Single-molecule quantum-dot fluorescence resonance energy transfer.

Colloidal semiconductor quantum dots are promising for single-molecule biological imaging due to their outstanding brightness and photostability. As a proof of concept for single-molecule fluorescence resonance energy transfer (FRET) applications, we measured FRET between a single quantum dot and a single organic fluorophore Cy5. DNA Holliday junction dynamics measured with the quantum dot/Cy5 pair are identical to those obtained with the conventional Cy3/Cy5 pair, that is, conformational changes of individual molecules can be observed by using the quantum dot as the donor.     

Continuous-flow protease assay based on fluorescence resonance energy transfer

A homogeneous continuous-flow assay using fluorescence resonance energy transfer (FRET) for detection was developed to measure the hydrolysis of HIV Protease Substrate 1 (to which two choromophores, EDANS and DABCYL are covalently attached) by a protease (e.g. Subtilisin Carlsberg) and the influence of inhibitors. In the continuous-flow assay, an inhibitor solution and an enzyme solution were first eluted into the system and allowed to react with each other in a reaction coil. Subsequently, the substrate solution was added to an enzyme-inhibitor mixture in a second reaction coil and incubated for 1 min. Finally, the fluorescence intensity was monitored.The system was also utilized to measure the inhibition of the protease by two weak acidity inhibitors which are 4-(2-aminoethyl)benzenesulfonyl fluoride hydrochloride (AEBSF) and ethylenediaminetetraacetic acid (EDTA). Using the obtained optimum conditions for AEBSF, a detection limit of 0.3 mmol/l was achieved and the relative standard deviation was below 3.7% in the 2.5-7.5 mmol/l range. For EDTA, which required a 20 times higher substrate concentration than AEBSF, a detection limit of 0.2 mmol/l was obtained and the relative standard deviation was below 9.6% in the 0.5-7.5 mmol/l range.The optimization of pH, substrate concentration, enzyme concentration, reaction time and temperature are described. Organic modifier effects were also investigated. Methanol, acetonitrile and DMSO could be tolerated up to 30%.     

A homogeneous fluorescence resonance energy transfer system for monitoring the activation of a protein switch in real time

A homogeneous fluorescence resonance energy transfer (FRET) system for the real-time monitoring of exchange factor-catalyzed activation of a ras-like small GTPase is described. The underlying design is based on supramolecular template effects exerted by protein-protein interactions between the GTPase adenosine diphosphate ribosylation factor (ARF) and its effector protein GGA3. The GTPase is activated when bound to guanosine triphosphate (GTP) and switched off in its guanosine diphosphate (GDP)-bound state. Both states are accompanied by severe conformational changes that are recognized by GGA3, which only binds the GTPase "on" state. GDP-to-GTP exchange, i.e., GTPase activation, is catalyzed by the guanine nucleotide exchange factor cytohesin-2. When GGA3 and the GTPase ARF1 are labeled with thoroughly selected FRET probes, with simultaneous recording of the fluorescence of an internal tryptophan residue in ARF1, the conformational changes during the activation of the GTPase can be monitored in real time. We applied the FRET system to a multiplex format that allows the simultaneous identification and distinction of small-molecule inhibitors that interfere with the cytohesin-catalyzed ARF1 activation and/or with the interaction between activated ARF1-GTP and GGA3. By screening a library of potential cytohesin inhibitors, predicted by in silico modeling, we identified new inhibitors for the cytohesin-catalyzed GDP/GTP exchange on ARF1 and verified their increased potency in a cell proliferation assay.     

