Two-step FRET as a structural tool

The power of FRET to study molecular complexes is expanded by the use of two or more donor/acceptor pairs. A general theoretical framework for distance measurements in three-chromophore systems is presented. Three energy transfer schemes applicable to many diverse situations are considered: (I) two-step FRET relay with FRET between the first and second chromophores and between the second and third, (II) FRET from a single donor to two different acceptors, and (III) two-step FRET relay with FRET also between the first and third chromophores. Equations for the efficiencies involving multiple energy transfer steps are derived for both donor quenching and sensitized emission measurements. The theory is supported by experimental data on model systems of known structure using steady-state donor quenching, lifetime quenching, and sensitized emission. The distances measured in the three-chromophore systems agree with those in two-chromophore systems and molecular models. Finally, labeling requirements for diagnosis of the energy transfer scheme and subsequent distance measurements are discussed.     

Fluorescence lifetime based distance measurement illustrates conformation changes of PYL10-CL2 upon ABA binding in solution state

The fluorescence lifetime based FRET distance measurements using sitespecific incorporated unnatural amino acid HC and Alexa488 as FRET pair revealed the different conformations of PYL10-CL2 upon ABA binding.     

General and reliable quantitative measurement of fluorescence resonance energy transfer using three fluorescence channels

In this paper, we describe a comprehensive general system adapted for quantitative fluorescence resonance energy transfer (FRET) measurement using signals from three channels of a fluorescence instrument. The general FRET measurement system involves two established methods, as well as two novel approaches. Unlike the previous measurements, which can be taken correctly only when the quantity of the acceptor is greater than or equal to that of the donor, one of our novel methods can overcome this obstacle and take quantitative FRET measurements when the donor is in excess of the acceptor. Hence the general FRET measurement system allowed one to determine the exact distance when the donor and acceptor were present in different quantities, and integrated the methods for quantitative FRET measurements. The uniformity of measured values and utility of each method were validated using molecular standards based on DNA oligonucleotide rulers. We also discussed and validated the use of a novel method for estimating the relative quantities of the donor and acceptor fluorophores when they were not known before an appropriate method of this system can be selected.     

β-NaYF4：Yb,Er纳米晶与四甲基异氰酸罗丹明染料分子间的发光共振能量转移研究

Yb^3＋和Er^3＋离子掺杂的NaYF4纳米晶在近红外光（980nm）激发下可产生中心位于539和655nm的上转换发光,其中位于539nm的发光与四甲基异氰酸罗丹明（tetrametrylrhodarnine isothiocyante,TRITC）染料分子的吸收光谱部分重叠.本文基于上述光谱重叠特性,构筑了以β-NaYF4：Yb,Er为能量给体、TRITC为能量受体的发光共振能量转移（LRET）体系.TRITC分子通过静电作用紧密吸附于纳米晶表面,其较近距离的相互作用利于提高LRET效率和体系的稳定性.在980nm近红外光激发下,LRET过程使NaYF4：Yb,Er位于539nm的上转换发光减弱,同时可观察到TRITC染料分子的发光.对发光寿命的研究也证实了β-NaYF4：Yb,Er到TRITC的能量传递.     

CdS量子点与曙红Y间的荧光共振能量转移研究

在水溶液中,量子点与有机荧光染料之间可能发生荧光共振能量转移(FRET)。本文以发射波长470nm的Cd S量子点为供体,曙红Y为受体,建立了Cd S量子点-曙红Y的FRET体系,研究了该体系的FRET参数。该体系受体供体数目比为8,猝灭效率为45.6%,增强效率为20.1%;供体-受体间的距离为4.4nm;临界能量转移距离为2.4nm。     

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.     

