Development of FRET-based high-throughput screening for viral RNase III inhibitors.

The class 1 ribonuclease III (RNase III) encoded by Sweet potato chlorotic stunt virus (CSR3) suppresses RNA silencing in plant cells and thereby counters the host antiviral response by cleaving host small interfering RNAs, which are indispensable components of the plant RNA interference (RNAi) pathway. The synergy between sweet potato chlorotic stunt virus and sweet potato feathery mottle virus can reduce crop yields by 90%. Inhibitors of CSR3 might prove efficacious to counter this viral threat, yet no screen has been carried out to identify such inhibitors. Here, we report a novel high-throughput screening (HTS) assay based on fluorescence resonance energy transfer (FRET) for identifying inhibitors of CSR3. For monitoring CSR3 activity via HTS, we used a small interfering RNA substrate that was labelled with a FRET-compatible dye. The optimized HTS assay yielded 109 potential inhibitors of CSR3 out of 6,620 compounds tested from different small-molecule libraries. The three best inhibitor candidates were validated with a dose-response assay. In addition, a parallel screen of the selected candidates was carried out for a similar class 1 RNase III enzyme from Escherichia coli (EcR3), and this screen yielded a different set of inhibitors. Thus, our results show that the CSR3 and EcR3 enzymes were inhibited by distinct types of molecules, indicating that this HTS assay could be widely applied in drug discovery of class 1 RNase III enzymes.

A novel low-cost approach for the semi-quantitative analysis of carbohydrate-deficient transferrin (CDT) based on fluorescence resonance energy transfer (FRET).

BACKGROUND AND AIM: The increase of the carbohydrate-deficient transferrin (CDT) as results of an heavy intake of alcohol for at least two weeks, is a well-known biochemical modification since the middle '70s. Notwithstanding the first commercial kit for the diagnosis of chronic alcohol abuse based on this biomarker was commercially accessible already thirty years ago, only expensive analytical methods are currently available for its determination. The present paper shows a new approach intrinsically sensitive and specific, based on a specific derivatization of transferrin, and not requiring sophisticated instrumentation. METHODS: The proposed procedure is based on a selective chelation of terbium (III) by transferrin followed by detection using an characteristic Fluorescence Resonance Transfer Energy (FRET) phenomenon (ex 298 nm - em 550 nm). RESULTS: The proposed procedure showed a limit of detection of 2.5 pmol/mL and a reproducibility intra-day and inter-days <15% and 20%, respectively. The results obtained analyzing 40 serum samples using the developed method, were compared with those obtained with HPLC-Vis and an R2 = 0.8854 was found. CONCLUSIONS: Considering its main features (low-cost, ease of operation, minimum need of instrumentation) the present method is suitable for application in screening contexts and in non-strictly regulated environments (e.g. clinical diagnosis) as well as in developing countries or remote areas.

A single tube system for the detection of Mycobacterium tuberculosis DNA using gold nanoparticles based FRET assay.

The global combat against MTB is limited by challenges in accurate affordable detection. In this study, a rapid, affordable, single tube system for detection of unamplified MTB16s rDNA was developed. Utilizing a AuNP based FRET system, this assay achieved a sensitivity and specificity of 98.6% and 90% respectively.

Simple, rapid detection of influenza A (H1N1) viruses using a highly sensitive peptide-based molecular beacon.

A peptide-based molecular beacon (PEP-MB) was prepared for the simple, rapid, and specific detection of H1N1 viruses using a fluorescence resonance energy transfer (FRET) system. The PEP-MB exhibited minimal fluorescence in its "closed" hairpin structure. However, in the presence of H1N1 viruses, the specific recognition of the hemagglutinin (HA) protein of H1 strains by the PEP-MB causes the beacon to assume an "open" structure that emits strong fluorescence. The PEP-MB could detect H1N1 viruses within 15 min or even 5 min and can exhibit strong fluorescence even at low viral concentrations, with a detection limit of 4 copies.

A graphene oxide-based FRET sensor for rapid and specific detection of unfolded collagen fragments.

The unstructured collagen species plays a critical role in a variety of important biological processes as well as pathological conditions. In order to develop novel diagnosis and therapies for collagen-related diseases, it is essential to construct simple and efficient methods to detect unfolded collagen fragments. We therefore have designed a FITC-labeled collagen mimic triple helical peptide, whose adsorption on the surface of GO effectively quenches its fluorescence. The newly constructed GO/FITC-GPO complex specifically detects unstructured collagen fragments, but not fully folded triple helix species. The detection shows a clear preference for the collagen targets with complementary GPO-rich sequences. The conformation-sensitive, sequence-specific GO-based approach can be applied as an efficient biosensor for rapid detection of unfolded collagen fragments at nM level, and may have great potential in drug screening for inhibitors of unfolded collagen. It may provide a prototype to develop GO-based assays to detect other important unstructured proteins involved in diseases.