Design and synthesis of an enzyme-cleavable sensor molecule for phosphodiesterase activity based on fluorescence resonance energy transfer

Ratiometric measurement is a technique that can provide precise data and even quantitative detection. To carry out ratiometric measurements, it is necessary that the sensor molecule exhibits a large shift in its emission or excitation spectrum after reaction with the target molecule. Fluorescence resonance energy transfer (FRET) is one mechanism used to obtain a large spectral shift. In this study, our aim was to develop a ratiometric fluorescent sensor molecule for phosphodiesterase activity based on FRET. We designed and synthesized CPF4 with a coumarin donor, a fluorescein acceptor, and two phenyl linkers having the phosphodiester moiety interposed between them. In the emission spectrum of CPF4 in aqueous buffer excited at 370 nm, the emission of the coumarin donor was strongly quenched and the emission of the fluorescein acceptor was observed. This emission spectrum demonstrates that energy transfer from the coumarin donor to the fluorescein acceptor proceeds efficiently. Addition of a phosphodiesterase to an aqueous solution of CPF4 resulted in an increase in the donor fluorescence and a decrease in the acceptor fluorescence. CPF4 exhibited a large shift in its emission spectrum after the hydrolysis of the phosphodiester group by the enzyme. This large shift of the emission spectrum indicates that ratiometric measurements can be made by using CPF4. The method described in this paper for designing enzyme-cleavable sensor molecules based on FRET should be readily applicable to other hydrolytic enzymes.     

Homogeneous non-competitive bioaffinity assay based on fluorescence resonance energy transfer

A homogeneous non-competitive assay principle for measurement of small analytes based on quenching of fluorescence is described. Fluorescence resonance energy transfer (FRET) occurs between the donor, intrinsically fluorescent europium(III)-chelate conjugated to streptavidin, and the acceptor, quencher dye conjugated to biotin derivative when the biotin-quencher is bound to Eu-streptavidin. Fluorescence can be measured only from those streptavidins that are bound to biotin of the sample, while the fluorescence of the streptavidins that are not occupied by biotin are quenched by quencher-biotin conjugates. The quenching efficiencies of the non-fluorescent quencher dyes were over 95% and one dye molecule was able to quench the fluorescence of more than one europium(III)-chelate. This, however, together with the quadrovalent nature of streptavidin limited the measurable range of the assay to 0.2-2 nmol L⁻¹. In this study we demonstrated that FRET could be used to design a non-competitive homogeneous assay for a small analyte resulting in equal performance with competitive heterogeneous assay.     

量子点荧光共振能量转移检测赭曲霉毒素A

基于量子点与荧光猝灭基团之间构成的荧光共振能量转移体系,以量子点标记赭曲霉毒素A适配体与荧光猝灭基团标记的补体杂交构成荧光传感探针,当有赭曲霉毒素A存在时,由于其适配体与赭曲霉毒素A的高度亲和作用,使传感探针上结合的荧光猝灭剂减少,荧光增强,从而建立了一种检测赭曲霉毒素A的荧光分析方法.该方法简单、快速、特异性强,在适...     

RNA degradation in cell extracts: real-time monitoring by fluorescence resonance energy transfer

Short noncoding RNAs are increasingly recognized as key regulators of essential cellular processes such as RNA interference. A better understanding of the processes by which such RNAs are degraded is necessary to expand our knowledge of these processes and our ability to harness them. To this end we have developed a novel fluorescence resonance energy transfer (FRET) assay to monitor in real-time the degradation kinetics of short RNAs by a purified RNase and S100 cytosolic HeLa cell extract. An unstructured RNA is found to be degraded more rapidly than a stem-loop RNA under all conditions tested except for low concentrations of cell extract, showing that secondary structure confers protection against RNase activity. The assay also allows for the quantitative comparison of inhibitors such as Contrad70 and aurin tricarboxylic acid (ATA). Finally, gel electrophoretic FRET analysis confirms that HeLa cell extract is dominated by 5' to 3' exonucleolytic activity.     