A Fluorescent Indicator for Imaging Lysosomal Zinc(II) with Förster Resonance Energy Transfer (FRET)‐Enhanced Photostability and a Narrow Band of Emission

We demonstrate a strategy to transfer the zinc(II) sensitivity of a fluoroionophore with low photostability and a broad emission band to a bright and photostable fluorophore with a narrow emission band. The two fluorophores are covalently connected to afford an intramolecular Förster resonance energy transfer (FRET) conjugate. The FRET donor in the conjugate is a zinc(II)‐sensitive arylvinylbipyridyl fluoroionophore, the absorption and emission of which undergo bathochromic shifts upon zinc(II) coordination. When the FRET donor is excited, efficient intramolecular energy transfer occurs to result in the emission of the acceptor boron dipyrromethene (4,4‐difluoro‐4‐bora‐3a,4a‐diaza‐s‐indacene or BODIPY) as a function of zinc(II) concentration. The broad emission band of the donor/zinc(II) complex is transformed into the strong, narrow emission band of the BODIPY acceptor in the FRET conjugates, which can be captured within the narrow emission window that is preferred for multicolor imaging experiments. In addition to competing with other nonradiative decay processes of the FRET donor, the rapid intramolecular FRET of the excited FRET‐conjugate molecule protects the donor fluorophore from photobleaching, thus enhancing the photostability of the indicator. FRET conjugates 3 and 4 contain aliphatic amino groups, which selectively target lysosomes in mammalian cells. This subcellular localization preference was verified by using confocal fluorescence microscopy, which also shows the zinc(II)‐enhanced emission of 3 and 4 in lysosomes. It was further shown using two‐color structured illumination microscopy (SIM), which is capable of extending the lateral resolution over the Abbe diffraction limit by a factor of two, that the morpholino‐functionalized compound 4 localizes in the interior of lysosomes, rather than anchoring on the lysosomal membranes, of live HeLa cells.     

Energy Relay from an Unconventional Yellow Dye to CdS/CdSe Quantum Dots for Enhanced Solar Cell Performance

A new design for a quasi‐solid‐state Forster resonance energy transfer (FRET) enabled solar cell with unattached Lucifer yellow (LY) dye molecules as donors and CdS/CdSe quantum dots (QDs) tethered to titania (TiO₂) as acceptors is presented. The Forster radius is experimentally determined to be 5.29 nm. Sequential energy transfer from the LY dye to the QDs and electron transfer from the QDs to TiO₂ is followed by fluorescence quenching and electron lifetime studies. Cells with a donor–acceptor architecture (TiO₂/CdS/CdSe/ZnS‐LY/S^2?‐multi‐walled carbon nanotubes) show a maximum incident photon‐to‐current conversion efficiency of 53 % at 530 nm. This is the highest efficiency among Ru‐dye free FRET‐enabled quantum dot solar cells (QDSCs), and is much higher than the donor or acceptor‐only cells. The FRET‐enhanced solar cell performance over the majority of the visible spectrum paves the way to harnessing the untapped potential of the LY dye as an energy relay fluorophore for the entire gamut of dye sensitized, organic, or hybrid solar cells.     

High-Efficiency FRET Processes in BODIPY-Functionalized Quantum Dot Architectures

Efficient FRET systems are developed combining colloidal CdSe quantum dots (QDs) donors and BODIPY acceptors. To promote effective energy transfer in FRET architectures, the distance between the organic fluorophore and the QDs needs to be optimized by a careful system engineering. In this context, BODIPY dyes bearing amino-terminated functionalities are used in virtue of the high affinity of amine groups in coordinating the QD surface. A preliminary QD surface treatment with a short amine ligand is performed to favor the interaction with the organic fluorophores in solution. The successful coordination of the dye to the QD surface, accomplishing a short donor–acceptor distance, provides effective energy transfer already in solution, with efficiency of 76 %. The efficiency further increases in the solid state where the QDs and the dye are deposited as single coordinated units from solution, with a distance between the fluorophores down to 2.2 nm, demonstrating the effectiveness of the coupling strategy.     

