Fluorescence resonance energy transfer assay for high-throughput screening of ADAMTS1 inhibitors

A disintegrin and metalloprotease with thrombospondin type I motifs-1 (ADAMTS1) plays a crucial role in inflammatory joint diseases and its inhibitors are potential candidates for anti-arthritis drugs. For the purposes of drug discovery, we reported the development and validation of fluorescence resonance energy transfer (FRET) assay for high-throughput screening (HTS) of the ADAMTS1 inhibitors. A FRET substrate was designed for a quantitative assay of ADAMTS1 activity and enzyme kinetics studies. The assay was developed into a 50-μL, 384-well assay format for high throughput screening of ADAMTS1 inhibitors with an overall Z' factor of 0.89. ADAMTS1 inhibitors were screened against a diverse library of 40,960 total compounds with the established HTS system. Four structurally related hits, naturally occurring compounds, kuwanon P, kuwanon X, albafuran C and mulberrofuran J, extracted from the Chinese herb Morus alba L., were identified for further investigation. The results suggest that this FRET assay is an excellent tool, not only for measurement of ADAMTS1 activity but also for discovery of novel ADAMTS1 inhibitors with HTS.     

Fluorescence resonance energy transfer (FRET) in chemistry and biology: Non-F?rster distance dependence of the FRET rate

Fluorescence resonance energy transfer (FRET) is a popular tool to study equilibrium and dynamical properties of polymers and biopolymers in condensed phases and is now widely used in conjunction with single molecule spectroscopy. In the data analysis, one usually employs the F?rster expression which predicts (l/R ⁶) distance dependence of the energy transfer rate. However, critical analysis shows that this e_xpression can be of rather limited validity in many cases. We demonstrate this by explicitly considering a donor-acceptor system, polyfluorene (PF₆)-tetraphenylporphyrin (TPP), where the size of both donor and acceptor is comparable to the distance separating them. In such cases, one may expect much weaker distance (as l/R ² or even weaker) dependence. We have also considered the case of energy transfer from a dye to a nanoparticle. Here we find l/R ⁴ distance dependence at large separations, completely different from F?rster. We also discuss recent application of FRET to study polymer conformational dynamics. Dedicated to Prof J Gopalakrishnan on his 62nd birthday.     

A photochromic acceptor as a reversible light-driven switch in fluorescence resonance energy transfer (FRET)

A method has been developed for the quantitative determination of fluorescence resonance energy transfer (FRET) based on the modulation of donor fluorescence upon the reversible photoconversion of a photochromic acceptor. A model system was devised, consisting of Lucifer Yellow cadaverine (LYC, donor) conjugated to the photochromic molecule, 6-nitroBIPS (1′,3′-dihydro-1′-(2-carboxyethyl)-3′,3′-dimethyl-6-nitrospiro[2H-1-benzopyran-2,2′-(2H)-indoline]). Near-ultraviolet irradiation catalyzes the conversion of the colorless spiropyran (SP) to the colored merocyanine (MC) form of 6-nitroBIPS. Only the MC form absorbs at the emission wavelengths of the donor, thereby potentiating FRET, as demonstrated by quenching of the donor. Subsequent irradiation in the visible MC absorption band reverts 6-nitroBIPS to the SP form and FRET is inactivated. The acceptor exhibited high photostability under repeated cycles of alternating UV–Vis irradiation. In this model system, the intramolecular FRET efficiency was close to 100%. The observed maximal donor quenching of 34±3% was indicative of an equilibrium determined by the high quantum efficiency of forward conversion (SP→MC) induced by near-UV irradiation and a low but finite quantum efficiency of the back reaction resulting from excitation of the MC form directly as well as indirectly (by FRET via the donor). A quantitative formalism for the photokinetic scheme was developed. Photochromic FRET (pcFRET) permits repeated, quantitative, and non-destructive FRET determinations for arbitrary relative concentrations of donor and acceptor and thus offers great potential for monitoring dynamic molecular interactions in living cells over extended observation times by fluorescence microscopy.     

