Donor Emission Research Articles

Photochromic Polymer Composites for Two-Photon 3D Optical Data Storage

In this paper we demonstrate 3D two-photon recording and two-photon readout in photochromic polymer composites containing a mixture of 1,2-bis(2-methylbenzo[b]thiophen-3-yl)hexafluorocyclopentene (diarylethene 1) and fluorene derivatives 2,2‘-(9,9-didecyl-9H-fluorene-2,7-diyl)bis(ethene-2,1-diyl)bis(4,1-phenylene)) dibenzo[d]thiazole (2) or poly(9,9-didecyl-2,7-dipheylaminofluorene) (3). The recording mechanism in this system is based on two-photon excitation of the closed form of diarylethene 1 at 800 nm. The readout mechanism is based on the modulation of the emission intensity of fluorene derivatives 2 or 3 by the closed form of diarylethene 1 through Resonance Energy Transfer (RET). Foster distances (R0) and critical concentrations (A0) were calculated from the spectral overlap of the donor's emission (fluorene derivatives) and the acceptor's absorption (closed form of diarylethene 1) in solution and in polymer films of PMMA-co-VBP. This system was demonstrated to be suitable for recording data by two...

Imaging FRET standards by steady‐state fluorescence and lifetime methods

Imaging fluorescence resonance energy transfer (FRET) between molecules labeled with fluorescent proteins is emerging as a powerful tool to study changes in ions, ligands, and molecular interactions in their physiological cellular environment. Different methods use either steady-state fluorescence properties or lifetime to quantify the FRET rate. In addition, some provide the absolute FRET efficiency whereas others are simply a relative index very much influenced by the actual settings and instrumentation used, which makes the interpretation of a given FRET rate very difficult. The use and exchange of FRET standards in laboratories using these techniques would help to overcome this drawback. We report here the construction and systematic evaluation of FRET standard probes of varying FRET efficiencies. The standards for intramolecular FRET were protein fusions of the cyan and yellow variants of A. victoria green fluorescent protein (ECFP and citrine) joined by short linkers or larger protein spacers, or ECFP tagged with a tetracysteine motif and labeled with the biarsenical fluorochrome, FlAsH. Negative and positive controls of intermolecular FRET were also used. We compared these FRET standards with up to four FRET quantification methods: ratioing of acceptor to donor emission, donor intensity recovery upon acceptor photobleach, sensitized emission after spectral unmixing of raw images, and fluorescence lifetime imaging (FLIM). The latter was obtained with a frequency-domain setup able to provide high quality lifetime images in less than a second, and is thus very well suited for live cell studies. The FRET rates or indexes of the standards were in good agreement regardless of the method used. For the CFP-tetraCys/FlAsH pair, the rate calculated from CFP quenching was faster than that obtained by FLIM.

Fluorescent polystyrene microspheres with large Stokes shift by fluorescence resonance energy transfer

We prepared fluorescent microspheres with notably large Stokes shift and long-wavelength fluorescence by applying fluorescence resonance energy transfer (FRET) between two common julolidine dyes. Short distance between dye molecules caused by high dye concentration results in efficient FRET in microspheres. However, adequate dye concentration and moderate molar ratio of the donor and acceptor should be chosen to avoid aggregation of dye molecules, which leads to the decrease of fluorescent intensity. Microrspheres with average distance between dye molecules of 1.94 nm and molar ratio of 3.08:1 realize highly efficient FRET with no fluorescence of donor and intense long-wavelength emission of acceptor. In addition, the applied solvent evaporation method for preparing microspheres provided better protection of dyes from ambient medium than traditional surface-labeled method. These results demonstrate the feasibility of applying FRET in microspheres to expand useful fluorescent probes, and reveal their potential application in bioassays field.