Three-dimensional orientational colocalization of individual donor--acceptor pairs

We report on the determination of the three-dimensional orientation of the donor and acceptor transition dipoles in individual fluorescence resonance energy transfer (FRET) pairs by means of scanning optical microscopy with annular illumination. Knowledge of the mutual orientation of the donor and acceptor dipole is mandatory for reliable distance determination based on FRET efficiency measurements. In our model system perylenediimide as the donor and terryelenediimide as the acceptor are coupled via a stiff p-terphenyl linker. The absorption dipoles of the donor and acceptor are selectively addressed by the 488 nm and 647 line of an Ar/Kr mixed gas laser, respectively. A clear deviation from collinearity is observed with a distribution of misalignment angles peaked around 22 degrees.     

Fluorescence resonance energy transfer between quantum dot donors and dye-labeled protein acceptors

We used luminescent CdSe-ZnS core-shell quantum dots (QDs) as energy donors in fluorescent resonance energy transfer (FRET) assays. Engineered maltose binding protein (MBP) appended with an oligohistidine tail and labeled with an acceptor dye (Cy3) was immobilized on the nanocrystals via a noncovalent self-assembly scheme. This configuration allowed accurate control of the donor-acceptor separation distance to a range smaller than 100 A and provided a good model system to explore FRET phenomena in QD-protein-dye conjugates. This QD-MBP conjugate presents two advantages: (1) it permits one to tune the degree of spectral overlap between donor and acceptor and (2) provides a unique configuration where a single donor can interact with several acceptors simultaneously. The FRET signal was measured for these complexes as a function of both degree of spectral overlap and fraction of dye-labeled proteins in the QD conjugate. Data showed that substantial acceptor signals were measured upon conjugate formation, indicating efficient nonradiative exciton transfer between QD donors and dye-labeled protein acceptors. FRET efficiency can be controlled either by tuning the QD photoemission or by adjusting the number of dye-labeled proteins immobilized on the QD center. Results showed a clear dependence of the efficiency on the spectral overlap between the QD donor and dye acceptor. Apparent donor-acceptor distances were determined from efficiency measurements and corresponding F?rster distances, and these results agreed with QD bioconjugate dimensions extracted from structural data and core size variations among QD populations.     

Separation‐free single‐base extension assay with fluorescence resonance energy transfer for rapid and convenient determination of DNA methylation status at specific cytosine and guanine dinucleotide sites

A separation‐free single‐base extension (SBE) assay utilizing fluorescence resonance energy transfer (FRET) was developed for rapid and convenient interrogation of DNA methylation status at specific cytosine and guanine dinucleotide sites. In this assay, the SBE was performed in a tube using an allele‐specific oligonucleotide primer (i.e., extension primer) labeled with Cy3 as a FRET donor fluorophore at the 5′‐end, a nucleotide terminator (dideoxynucleotide triphosphate) labeled with Cy5 as a FRET acceptor, a PCR amplicon derived from bisulfite‐converted genomic DNA, and a DNA polymerase. A single base‐extended primer (i.e., SBE product) that was 5′‐Cy3‐ and 3′‐Cy5‐tagged was formed by incorporation of the Cy5‐labeled terminator into the 3′‐end of the extension primer, but only if the terminator added was complementary to the target nucleotide. The resulting SBE product brought the Cy3 donor and the Cy5 acceptor into close proximity. Illumination of the Cy3 donor resulted in successful FRET and excitation of the Cy5 acceptor, generating fluorescence emission from the acceptor. The capacity of the developed assay to discriminate as low as 10% methylation from a mixture of methylated and unmethylated DNA was demonstrated at multiple cytosine and guanine dinucleotide sites.     