Self-assembled pi-nanotapes as donor scaffolds for selective and thermally gated fluorescence resonance energy transfer (FRET)

Self-assembled nanotapes of a few tailor-made oligo(p-phenylenevinylene)s (OPVs) have been prepared and used as supramolecular donor scaffold to study the fluorescence resonance energy transfer (FRET) to a suitable acceptor. In nonpolar solvents, FRET occurs with nearly 63-81% efficiency, exclusively from the self-assembled OPVs to entrapped Rhodamine B, resulting in the quenching of the donor emission with concomitant formation of the acceptor emission at 625 nm. The efficiency of FRET is considerably influenced by the ability of the OPVs to form the self-assembled aggregates and hence could be controlled by structural variation of the molecules, and polarity of the solvent. Most importantly, FRET could be controlled by temperature as a result of the thermally reversible self-assembly process. The FRET efficiency was significantly enhanced (ca. 90%) in a xerogel film of the OPV1 which is dispersed with relatively less amount of the acceptor (33 mol %), when compared to that of the aggregates in dodecane gel. FRET is not efficient in polar solvents due to weak self-organization of the chromophores. These results indicate that energy transfer occurs exclusively from the self-assembled donor and not directly from the individual donor molecules. The present study illustrates that the self-assembly of chromophores facilitates temperature and solvent controlled FRET within pi-conjugated nanostructures.     

Fluorescence resonance energy transfer disposable sensor for copper(II)

A disposable sensor has been developed for the measurement of copper(II) concentration in aqueous solution based on a change in the fluorescence of porphyrazine 2,7,12,17-tetra-tert-butyl-5,10,15,20-tetraaza-21H,23H-porphine (TP). The sensor was constructed by spin-coating a polyester support with a PVC solution containing TP, a plasticizer, the chelating agent Zincon and the ion-pairing benzetonium chloride. The measurement principle is based on the radiationless resonance energy transfer (RET) from TP immobilized in membrane, and acting as fluorescence donor, to Zincon acting as an acceptor induced by copper(II). The absorption spectrum of the Zincon-Cu(II) complex presents adequate overlapping with the emission spectrum of TP, producing a useful analytical signal by the RET process.The disposable sensor responds to copper(II) irreversibly over a dynamic range from 0.039 to 14 μmol L⁻¹ (2.5-890 μg L⁻¹) with a sensor-to-sensor reproducibility (relative standard deviation RSD) of 1.9%, as log aCu2+, at the medium level of the range and a response time of 10 min. The performance of the optical disposable sensor was tested for the analysis of copper in different types of natural waters (river, well, spring and swimming pool), validating results against a reference procedure.     

Inhibition assay of biomolecules based on fluorescence resonance energy transfer (FRET) between quantum dots and gold nanoparticles

An inhibition assay method was developed based on the modulation in the FRET efficiency between quantum dots (QDs) and gold nanoparticles (AuNPs) in the presence of the molecules which inhibit the interactions between QD- and AuNP-conjugated biomolecules. For the functionalization, AuNPs were first stabilized by chemisorption of n-alkanethiols and then capped with the first generation polyamidoamine (G1 PAMAM) dendrimers. By employing a streptavidin-biotin couple as a model system, avidin was quantitatively analyzed as an inhibitor by sensing the change in photoluminescence (PL) quenching of SA-QDs by biotin-AuNPs. The detection limit for avidin was about 10 nM. It is anticipated that the PL quenching-based sensing system can be used for the quantitative analysis and high throughput screening of molecules which inhibit the specific biomolecular interactions.     