Solvent dependent tunable energy transfer of d 10 metal dicyanide nanoclusters with Eu 3+ and Tb 3+ rare earth ions

The luminescence energy and intensity of d 10 copper(I), silver(I) and gold(I) dicyanide nanoclusters exhibit high tunability as energy transfer donors in different organic solvents. For Tb 3+ acceptor ions, the energy transfer efficiency, which is proportional to the spectral overlap between the donor emission and the acceptor absorption, depends on the solvent tunability of the donor emission energy. For Eu 3+ acceptor ions, energy transfer can be ‘tuned off’ or ‘tuned on’ as the solvent dependent donor emission energy becomes in resonance with a charge transfer state or with the 5L 6 Eu 3+ ion state, respectively.

Tandem Dye Acceptor Used To Enhance Upconversion Fluorescence Resonance Energy Transfer in Homogeneous Assays

In fluorescence resonance energy transfer (FRET)-based assays, spectral separation of acceptor emission from donor emission is a common problem affecting the assay sensitivity. The challenge derives from small Stokes shifts characteristic to conventional fluorescent dyes resulting in leakage of donor emission to the measurement window intended only to collect the acceptor emission. We have studied a FRET-based homogeneous bioaffinity assay utilizing a tandem dye acceptor with a large pseudo-Stokes shift (139 nm). The tandem dye was constructed using B-phycoerythrin as an absorber and multiple Alexa Fluor 680 dyes as emitters. As a donor, we employed upconverting phosphor particles, which uniquely emit at visible wavelengths under low-energy infrared excitation enabling the fluorescence measurements free from autofluorescence even without time-resolved detection. With the tandem dye, it was possible to achieve four times higher signal from a single binding event compared to the conventional Alexa Fluor 680 dye alone. Tandem dyes are widely used in cytometry and other multiplex purposes, but their applications can be expanded to fluorescence-based homogeneous assays. Both the optimal excitation and emission wavelengths of tandem dye can be tuned to a desired region by choosing appropriate fluorophores enabling specifically designed acceptor dyes with large Stokes shift.

Enhanced energy transfer in single glycerol/water microdroplets standing on a superhydrophobic surface

We demonstrate resonant enhancement of energy transfer from donor to acceptor molecules in single glycerol/water microdroplets standing on a superhydrophobic surface. At donor emission wavelengths resonant with a whispering gallery mode, we recorded energy transfer rates up to 10 times higher than the non-radiative (Förster) energy transfer rate, by using the gradual acceptor photobleaching technique. Optical images taken with donor and acceptor emission filters revealed the radiative (long-range) nature of the energy transfer mediated by the whispering gallery modes.

An experimental study of GFP‐based FRET, with application to intrinsically unstructured proteins

We have experimentally studied the fluorescence resonance energy transfer (FRET) between green fluorescent protein (GFP) molecules by inserting folded or intrinsically unstructured proteins between CyPet and Ypet. We discovered that most of the enhanced FRET signal previously reported for this pair was due to enhanced dimerization, so we engineered a monomerizing mutation into each. An insert containing a single fibronectin type III domain (3.7 nm end-to-end) gave a moderate FRET signal while a two-domain insert (7.0 nm) gave no FRET. We then tested unstructured proteins of various lengths, including the charged-plus-PQ domain of ZipA, the tail domain of alpha-adducin, and the C-terminal tail domain of FtsZ. The structures of these FRET constructs were also studied by electron microscopy and sedimentation. A 12 amino acid linker and the N-terminal 33 amino acids of the charged domain of the ZipA gave strong FRET signals. The C-terminal 33 amino acids of the PQ domain of the ZipA and several unstructured proteins with 66-68 amino acids gave moderate FRET signals. The 150 amino acid charged-plus-PQ construct gave a barely detectable FRET signal. FRET efficiency was calculated from the decreased donor emission to estimate the distance between donor and acceptor. The donor-acceptor distance varied for unstructured inserts of the same length, suggesting that they had variable stiffness (persistence length). We conclude that GFP-based FRET can be useful for studying intrinsically unstructured proteins, and we present a range of calibrated protein inserts to experimentally determine the distances that can be studied.

