

Ultraviolet laser induced fluorescence of human aorta

Laser induced fluorescence from normal human aorta is studied with u.v. excitations of 305 to 310 nm, observing emission from 320 to 500 nm. In this region LIF lineshapes are strongly dependent on the excitation wavelength, suggesting that at least two fluorophores are being observed. The short wavelength fluorophore, peaking at 34Onm, is identified as tryptophan, while the longer wavelength fluorophore, peaking at 387 nm, is associated with collagen and elastin. In addition, fluorescence time decays of each component are measured with a time correlated photon counting system. A four-exponential fit of each decay is necessary to extract fluorescence lifetimes, which range from 33 ps to 8.6 ns.     

Fabrication of Novel Polymer Nanoparticle-Based Fluorescence Resonance Energy Transfer Systems and their Tunable Fluorescence Properties

In this study, two hydrophobic fluorescent dyes, nitrobenzoxadiazolyl (NBD) and 9-(diethylamino)benzo[a]phenoxazin-5-one (NR) with different doping ratios were incorporated into polymer nanoparticles to constitute novel polymer nanoparticle-based fluorescence resonance energy transfer (FRET) systems via a facile one-step mini-emulsion polymerization. Spectroscopic characteristics demonstrate that the two fluorophores have been successfully embedded into the nanoparticles, and the fluorescence emission intensity of the two hydrophobic dyes can be greatly enhanced in aqueous media. The as-prepared fluorescent nanoparticles also display a uniform small size (ca. 55 nm), high dye load, intense fluorescence, as well as controllable amount and ratio of the two dyes. The observed FRET efficiencies (16.0–75.2%), as well as the distance (r) between NBD (donor) and NR (acceptor), is closely correlated to the doping ratio of two dyes. Moreover, by varying the doping ratio of two dyes, the fluorescent nanoparticles would exhibit multicolor through FRET upon a single wavelength excitation, and the fluorescence emission signals of the dye-doped nanoparticles could be accurately tuned. These results indicate that the as-prepared uniform FRET-mediated nanoparticles are of high interest in multiplexed bioanalysis.     

Covalent Attachment of Active Enzymes to Upconversion Phosphors Allows Ratiometric Detection of Substrates

Upconverting phosphors (UCPs) convert multiple low energy photons into higher energy emission via the process of photon upconversion and offer an attractive alternative to organic fluorophores for use as luminescent probes. Here, UCPs were capped with functionalized silica in order to provide a surface to covalently conjugate proteins with surface-accessible cysteines. Variants of green fluorescent protein (GFP) and the flavoenzyme pentaerythritol tetranitrate reductase (PETNR) were then attached via maleimide-thiol coupling in order to allow energy transfer from the UCP to the GFP or flavin cofactor of PETNR, respectively. PETNR retains its activity when coupled to the UCPs, which allows reversible detection of enzyme substrates via ratiometric sensing of the enzyme redox state.     

Biosynthesis of a fluorescent protein with extreme pseudo-Stokes shift by introducing a genetically encoded non-natural amino acid outside the fluorophore

A novel kind of fluorescent protein relying on the intramolecular interplay between two different fluorophores, one of chemical origin and one of biological origin, was developed. The fluorescent non-natural amino acid l-(7-hydroxycoumarin-4-yl)ethylglycine was site-specifically incorporated into the recombinant enhanced cyan fluorescent protein (eCFP) at a permissible surface position ～20 ? away from the protein fluorophore using amber suppression in Escherichia coli with an engineered cognate Methanococcus jannaschii tRNA synthetase. The resulting eCFP(Cou) exhibited almost quantitative intramolecular Fo?rster resonance energy transfer (FRET) between its two fluorophores, showing brilliant cyan emission at 476 nm upon excitation in the near-UV at 365 nm (a wavelength easily accessible via conventional laboratory UV sources), in contrast to its natural counterpart. Thus, this fluorescent protein with unprecedented spectroscopic properties reveals an extreme apparent Stokes shift of ～110 nm between the absorption wavelength of the coumaryl group and the emission wavelength of eCFP.     

Giant Amplification of Photoswitching by a Few Photons in Fluorescent Photochromic Organic Nanoparticles

Controlling or switching the optical signal from a large collection of molecules with the minimum of photons represents an extremely attractive concept. Promising fundamental and practical applications may be derived from such a photon‐saving principle. With this aim in mind, we have prepared fluorescent photochromic organic nanoparticles (NPs), showing bright red emission, complete ON–OFF contrast with full reversibility, and excellent fatigue resistance. Most interestingly, upon successive UV and visible light irradiation, the NPs exhibit a complete fluorescence quenching and recovery at very low photochromic conversion levels (<5 %), leading to the fluorescence photoswitching of 420±20 molecules for only one converted photochromic molecule. This “giant amplification of fluorescence photoswitching” originates from efficient intermolecular energy‐transfer processes within the NPs.     

Spectral identification of specific photophysics of cy5 by means of ensemble and single molecule measurements

The triplet-state characteristics of the Cy5 molecule related to trans-cis isomerization are investigated by means of ensemble and single molecule measurements. Cy5 has been used frequently in the past 10 years in single molecule spectroscopic applications, e.g., as a probe or fluorescence resonance energy transfer acceptor in large biomolecules. However, the unknown spectral properties of the triplet state and the lack of knowledge on the photoisomerization do not allow us to interpret precisely the unexpected single molecule behaviors. This limits the application of Cy5. The laser photolysis experiments demonstrate that the trans triplet state of Cy5 absorbs about 625 nm, the cis ground state absorbs about 690 nm, and the cis triplet state also absorbs about 690 nm. In other words, the T1-Tn absorptions largely overlap the ground-state absorptions for both trans and cis isomers, respectively. Furthermore, the observation of the cis triplet state indicates an important isomerization pathway from the trans-S1 state to the cis-T1 state upon excitation. The detailed spectra presented in this article let us clearly interpret the exact mechanisms responsible for several important and unexpected photophysical behaviors of single Cy5 molecules such as reverse intersystem crossing (RISC), the observation of dim states with a lower emission intensity and slightly red-shifted fluorescence, and unusual energy transfer from donor molecules to dark Cy5 molecules acting as acceptors in single molecule fluorescence resonance energy transfer (FRET) measurements. Spectral results show that the dim state in the single molecule fluorescence intensity time traces originated from cis-Cy5 because of a lower excitation rate, resulting from the red-shifted ground-state absorption of cis-Cy5 compared to that of the trans-Cy5.     