Rapid and efficient pesticide detection via cyclodextrin-promoted energy transfer.

Cyclodextrins facilitate non-covalent fluorescence energy transfer from a variety of pesticides to high quantum-yield fluorophores, resulting in a rapid, sensitive detection scheme for these compounds with detection limits as low as two micromolar. Such a facile detection tool has significant potential applications in agriculture and public health research.

FRET-based homogeneous immunoassay on a nanoparticle-based photonic crystal.

The potential of fluorescence resonance energy transfer (FRET) in a photonic crystal (PC) nanostructured array to enhance the speed and sensitivity of a protein-based immunoassay was tested. Forty-nanometer carboxylated particles conjugated with donor-labeled capture antibodies were trapped by electrophoresis and used as a FRET energy donor. The PC array was able to enhance fluorescent excitation and emission by phase matching. To provide a proof of concept for this FRET-based homogeneous assay on a PC chip, an immunoassay was tested with a simple immunoglobulin G (IgG)-based reaction. A standard curve was generated by testing two different antibody reaction times: 20 min. and 1 min. The results were compared directly to those obtained from a FRET assay that used a modern, high-sensitivity plate reader with a 96-well plate and a reaction time of 1 h. The rabbit-IgG detection limits of the FRET-based homogeneous assay on the PC were 0.001 and 0.1 µg/mL for incubation times of 20 and 1 min, respectively; the sensitivities were 10(3) and 10 times better than the 96-well plate reader, respectively. Thus, FRET on a PC immunoplatform was shown to be a facile, effective, rapid, and sensitive detection technology.

Highly efficient förster resonance energy transfer in a fast, serum-compatible immunoassay.

Highly efficient FRET leads to important enhancements for homogeneous immunoassays. By using the novel phosphorescent dye EuLH and BHQ-10 as a donor-acceptor pair, the FRET efficiency increases to >99.5 %, leading to significantly improved signal-to-background ratio, precision and linear range. The phosphorescence detection enabled full compatibility to serum samples for this fast-responding immunoassay.

FRETex: a FRET-based, high-throughput technique to analyze protein-protein interactions.

Protein-protein interactions (PPIs) are essential for cellular viability and activity. Here, we present a rapid, semi-quantitative method (termed FRETex) to analyze PPIs, taking advantage of the strong and specific FRET signal between fused CyPET donor and YPET acceptor molecules. To demonstrate the robustness of this approach, we analyzed the interactions between three protein pairs and their muteins: TEM1-ß-lactamase binding its inhibitor BLIP, barnase binding barstar and ornithine decarboxylase binding its inhibitor antizyme. The CyPET/YPET fused proteins were produced in small quantities, and the measurements were conducted directly in the proteins crude Escherichia coli lysates without any purification step. Protein concentrations were determined from the fluorescence intensities of the lysates. While binding titration curves were produced, the resulting affinities were not always precise. Therefore, we also conducted time-resolved chase experiments using non-labeled binding partners as chasers. The acquired dissociation rate constants were in a good agreement with those measured by surface plasmon resonance. Due to the simplicity of FRETex, and the ability to obtain semi-quantitative binding data, FRETex is a suitable method for tasks such as mutant scans, protein-engineering, scanning for inhibitors and more.

Novel peptide-protein assay for identification of antimicrobial peptides by fluorescence quenching.

The specific interaction of peptides with proteins is often a key factor which determines biological activities. The determination of K(d) values of such interactions is commonly performed with fluorescence polarization. However, fluorescence polarization assays are prone to false-positive results due to the potential for non-specific interactions and only afford very low signal-to-background ratios. Here, we present as an alternative a fluorescence resonance energy transfer based quenching assay to measure peptide-protein interactions in solution. In a test setup where antimicrobial peptides were tested for their affinity towards the protein DnaK, the assay provided high specificity and good reproducibility and correlated with the results obtained by fluorescence polarization methods. Furthermore, we established a fast prescreening method which will allow a highly efficient screening of peptide libraries by reducing the amount of sample by 98% compared to conventional fluorescence polarization assays.

Detection of biologically active botulinum neurotoxin--A in serum using high-throughput FRET-assay.