Enhanced Sensitivity of FRET‐Based Protease Sensors by Redesign of the GFP Dimerization Interface

changes in a sensor domain are translated into a change in energy-transfer efficiency between donor and acceptor fluorescent domains, which is detected by a change in the ratio of donor and acceptor emission. This ratiometric response is independent of the sensor concentration, which is an important advantage of FRET-based sensors. In practice, however, most FRET-based sensors display only a relatively small difference in emission ratio upon activation. Improvement of these ratiometric changes has been recognized as an important prerequisite for use of these sensor systems in high-throughput applications based on fluorescence plate readers and fluorescence assisted cell sorting (FACS). [14, 15] Recently a pair of CFP (cyan fluorescent protein) and YFP (yellow fluorescent protein) variants, CyPet and YPet, respectively, have been reported that were optimized for FRET through a process of directed evolution. [16] When incorporated in a protease sensor, a 20-fold change in emission ratio was observed upon cleavage of a flexible peptide that linked CyPet and YPet, compared to only a fourfold change for the same construct with enhanced CFP (ECFP) and enhanced YFP (EYFP) domains. However, the mechanism behind their remarkable FRET properties has remained unclear. A total of eighteen mutations were introduced in the course of their development, many of which were at the exterior of the protein, at a large distance from the fluorophore. Moreover, no large differences in quantum yield or extinction coefficient were reported; this suggests that the photophysical properties of the fluorescent proteins were not significantly altered. We therefore hypothesized that the increase in FRET observed for CyPet and YPet could be due to an enhanced tendency to interact when connected by a peptide linker. The parent green fluorescent protein (GFP) has a known tendency to dimerize, [17] and analysis of the mutations in YPet have identified two residues, S208F and V224L, that are present at the dimer interface, as shown by the X-ray structure of the GFP dimer. Here, we show that A of just these two mutations in both fluorescent domains of ECFP–linker–EYFP constructs results in a fourfold increase in the EYFP-to-ECFP emission ratio, which yields a 16fold change in emission ratio upon protease cleavage of the peptide linker (Figure 1). Additional biophysical evidence is provided, which shows that the mutations indeed result in A of an intramolecular complex.

Tunable energy transfer from d 10 heterobimetallic dicyanide(I) donor ions to terbium(III) acceptor ions in luminescent Tb[Ag xAu 1− x(CN) 2] 3 ( x = 0 → 1)

We report on the heterobimetallic system, Tb[Ag x Au 1− x (CN) 2] 3 ( x = 0 → 1), in which sensitization of terbium luminescence occurs by energy transfer from [Ag x Au 1− x (CN) 2] − donor excited states. The donor states have energies which are tunable and dependent on the Ag/Au stoichiometric ratio. We report on their use as donor systems with Tb(III) ions as acceptor ions in energy transfer studies. Luminescence results show that the mixed metal dicyanides with the higher silver loading have a better energy transfer efficiency than the pure Ag ( CN ) 2 - and Au ( CN ) 2 - donors. The better energy transfer efficiency is due to the greater overlap between the donor emission and acceptor excitation.

Fluorescence resonance energy transfer in short linear peptides carrying 3-[2-(2-benzofuranyl)benzoxazol-5-yl]-alanine and 3-nitro- l-tyrosine molecules in poly(vinyl alcohol) film

Excitation energy transfer between donor (Box(benzfur)) and acceptor (Tyr(NO 2)) is studied for uniaxially stretched and unstretched poly(vinyl) alcohol films. Free D–A pair and short linear peptides are examined. D–A distance for the longest peptide in unstretched poly(vinyl alcohol) film is very similar to that determined in aqueous solution which indicates the immobilization of the peptide native conformation chain in PVA. The results for stretched PVA matrix indicate partial stretching of the peptide chain. However, for free non-linked D–A pair for stretched PVA matrix substantial increase of D–A distance is observed. Emission anisotropy increases with the degree of stretching but for the longest peptide the saturation effect is not reached. Moreover, the donor emission anisotropy spectra remain practically constant for a given stretching factor R S of the film.