Fluorescence Quenching over Short Range in a Donor‐DNA‐Acceptor System

A new donor‐DNA‐acceptor system has been synthesized containing Nile red‐modified 2′‐deoxyuridine as charge donor and 6‐N,N‐dimethylaminopyrene‐modified 2′‐deoxyuridine as acceptor to investigate the charge transfer in DNA duplexes using fluorescence spectroscopy and time‐resolved femtosecond pump‐probe techniques. Fluorescence quenching experiments revealed that the quenching efficiency of Nile red depends on two components: 1) the presence of a charge acceptor and 2) the number of intervening CG and AT base pairs between donor and acceptor. Surprisingly, the quenching efficiency of two base pairs (73 % for CG and the same for AT) is higher than that for one base pair (68 % for CG and 37 % for AT), while at a separation of three base pairs less than 10 % quenching is observed. A comparison with the results of time‐resolved measurements revealed a correlation between quenching efficiency and the first ultrafast time constant suggesting that quenching proceeds via a charge transfer from the donor to the acceptor. All transients are satisfactorily described with two decays: a rapid charge transfer with 600 fs (～10¹² s^?1) that depends strongly and in a non‐linear fashion on the distance between donor and acceptor, and a slower time constant of a few picoseconds (～10¹¹ s^?1) with weak distance dependence. A third time constant on a nanosecond time scale represents the fluorescence lifetime of the donor molecule. According to these results and time‐dependent density functional theory (TDDFT) calculations a combination of single‐step superexchange and multistep hopping mechanisms can be proposed for this short‐range charge transfer. Furthermore, significantly less quenching efficiency and slower charge transfer rates at very short distances indicate that the direct interaction between donor and acceptor leads to a local structural distortion of DNA duplexes which may provide some uncertainty in identifying the charge transfer rates in short‐range systems.     

Fluorescent resonant energy transfer: correlated fluctuations of donor and acceptor

Mounting evidence suggests that in single-molecule fluorescent resonant energy transfer (FRET) measurements, correlation between fluctuations in donor and acceptor may be important. We present a general theory to describe this correlation and its effect on the FRET rate. The correlation arises from low-energy excitations (e.g., acoustic phonons) of the molecule to which a donor-acceptor pair is attached, and results in an effective interaction between local environments or baths associated with the donor and the acceptor. The correlation is found to reduce the transfer rate, in particular, at short donor-acceptor distances. The theory can quantitatively explain recent measurements of polyproline peptides.     

Estimating the size of laterally phase separated cholesterol domains in model membranes with Förster resonance energy transfer: a simulation study

In this work, we use two vertically-coupled square two-dimensional lattices to simulate membrane bilayers containing a uniform size distribution of cholesterol immiscible domains of a predetermined size distribution. We substitute cholesterols and phospholipids with their fluorescent analogs and calculate the efficiency of energy transfer as a function of acceptor concentration for four membrane configurations. The simulated efficiency of energy transfer as a function of acceptor concentration data is then fit with an analytical FRET model to estimate the domain size, in the same manner in which experimental FRET data is analyzed. The fitted model parameters (domain size and donor partition coefficient) are compared to the simulation inputs to test the applicability of the FRET model to estimating the size of laterally phase separated cholesterol domains. We show that the FRET model yields good size estimates for domains that range between 1 and 25 nm. We also find that the assumed fluorophore configuration in the FRET model leads to a constant under-prediction of these values. Finally, we demonstrate that when two parameters are open to the fit, the FRET model adequately predicts the donor partition coefficient in addition to the domain size.     

Probing Deviation of Adhered Membrane Dynamics between Reconstituted Liposome and Cellular System

The dynamics of cell‐cell adhesion are complicated due to complexities in cellular interactions and intra‐membrane interactions. In the present work, we have reconstituted a liposome‐based model system to mimic the cell‐cell adhesion process. Our model liposome system consists of one fluorescein‐tagged and one TRITC (tetramethyl‐rhodamine isothiocyanate)‐tagged liposome, adhered through biotin‐neutravidin interaction. We monitored the adhesion process in liposomes using Förster Resonance Energy Transfer (FRET) between fluorescein (donor) and TRITC (acceptor). Occurrence of FRET is confirmed by the decrease in donor lifetime as well as distinct rise time of the acceptor fluorescence. Interestingly, the acceptor's emission exhibits fluctuations in the range of ≈3±1 s. This may be attributed to structural oscillations associated in two adhered liposomes arising from the flexible nature of biotin‐neutravidin interaction. We have compared the dynamics in a cell‐mimicking liposome system with that in an in vitro live cell system. In the adhered live cell system, we used CPM (7‐diethylamino‐3‐(4‐maleimido‐phenyl)‐4‐methylcoumarin, donor) and nile red (acceptor), which are known to stain the membrane of CHO (Chinese Hamster Ovary) cells. The dynamics of the adhered membranes of two live CHO cells were observed through FRET between CPM and nile red. The acceptor fluorescence intensity exhibits an oscillation in the time‐scale of ≈1±0.75 s, which is faster compared to the reconstituted liposome system, indicating the contributions and involvement of multiple dynamic protein complexes around the cell membrane. This study offers simple reconstituted model systems to understand the complex membrane dynamics using a FRET‐based physical chemistry approach.     