INTRODUCTION: The goals of this project were to compare fluorescent resonance energy transfer (FRET) assays using a customized FRET substrate (substrate-substrate-A, SSA) with a commercially available FRET substrate (SNAPtide); optimize the assay conditions for SSA for lowest level of detection; and apply SSA to detect botulinum neurotoxin-A (BoNTA) in serum samples. METHODS: Biological activity of BoNTA and light-chain-A (LCA) was verified by murine phrenic nerve-hemidiaphragm bioassay and western blot before use in both FRET assays. The reaction conditions were optimized to determine the smallest amount of toxin that could be detected. A range of serum samples was investigated for interference in the SSA-based FRET assay. Detection of BoNTA from rat serum samples was performed over time. RESULTS: We found that BoNTA and LCA were able to cleave the substrates whereas mutated LCA and a different serotype of BoNT, BoNTB, could not. SSA had significantly more arbitrary fluorescing units compared to the FRET substrate SNAPTide, and the SSA assay could detect 0.1nM of BoNTA or LCA comfortably (p=<0.05) in a 20-µl reaction. No significant interference was observed when serum was present in the reaction buffer. Due to negligible background noise, the SSA FRET assay could detect BoNTA from spiked rat serum even after 256min. DISCUSSION: The greatest advantage of the FRET assay is its extreme rapidity, its cost effectiveness, and unlike ELISA, its ability to detect biologically active toxin. SSA is a better FRET substrate for detecting BoNTA toxin (detected 0.1nM concentration). Because serum present in the assay reaction did not cause any appreciable interference, the assay can be used to detect BoNTA in serum samples. Therefore, the SSA FRET assay can be used for pharmacokinetic and pharmacodynamic studies, screening inhibitors, and detecting BoNTA in serum samples.

FRET imaging of cells transfected with siRNA/liposome complexes.

By monitoring the efficiency of fluorescence resonance energy transfer of dyes attached to the different strands of siRNA, the structural integrity of the latter can be traced inside cells. Here, the experimental details of dye-labeled siRNA construction, tissue culture, and transfection with liposomally formulated siRNAs are given, as well as the conditions for confocal microscopy and an algorithm allowing the visualization of intact siRNA after image data treatment. The method allows rapid screening of different liposomal siRNA formulations, obtained by small scale dual asymmetric centrifugation with high entrapping efficiency.

Temperature-dependent FRET spectroscopy for the high-throughput analysis of self-assembled DNA nanostructures in real time.

We describe a method for the real-time and high-throughput monitoring of the self-assembly and disassembly of complex DNA superstructures, using temperature-dependent Förster resonance energy transfer (FRET) spectroscopy. Compared with other spectroscopic approaches, such as UV-visible and circular dichroism, the method described has advantages in terms of sensitivity, feasibility for high-throughput analysis and applicability to virtually any kind of supramolecular structure. To this end, two oligonucleotides out of the entire set building up the superstructure are labeled with a fluorescein and a tetramethylrhodamine, as FRET donor and acceptor, respectively. Correct assembly of the superstructure induces maximum FRET efficiency, whereas complete dissociation leads to minimal FRET. Monitoring of temperature-dependent FRET efficiency yields a thermal profile that is used for thermodynamic analysis. In the case of reversible and cooperative assembly/disassembly of the DNA superstructure, application of the van't Hoff law allows for the determination of the thermodynamic parameters of the process. Owing to slow temperature ramping, the entire assay requires about 17 h. The protocol allows to simultaneously analyze up to 384 samples with only 30 microl sample volume each.

A FRET-based analysis of SNPs without fluorescent probes.

Fluorescence resonance energy transfer (FRET) is a simple procedure for detecting specific DNA sequences, and is therefore used in many fields. However, the cost is relatively high, because FRET-based methods usually require fluorescent probes. We have designed a cost-effective way of using FRET, and developed a novel approach for the genotyping of single nucleotide polymorphisms (SNPs) and allele frequency estimation. The key feature of this method is that it uses a DNA-binding fluorogenic molecule, SYBR Green I, as an energy donor for FRET. In this method, single base extension is performed with dideoxynucleotides labeled with an orange dye and a red dye in the presence of SYBR Green I. The dyes incorporated into the extended products accept energy from SYBR Green I and emit fluorescence. We have validated the method with ten SNPs, which were successfully discriminated by end-point measurements of orange and red fluorescence intensity in a microplate fluorescence reader. Using a mixture of homozygous samples, we also confirmed the potential of this method for estimation of allele frequency. Application of this strategy to large-scale studies will reduce the time and cost of genotyping a vast number of SNPs.