Towards multi-colour strategies for the detection of oligonucleotide hybridization using quantum dots as energy donors in fluorescence resonance energy transfer (FRET)

The potential for a simultaneous two-colour diagnostic scheme for nucleic acids operating on the basis of fluorescence resonance energy transfer (FRET) has been demonstrated. Upon ultraviolet excitation, two-colours of CdSe/ZnS quantum dots with conjugated oligonucleotide probes act as energy donors yielding FRET-sensitized acceptor emission upon hybridization with fluorophore (Cy3 and Alexa647) labeled target oligonucleotides. Energy transfer efficiencies, Förster distances, changes in quantum yield and lifetime, and signal-to-noise with respect to non-specific adsorption have been investigated. The dynamic range and limit-of-detection are tunable with the concentration of QD-DNA conjugate. The Cy3 and Alexa647 acceptor schemes can detect target from 4 to 100% or 10 to 100% of the QD-DNA conjugate concentration, respectively. Nanomolar limits of detection have been demonstrated in this paper, however, results indicate that picomolar detection limits can be achieved with standard instrumentation. The use of an intercalating dye (ethidium bromide) as an acceptor to alleviate non-specific adsorption is also described and increases signal-to-noise from S/N < 2 to S/N = 9-10. The ethidium bromide system had a dynamic range from 8 to 100% of the QD-DNA conjugate concentration and could detect target in a matrix containing an excess of non-complementary nucleic acid.     

Energy transfer in zinc porphyrin-phthalocyanine heterotrimer and heterononamer studied by fluorescence resonance energy transfer (FRET)

Two or eight zinc triphenyl porphyrins were conjugated with Zn-phthalocyanine or H2-phthalocyanine to form ZnPc-(ZnTPP)2, ZnPc-(ZnTPP)8, H2Pc-(ZnTPP)2 and H2Pc-(ZnTPP)8. Energy transfers from the porphyrin moiety to phthalocyanine part were quantitatively studied with the modality of fluorescence resonance energy transfer (FRET). By measuring the fluorescence increment from the phthalocyanine moiety and the decrease from porphyrin part under selective excitation at the B band of the porphyrin part in those conjugated compounds and their equimolar mixture of compositions, energy transfer efficiencies were estimated to be 90% for H2Pc-(ZnTPP)8 and ZnPc-(ZnTPP)8, and 60%, 30% for ZnPc-(ZnTPP)2 and H2Pc-(ZnTPP)2, respectively.     

Fluorescence resonance energy transfer across a mechanical bond of a rotaxane

Fluorescence transfer across a donor-acceptor tagged rotaxane was studied and a small conformational change of the rotaxane observed using fluorescent spectroscopy and ROESY NMR.     

Upconversion nanoparticle-based fluorescence resonance energy transfer assay for Cr(III) ions in urine

A novel assay of chromium(III) ion based on upconversion fluorescence resonance energy transfer was designed and established. Lysine-capped NaYF₄:Yb/Er upconversion nanoparticles (UCNPs) and dimercaptosuccinic acid-capped gold nanoparticles (AuNPs) were used as the energy donor and acceptor, respectively. They were bound together via electrostatic interaction, resulting in the quenching of the fluorescence of UCNPs by AuNPs. Chromium(III) ions can specifically and strongly interact with dimercaptosuccinic acid that was modified on the surface of AuNPs, leading to the separation of AuNPs from UCNPs and the recovery of fluorescence of UCNPs. The fluorescence recovery of UCNPs showed a good linear response to Cr³⁺ concentration in the range of 2–500 nM with a detection limit of 0.8 nM. This method was further applied to determine the levels of Cr³⁺ in urine. Compared with other fluorescence methods, current method displayed very high sensitivity and signal-to-noise ratio because of the excitation of near-infrared that can eliminate autofluorescence, providing a promising examination of biological samples for the diagnostic purposes.     

Fluorescence resonance energy transfer as a probe of peptide cyclization catalyzed by nonribosomal thioesterase domains

Macrocyclization of synthetic peptides by thioesterase (TE) domains excised from nonribosomal peptide synthetases (NRPS) has been limited to peptides that contain TE-specific recognition elements. To alter substrate specificity of these enzymes by evolution efforts, macrocyclization has to be detected under high-throughput conditions. Here we describe a method to selectively detect cyclic peptides by fluorescence resonance energy transfer (FRET). Using this method, picomolar detection limits were easily realized, providing novel entry for kinetic studies of catalyzed macrocyclization. Application of this method also provides an ideal tool to track TE-mediated peptide cyclization in real time. The general utility of FRET-assisted detection of cyclopeptides was demonstrated for two cyclases, namely tyrocidine (Tyc) TE and calcium-dependent antibiotic (CDA) TE. For the latter cyclase, this approach was combined with site-directed affinity labeling, opening the possibility for high-throughput enzymatic screening.     