Molecular distribution sensing in a fluorescence resonance energy transfer based affinity assay for glucose

A newly developed method for determining molecular distribution functions is applied to a widely researched glucose affinity sensor. The reduction in fluorescence resonance energy transfer (FRET) to a malachite green (MG)-dextran complex from allophycocyanin (APC) bound to concanavalin A (ConA) due to displacement of the complex by glucose from ConA provides the basis of the assay. The higher sensitivity and specificity of a new approach to fluorescence decay analysis, over the methods based on conventional Forster-type models, is demonstrated and critical parameters in competitive binding FRET sensing derived.     

Modulating fluorescence resonance energy transfer in conjugated liposomes

We report here a novel system where the rate of energy transfer is based on changes in the spectral overlap between the emission of the donor and the absorption of the acceptor (J) as well as changes in the quantum yield of the acceptor. We use the fluorophore dansyl as the donor and polydiacetylene (PDA) as the acceptor to demonstrate the modulation of FRET through conformationally induced changes in the PDA absorption spectrum following thermal treatment that converts the PDA backbone of the liposome from the blue form to the red form. Energy transfer was found to be significantly more efficient from dansyl to the red-form PDA. These findings support the basis of a new sensing platform that utilizes J-modulated FRET as an actuating mechanism.     

Ultrafast fluorescence resonance energy transfer in a micelle

Ultrafast fluorescence resonance energy transfer (FRET) from coumarin 153 (C153) to rhodamine 6G (R6G) is studied in a neutral PEO(20)-PPO(70)-PEO(20) triblock copolymer (P123) micelle and an anionic micelle (sodium dodecyl sulfate, SDS) using a femtosecond up-conversion setup. Time constants of FRET were determined from the rise time of the acceptor emission. It is shown that a micelle increases efficiency of FRET by holding the donor and the acceptor at a close distance (intramicellar FRET) and also by tuning the donor and acceptor energies. It is demonstrated that in the P123 micelle, intramicellar FRET (i.e., donor and acceptor in same micelle) occurs in 1.2 and 24 ps. In SDS micelle, there are two ultrafast components (0.7 and 13 ps) corresponding to intramicellar FRET. The role of diffusion is found to be minor in the ultrafast components of FRET. We also detected a much longer component (1000 ps) for intramicellar FRET in the larger P123 micelle.     

Sensitive turn-on fluorescent detection of tartrazine based on fluorescence resonance energy transfer

We introduce a sensitive, rapid, label-free and general fluorescent method for the determination of tartrazine by competitive binding to reduced graphene oxide (rGO) against fluorescein, and the fluorescence recovery upon fluorescein desorption from rGO provides a quantitative readout for tartrazine, giving a detection limit of 0.53 ng mL(-1).     

Sensitive turn-on fluorescent detection of melamine based on fluorescence resonance energy transfer

We here report a novel fluorescent method for the detection of melamine based on the high fluorescence quenching ability of gold nanoparticles. The fluorescence was significantly quenched via fluorescence resonance energy transfer when fluorescein molecules were attached to the surface of gold nanoparticles by electrostatic interaction. Upon addition of melamine, the fluorescence was enhanced due to the competitive adsorption of gold nanoparticles between melamine and fluorescein. Under the optimum conditions, the fluorescence enhancement efficiency [(I-I(0))/I(0)] showed a linear relationship with the concentration of melamine in the range of 1.0 × 10(-7) mol L(-1)~4.0 × 10(-6) mol L(-1), and the detection limit was calculated to be 1.0 × 10(-9) mol L(-1). The proposed method showed several advantages such as high sensitivity, short analysis time, low cost and ease of operation.     

Two-dimensional fluorescence resonance energy transfer as a probe for protein folding: a theoretical study

We describe a two-dimensional (2D), four-color fluorescence resonance energy transfer (FRET) scheme, in which the conformational dynamics of a protein is followed by simultaneously observing the FRET signal from two different donor-acceptor pairs. For a general class of models that assume Markovian conformational dynamics, we relate the properties of the emission correlation functions to the rates of elementary kinetic steps in the model. We further use a toy folding model that treats proteins as chains with breakable cross-links to examine the relationship between the cooperativity of folding and FRET data and to establish what additional information about the folding dynamics can be gleaned from 2D, as opposed to one-dimensional FRET experiments. We finally discuss the potential advantages of the four-color FRET over the three-color FRET technique.     