Multi‐dimensional fluorescence lifetime and FRET measurements

When and where proteins associate with each other in living cells are key questions in many biological research projects. One way to address these questions is to measure the extent of Förster resonance energy transfer (FRET) between proteins that have been labeled with appropriate donor and acceptor fluorophores. When both proteins interact, donor and acceptor fluorophores are brought into close vicinity so that the donor can transmit a part of its excitation energy to the acceptor. As a result, both the intensity and the lifetime of the donor fluorescence decrease, whereas the intensity of the acceptor emission increases. This offers different approaches to determine FRET efficiency: One is to detect changes in the intensity of donor and acceptor emission, the other is to measure changes in the lifetime of the donor molecule. One important advantage of the fluorescence lifetime approach is that it allows to distinguish between free and associated donor molecules. However, like intensity measurements it lacks an intrinsic control ensuring that changes in the measured parameters are only due to FRET and not other quenching processes. Here, we show how this limitation can be overcome by spectrally resolved fluorescence lifetime measurements in the time domain. One technique is based on a streak camera system, the other technique is based on a time-correlated-single-photon-counting approach. Both approaches allow biologists to record both donor and acceptor fluorescence emitted by the sample in a single measurement.

Design and characterization of two-dye and three-dye binary fluorescent probes for mRNA detection

We report the design, synthesis, and characterization of binary oligonucleotide probes for mRNA detection. The probes were designed to avoid common problems found in standard binary probes such as direct excitation of the acceptor fluorophore and overlap between the donor and acceptor emission spectra. Two different probes were constructed that contained an array of either two or three dyes and were characterized using steady-state fluorescence spectroscopy, time-resolved fluorescence spectroscopy, and fluorescence depolarization measurements. The three-dye binary probe ( BP-3d) consists of a Fam fluorophore which acts as a donor, collecting light and transferring it as energy to Tamra, which subsequently transfers energy to Cy5 when the two probes are hybridized to mRNA. This design allows the use of 488 nm excitation, which avoids the direct excitation of Cy5 and at the same time provides a good fluorescence resonance energy transfer (FRET) efficiency. The two-dye binary probe system ( BP-2d) was constructed with Alexa488 and Cy5 fluorophores. Although the overlap between the fluorescence of Alexa488 and the absorption of Cy5 is relatively low, FRET still occurs due to their close physical proximity when the probes are hybridized to mRNA. This framework also decreases the direct excitation of Cy5 and reduces the fluorescence overlap between the donor and the acceptor. Picosecond time-resolved spectroscopy showed a reduction in the fluorescence lifetime of donor fluorophores after the formation of the hybrid between the probes and target mRNA. Interestingly, BP-2d in the presence of mRNA shows a slow rise in the fluorescence decay of Cy5 due to a relatively slow FRET rate, which together with the reduction in the Alexa488 lifetime provides a way to improve the signal to background ratio using time-resolved fluorescence spectra (TRES). In addition, fluorescence depolarization measurements showed complete depolarization of the acceptor dyes (Cy5) for both BP-3d (due to sequential FRET steps) and BP-2d (due to the relatively low FRET rate) in the presence of the mRNA target.

Origin of Simultaneous Donor−Acceptor Emission in Single Molecules of Peryleneimide−Terrylenediimide Labeled Polyphenylene Dendrimers

Förster 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.

Fluorescence ratiometric assays of hydrogen peroxide and glucose in serum using conjugated polyelectrolytes

A new water-soluble cationic polyfluorene with boronate-protected fluorescein (peroxyfluor-1) covalently linking to the polymer backbone (PF-FB) was synthesized as a fluorescence probe to optically detect hydrogen peroxide (H2O2) and glucose in serum. The peroxyfluor-1 exists as a lactone form which is colorless and non-fluorescent. Without addition of H2O2, the fluorescence resonance energy transfer (FRET) from fluorene units (donor) to peroxyfluor-1 (acceptor) is absent and only blue donor emission is observed upon excitation of the fluorene units. In the presence of H2O2, the peroxyfluor-1 can specifically react with H2O2 to deprotect the boronate protecting groups and to generate green fluorescent fluorescein. The absorption of fluorescein overlaps the emission of polyfluorene, which encourages efficient FRET from the fluorene units to the fluorescein. By triggering the shift in emission color and the ratio change of blue to green emission intensities, it is possible to assay H2O2 and its concentration change in buffer solution and in serum. The PF-FB probe can detect H2O2 in the range from 4.4 to 530 µM. Since glucose oxidases (GOx) can specifically catalyze the oxidation of β-D-(+)-glucose to generate H2O2, glucose detection is also realized with the PF-FB probe as the signal transducer. Thus, an optical assay for hydrogen peroxide (H2O2) and glucose in serum was created which combines a fluorescent ratiometric technique based on FRET with the light-harvesting properties of conjugated polymers.