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.     

A New Robust and Highly Sensitive FRET Donor–Acceptor Pair: Synthesis,Characterization, and Application in a Thrombin Assay

The synthesis of a new, robust fluorescence‐resonance‐energy‐transfer (FRET) system is described. Its donor chromophore is derived from an N‐allyl‐substituted quinolinone attached to 4‐bromophenylalanine via Heck cross‐coupling. The resulting Fmoc‐protected derivative 11 was used as building block in solid‐phase peptide synthesis (SPPS). As FRET acceptor, a sulfonylated ruthenium(II)–bathophenanthroline complex with a peripheral COOH function was prepared for covalent attachment to target molecules. The UV/VIS absorption and emission spectra of peptides bearing only the donor (D) or acceptor (A) dye showed a good overlap of the emission band of the donor with the absorption band of the acceptor. The fluorescence spectra of a peptide bearing both dyes revealed an additional emission after excitation of the donor, which is due to indirect excitation of the acceptor via FRET. The long fluorescence lifetime of the Ru^II complex (0.53 μs) makes it well‐suited for time‐resolved measurements. As a first application of this new FRET system, the peptide 18 , with the recognition sequence for the protease thrombin, flanked by the two dyes, was synthesized and successfully cleaved by the enzyme. The change in the ratio of the fluorescence intensities could be determined.     

High‐Performance Förster Resonance Energy Transfer (FRET)‐Based Dye‐Sensitized Solar Cells: Rational Design of Quantum Dots for Wide Solar‐Spectrum Utilization

High‐performance Förster resonance energy transfer (FRET)‐based dye‐sensitized solar cells (DSSCs) have been successfully fabricated through the optimized design of a CdSe/CdS quantum‐dot (QD) donor and a dye acceptor. This simple approach enables quantum dots and dyes to simultaneously utilize the wide solar spectrum, thereby resulting in high conversion efficiency over a wide wavelength range. In addition, major parameters that affect the FRET interaction between donor and acceptor have been investigated including the fluorescent emission spectrum of QD, and the content of deposited QDs into the TiO₂ matrix. By judicious control of these parameters, the FRET interaction can be readily optimized for high photovoltaic performance. In addition, the as‐synthesized water‐soluble quantum dots were highly dispersed in a nanoporous TiO₂ matrix, thereby resulting in excellent contact between donors and acceptors. Importantly, high‐performance FRET‐based DSSCs can be prepared without any infrared (IR) dye synthetic procedures. This novel strategy offers great potential for applications of dye‐sensitized solar cells.     

G‐Tetraplex‐Induced FRET within Telomeric Repeat Sequences Using PyA‐PerA as Energy Donor–Acceptor Pair

G‐tetraplex induced fluorescence resonance energy transfer (FRET) within telomeric repeat sequences has been studied using a nucleoside‐tethered FRET pair embedded in the human telomeric G‐quadruplex forming sequence (5′‐A GGG TT ^Py A GGG TT ^Per A GGG TTA GGG‐3′, Py=pyrene, Per=perylene). Conformational change from a single strand to an anti‐parallel G‐quadruplex leads to FRET from energy donor ( ^Py A ) to acceptor ( ^Per A ). The distance between the FRET donor/acceptor partners was controlled by changing the number of G‐quartet spacer units. The FRET efficiency decreases with increase in G‐quartet units. Overall findings indicate that this could be further used for the development of FRET‐based sensing and measurement techniques.