A fluorescence turn-on method for real-time monitoring of protease activity based on the electron transfer between a fluorophore labeled oligonucleotide and cytochrome c

A new continuous fluorescence turn-on assay for protease activity and inhibitor screening has been developed. A fluorophore labeled single stranded DNA (FAM-DNA) and cytochrome c (cyt c) were employed. The fluorescence of the FAM-DNA was efficiently quenched when binding to cyt c, through the electron transfer between the FAM fluorophore and the heme cofactor of cyt c. In the presence of a protease, such as trypsin, cyt c was digested into small peptide fragments. The FAM-DNA was released, which resulted in the recovery of the FAM fluorescence. The rate of the cyt c digestion could be reduced via the addition of an inhibitor. As a result, reduced degree of the fluorescence recovery was obtained. The limit of detection of our assay is 1 nM trypsin and the IC₅₀ values are 3.23 μg mL⁻¹ and 0.303 μg mL⁻¹ for the inhibitor from egg white and the inhibitor from soybean, respectively. Our method could be used for the sensing of protease activity for various biochemical applications, and for the screening of protease inhibitors as drugs for the treatment of various related diseases.     

Clear evidence of fluorescence resonance energy transfer in gas-phase ions

Fluorescence resonance energy transfer (FRET) is a distance-sensitive method that correlates changes in fluorescence intensity with conformational changes, for example, of biomolecules in the cellular environment. Applied to the gas phase in combination with Fourier transform ion cyclotron resonance mass spectrometry, it opens up possibilities to define structural/conformational properties of molecular ions, in the absence of solvent, and without the need for purification of the sample. For successfully observing FRET in the gas phase it is important to find suitable fluorophores. In this study several fluorescent dyes were examined, and the correlation between solution-phase and gas-phase fluorescence data were studied. For the first time, FRET in the gas phase is demonstrated unambiguously.     

A fluorometric aptasensor for methamphetamine based on fluorescence resonance energy transfer using cobalt oxyhydroxide nanosheets and carbon dots

Cobalt oxyhydroxide (CoOOH) nanosheets are efficient fluorescence quenchers due to their specific optical properties and high surface area. The combination of CoOOH nanosheets and carbon dots (CDs) has not been used in any aptasensor based on fluorescence quenching so far. An aptamer based fluorometric assay is introduced that is making use of fluorescent CDs conjugated to the aptamer against methamphetamine (MTA), and of CoOOH nanosheets which reduce the fluorescence of the CDs as a quencher. The results revealed that the conjugated CDs with aptamers were able to enclose the CoOOH nanosheets. Consequently, fluorescence is quenched. If the aptamer on the CD binds MTA, the CDs are detached from CoOOH nanosheets. As a result, fluorescence is restored proportionally to zhe MTA concentration. The fluorometric limit of detection is 1 nM with a dynamic range from 5 to 156 nM. The method was validated by comparing the results obtained by the new method to those obtained by ion mobility spectroscopy. Theoretical studies showed that the distance between CoOOH nanosheet and C-Ds is approximately 7.6 Å which can illustrate the possibility of FRET phenomenon. The interactions of MTA and the aptamer were investigated using molecular dynamic simulation (MDS).

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Graphical abstract Carbon dots (C-Ds) were prepared from grape leaves, conjugated to aptamer, and adsorbed on CoOOH nanosheets. So, the fluorescence of C-Ds is quenched. On addition of MTA, fluorescence is restored.