A Mouse Model for Monitoring Calpain Activity under Physiological and Pathological Conditions

Calpains are Ca(2+)-dependent cysteine proteases known to be important for the regulation of cell functions and which aberrant activation causes cell death in a number of degenerative disorders. To provide a tool for monitoring the status of calpain activity in vivo under physiological and pathological conditions, we created a mouse model that expresses ubiquitously a fluorescent reporter consisting of eCFP and eYFP separated by a linker cleavable by the ubiquitous calpains. We named this mouse CAFI for calpain activity monitored by FRET imaging. Our validation studies demonstrated that the level of calpain activity correlates with a decrease in FRET (fluorescence resonance energy transfer) between the two fluorescent proteins. Using this model, we observed a small level of activity after denervation and fasting, a high level of activity during muscle regeneration and ischemia, and local activity in damaged myofibers after exercise. Finally, we crossed the CAFI mouse with the alpha-sarcoglycan-deficient model, demonstrating an increase of calpain activity at the steady state. Altogether, our results present evidence that CAFI mice could be a valuable tool in which to follow calpain activity at physiological levels and in disease states.

Imaging Protein Interactions by FRET Microscopy: FRET Measurements by Acceptor Photobleaching: Figure 1.

This protocol describes the detection of fluorescence resonance energy transfer (FRET) by measuring the quenching of donor emission alone. As opposed to sensitized emission measurements, photobleaching can be performed with high selectivity of the acceptor because absorption spectra are steep at their red edge, allowing the acceptor to be bleached without excitation of the donor. When using acceptor photobleaching FRET measurements, care should be taken that the photochemical product of the bleached acceptor does not have residual absorption at the donor emission and, more importantly, that it does not fluoresce in the donor spectral region. Because of mass movement of protein during the extended time required for photobleaching (typically 1-20 min), it is preferable to perform this type of FRET determination on fixed cell samples. Live-cell FRET measurements based only on donor fluorescence are more feasible using fluorescence lifetime imaging (FLIM), because lifetimes are independent of probe concentration and light path length. The former is not easy to determine in cells, and the latter means that cell shape is not a factor.

Fluorometric Measurements of Intermolecular Distances between the α- and β-Subunits of the Na+/K+-ATPase

The Na+/K+-ATPase maintains the physiological Na+ and K+ gradients across the plasma membrane in most animal cells. The functional unit of the ion pump is comprised of two mandatory subunits including the alpha-subunit, which mediates ATP hydrolysis and ion translocation, as well as the beta-subunit, which acts as a chaperone to promote proper membrane insertion and trafficking in the plasma membrane. To examine the conformational dynamics between the alpha- and beta-subunits of the Na+/K+-ATPase during ion transport, we have used fluorescence resonance energy transfer, under voltage clamp conditions on Xenopus laevis oocytes, to differentiate between two models that have been proposed for the relative orientation of the alpha- and beta-subunits. These experiments were performed by measuring the time constant of irreversible donor fluorophore destruction with fluorescein-5-maleimide as the donor fluorophore and in the presence or absence of tetramethylrhodamine-6-maleimide as the acceptor fluorophore following labeling on the M3-M4 or M5-M6 loop of the alpha-subunit and the beta-subunit. We have also used fluorescence resonance energy transfer to investigate the relative movement between the two subunits as the ion pump shuttles between the two main conformational states (E1 and E2) as described by the Albers-Post scheme. The results from this study have identified a model for the orientation of the beta-subunit in relation to the alpha-subunit and suggest that the alpha- and beta-subunits move toward each other during the E2 to E1 conformational transition.