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.     

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.     

Application of fluorescence resonance energy transfer (FRET) to investigation of light-induced conformational changes of the phoborhodopsin/transducer complex

The photoreceptor phoborhodopsin (ppR; also called sensory rhodopsin II) forms a complex with its cognate the Halobacterial transducer II (pHtrII) in the membrane, through which changes in the environmental light conditions are transmitted to the cytoplasm in Natronomonas pharaonis to evoke negative phototaxis. We have applied a fluorescence resonance energy transfer (FRET)-based method for investigation of the light-induced conformational changes of the ppR/pHtrII complex. Several far-red dyes were examined as possible fluorescence donors or acceptors because of the absence of the spectral overlap of these dyes with all the photointermediates of ppR. The flash-induced changes of distances between the donor and an acceptor linked to cysteine residues which were genetically introduced at given positions in pHtrII(1-159) and ppR were determined from FRET efficiency changes. The dye-labeled complex was studied as solubilized in 0.1% n-dodecyl-beta-D-maltoside (DDM). The FRET-derived changes in distances from V78 and A79 in pHtrII to V185 in ppR were consistent with the crystal structure data (Moukhametzianov, R. et al. [2006] Nature, 440, 115-119). The distance from D102 in pHtrII linker region to V185 in ppR increased by 0.33 angstroms upon the flash excitation. These changes arose within 70 ms (the dead time of instrument) and decayed with a rate of 1.1 +/- 0.2 s. Thus, sub-angstrom-scale distance changes in the ppR/pHtrII complex were detected with this FRET-based method using far-red fluorescent dyes; this method should be a valuable tool to investigate conformation changes in the transducer, in particular its dynamics.     

Langmuir-Blodgett thin films of quantum dots: synthesis, surface modification, and fluorescence resonance energy transfer (FRET) studies

We describe herein studies on as-prepared hydrophobic ZnS-CdSe quantum dots (QDs) at the air-water interface. Surface pressure-area (pi-A) isotherms have been used to study the monolayer behavior. Uniform, lamellar multilayer thin films of QDs were deposited by the Langmuir-Blodgett (LB) technique. The role of two different surfactant systems commonly employed in the synthesis of these QDs (trioctylphosphine oxide-octadecylamine (TOPO-ODA) system and trioctylphosphine oxide-tetradecylphosphonic acid (TOPO-TDPA) system) on the monolayer behavior and the quality of thin films produced has been investigated. The thin films were characterized by quartz crystal microgravimetry (QCM), contact angle measurements, fluorescence spectroscopy, and transmission electron microscopy (TEM). These QD films were further modified by an amphiphilic polymer, poly(maleic anhydride-alt-1-tetradecene) (PMA). The hydrophobic interaction between the polymers and the surfactants attached to the QDs drove the self-assembly process. The carboxylic acid functional groups in the polymer were also used to immobilize avidin. We have demonstrated a proof of concept for the biosensing strategy wherein the avidin-coated QD films attracted biotinylated gold nanoparticles, resulting in fluorescence resonance energy transfer (FRET) quenching of the thin films.     

Fluorescence resonance energy transfer measurements on cell surfaces. A spectroscopic tool for determining protein interactions.

The interaction of cell surface components may influence several events during the process of transmembrane signalling. Receptor clustering, conformational changes and altered molecular interactions often play essential roles in the final outcome of ligand receptor interactions. Fluorescence resonance energy transfer (FRET) is an excellent tool which can be used to determine distance relationships and supramolecular structure on cell surfaces. This paper reviews the theoretical basis of fluorescence resonance energy transfer, its spectrofluorometric and flow cytometric applications, and provides a critical evaluation of the methods. Finally, examples are given to illustrate the use of the method of fluorescence resonance energy transfer in solving biological problems.