     

Biotin induced fluorescence enhancement in resonance energy transfer and application for bioassay

A novel method to significantly enhance fluorescence resonance energy transfer (FRET) signal which occurred from fluoresceine isothiocyanate (FITC) to Dylight 549 was studied in this paper. Streptavidin was labeled with the donor fluorophore FITC and biotinamide was conjugated to the acceptor Dylight 549. When biotinamide bound to streptavidin, FRET would occur from FITC to Dylight 549 while a remarkable fluorescence enhancement of streptavidin-FITC was observed. The fluorescence enhancement of streptavidin-FITC in the presence of biotin was utilized in the FRET system to obtain higher fluorescence signal. Increase of fluorescence intensity of FITC and decrease of Dylight 549 depended on the concentration of competitive biotin. A homogeneous analysis method was established based on the fluorescence recovery of FITC in the FRET system with fluorescence enhancement. This method is highly sensitive and simple to determine the concentration of biotin. The detection limit for biotin was 0.5 nM and the linear range of the assay was 0.8-9.8 nM. The response time is no more than 15 min during the one-step assay due to the high affinity between streptavidin and biotin.     

Split aptamer-based sandwich fluorescence resonance energy transfer assay for 19-nortestosterone

In order to develop an aptamer based fluorescence resonance energy transfer (FRET) assay for 19-nortestosterone, a 76-mer 17β-estradiol aptamer was split into two pieces (referred to as P1 and P2, respectively). P1 was labeled with a quencher (BHQ), and P2 with a fluorophore (6FAM). The two aptamer pieces were employed to detect NT via FRET quenching in a homogeneous solution. This method has a low detection limit (5 μM) within a wide dynamic range (5 to 1000 μM). The approach was used to analyze spiked urine samples, and the results showed that the average recovery of three samples containing different NT concentrations ranged from 58 to 118 % with a relative standard deviation (RSD) of less than 1 %. In our perception, the method has a wide scope for future applications to other analytes by using dually labeled split aptamers.

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Graphical abstract A split aptamer-based fluorescence resonance energy transfer assay for 19-nortestosterone was developed with a wide dynamic range of 5 to 1000 μM and low detection limit (5 μM). The average recovery from spiked urine samples ranged from 58 to 118 %, with a relative standard deviation (RSD) of less than 1 %.

     

Development of a new fluorescent probe for transition metal cations based upon fluorescence resonance energy transfer

A novel fluorescent probe for metal cations, which has a large Stokes shift, was synthesized from the reaction of N-(3-carboxy-2-naphthyl)-ethylenediamine-N,N′,N′-triacetic acid (CNEDTA) with 4-(N,N-dimethylaminosulfonyl)-7-(2-aminoethylamino)-2,1,3-benzoxadiazole (DBD-ED). The large Stokes shift is due to the FRET phenomenon between a donor (CNEDTA) and an acceptor (DBD-ED) fluorophore. When the fluorescent probe, DBD-ED-CNEDTA, was excited at 240, 340 and 440 nm, an emission maximum was observed only at 560 nm. However, the fluorescence (FL) at 480 nm, based upon the CNEDTA moiety, was not detected with excitation at 340 nm. The FL intensity of DBD-ED-CNEDTA was dependent upon the acidity of the medium and highest at pH 4.1. DBD-ED-CNEDTA reacted with metal cations, i.e., Zn, Cd, Al, Y, and La, in aqueous medium to form chelates. The spectral change of FL excitation and emission was small before and after the addition of the metal ions. However, the FL intensity was dependent upon the concentrations of the metal ions. In the case of Zn²⁺, the molar ratio bound with DBD-ED-CNEDTA was calculated as 1:1. The FL intensities after chelate formation of Zn/DBD-ED-CNEDTA (1:1) were enhanced by 3.8-fold (excitation at 340 nm, emission at 560 nm), 4.2-fold (excitation at 440 nm, emission at 560 nm), and 5.9-fold (excitation at 240 nm, emission at 560 nm), respectively. The FL probe was applied to the determination of Zn in a food supplement.