FRET and colocalization analyzer—A method to validate measurements of sensitized emission FRET acquired by confocal microscopy and available as an ImageJ Plug‐in

Fluorescence resonance energy transfer (FRET) between an adequate pair of fluorophores is an indication of closer proximity than colocalization and is used by biologists to study fluorescently modified protein interactions inside cells. We present a method for visualization of FRET images acquired by confocal sensitized emission, involving excitation of the donor fluorophore and detection of the energy transfer as an emission from the acceptor fluorophore into the FRET channel. Authentic FRET signal measurements require the correction from the FRET channel of the undesired bleed-through signals (BT) resulting from both the leak-through of the donor emission and the direct acceptor emission. Our method reduces the interference of the user to a minimum by analyzing the entire image, pixel by pixel. It proposes imaging treatments and the display of control images to validate the BT calculation and the image corrections. It displays FRET images as a function of the colocalization of the two fluorescent partners. Finally, it proposes an alternative to normalization of the FRET intensities to compare FRET signal variations between samples. This method called "FRET and Colocalization Analyzer" has been implemented in a Plug-in of the freely available ImageJ software. It is particularly adapted when transient expression of the fluorescent proteins is used thereby giving very variable expression levels or when the colocalization of the two partners is varying in proportion, in amount, and in size, as a function of time. The method and program are validated using the analysis of the spatio-temporal interactions between a G-protein coupled receptor, the tachykinin NK2 receptor, and the beta-arrestin 2 as an example.

Synthesis of a PEGylated Polymeric pH Sensor and Its pH Sensitivity by Fluorescence Resonance Energy Transfer

A new pH-sensitive polymeric sensor with dispersion stability and biocompatibility is synthesized, and its pH sensitivity is examined on the basis of the fluorescence resonance energy transfer (FRET) efficiency. The polymeric pH sensor has a FRET donor and a FRET acceptor attached to both ends of a pH-sensitive polymeric linker and is also PEGylated to enhance the dispersion stability in aqueous media and biocompatibility. The pH sensor emits the blue color corresponding to the emission of the FRET donor at pHs higher than 7.6, but the pH sensor emits the green color corresponding to the emission of the FRET acceptor at pHs lower than 6.8 when both samples are irradiated at 330 nm, indicating that lowering the pH from 7.6 to 6.8 induces the FRET due to the conformational change of polymeric linker from coil to globule.

Lanthanides to Quantum Dots Resonance Energy Transfer in Time-Resolved Fluoro-Immunoassays and Luminescence Microscopy

A time-resolved fluoro-immunoassay (TR-FIA) format is presented based on resonance energy transfer from visible emitting lanthanide complexes of europium and terbium, as energy donors, to semiconductor CdSe/ZnS core/shell nanocrystals (quantum dots, QD), as energy acceptors. The spatial proximity of the donor-acceptor pairs is obtained through the biological recognition process of biotin, coated at the surface of the dots (Biot-QD), and streptavidin labeled with the lanthanide markers (Ln-strep). The energy transfer phenomenon is evident from simultaneous lanthanide emission quenching and QD emission sensitization with a 1000-fold increase of the QD luminescence decay time reaching the hundred mus regime. Delayed emission detection allows for quantification of the recognition process and demonstrated a nearly quantitative association of the biotins to streptavidin with sensitivity limits reaching 1.2 pM of QD. Spectral characterization permits calculation of the energy transfer parameters. Extremely large Förster radii (R(0)) values were obtained for Tb (104 A) and Eu (96 A) as a result of the relevant spectral overlap of donor emission and acceptor absorption. Special attention was paid to interactions with the varying constituents of the buffer for sensitivity and transfer efficiency optimization. The energy transfer phenomenon was also monitored by time-resolved luminescence microscopy experiments. At elevated concentration (>10(-)(5) M), Tb-strep precipitated in the form of pellets with long-lived green luminescence, whereas addition of Biot-QD led to red emitting pellets, with long excited-state decay times. The Ln-QD donor-acceptor hybrids appear as highly sensitive analytical tools both for TR-FIA and time-resolved luminescence microscopy experiments.