Single-molecule tracking of sub-millisecond domain motion in calmodulin

We used single-pair fluorescence resonance energy transfer (spFRET) to track distance changes between domains of fluorescently labeled calmodulin (CaM) on the sub-millisecond time scale. In most cases, CaM remained in the same conformational substate over time periods of up to 1 ms, showing that conformational interchange occurs on a longer time scale. However, in some instances, apparent transitions between conformational substates could be detected. The magnitude of sub-millisecond motion within the dominant conformational substate also revealed fluctuations in distance between domains that were dependent on pH and ionic strength.     

A novel fluorophore with dual fluorescence: local excited state and photoinduced electron-transfer-promoted charge-transfer state.

Absorption and emission spectra of 9-N,N-dimethylaniline decahydroacridinedione (DMAADD) have been studied in different solvents. The fluorescence spectra of DMAADD are found to exhibit dual emission in aprotic solvents and single emission in protic solvents. The effect of solvent polarity and viscosity on the absorption and emission spectra has also been studied. The fluorescence excitation spectra of DMAADD monitored at both the emission bands are different. The presence of two different conformation of the same molecule in the ground state has lead to two close lying excited states, local excited (LE) and charge transfer (CT), and thereby results in the dual fluorescence of the dye. A CTstate involving the N,N-dimethylaniline group and the decahy droacridinedione chromophore as donor and acceptor, respectively, has been identified as the source of the long wavelength anomalous fluorescence. The experimental studies were supported by ab initio time dependent-density functional theory (TDDFT) calculations performed at the B3LYP/6-31G* level. The molecule possesses photoinduced electron transfer (PET) quenching in the LE state, which is confirmed by the fluorescence lifetime and fluorescent intensity enhancement in the presence of transition metal ions.     

Novel diode laser-compatible fluorophores and their application to single molecule detection, protein labeling and fluorescence resonance energy transfer immunoassay

We describe a series of new long-wave absorbing and fluorescing cyanine dyes and labels (based on a general logic for the design of such dyes), their spectra, covalent and noncovalent linkage to proteins, their use in single molecule detection (SMD) and as donors and acceptors, respectively, in fluorescence resonance energy transfer studies. The new labels represent water-soluble and reactive fluorophores whose quantum yields increase substantially if noncovalently or covalently bound to proteins. Due to their strong absorptions between 550 and 700 nm they are excitable by light-emitting diodes or diode lasers. Their high absorbances (epsilon around 100,000) and adequate fluorescence quantum yields (phi up to 0.68 if bound to proteins) along with their availability as reactive NHS esters make them viable labels for proteins and oligomers, e.g. in context with SMD or fluorescence energy transfer immunoassay which is demonstrated for the system HSA/anti-HSA.     

Fluorophore-quencher distance correlation functions from single-molecule photon arrival trajectories

We generalize and simplify the method of Yang and Xie (J. Chem. Phys. 2002, 117, 10965) to obtain distance correlation functions from photon arrival trajectories of single fluorophores whose lifetime, [k(r)](-1), depends on the distance to a quencher. It is assumed that this distance does not change during the fluorescence lifetime. The experimental trajectory is first transformed by replacing the delay time (i.e., the interval between the photon arrival and the nearest laser pulse) by a certain function of this delay time. This function is the inverse Laplace transform of r(k), which is the solution of k(r) = 1. The correlation function of the transformed data then directly gives the distance correlation function. Illustrative examples include F?rster energy transfer and quenching due to electron transfer.     

Deconvolution of fluorescence spectra: contribution to the structural analysis of complex molecules

Fluorescence spectroscopy is a sensitive analytical tool in the studies of both simple and complex molecular structures. In complex molecules, however, determining the number and position of components may give a specific insight into the structure, complementary to the other analytical techniques. We applied log–normal model to analyze fluorescence of simple monofluorophore molecule. In order to analyze spectra where both fluorophores and Raman emission bands were present, we developed a method obtained by combination of the symmetric, Gaussian, for Raman and asymmetric, log–normal model, for fluorescence, applicable to the molecules of different complexity. Technically, for each sample we varied excitation wavelength with 5 nm step and recorded the corresponding emission spectra. They were subsequently used for component analysis. Position of each component was plotted against the excitation wavelength. Applying this approach we could identify minimal number of components having stable positions, while their approximate probability density (APD) in a spectral series was correlated with the probable number of fluorophores in the molecule. The method was tested on molecules containing different number of fluorophores: monomers involved in the synthesis of plant polymer lignin—coniferyl alcohol (one fluorophore), ferulic acid (two fluorophores) and on lignin model compound produced from these monomers (many fluorophores). All investigated species belong to benzene-substituted class of compounds, and it is reasonable to assume that they have similar fluorescence band contour. We also report the results of environmental scanning electron microscopy (ESEM) studies showing multilayered dehydrogenative polymer (DHP) structure, in order to show complexity of the polymer. Our results present complementarity of these two approaches in the structural studies of the lignin model compound.