Förster Resonance Energy Transfer System Research Articles

A molecularly imprinted polymer-coated CdTe quantum dot nanocomposite for tryptophan recognition based on the Förster resonance energy transfer process

A new ‘turn-on’ Förster resonance energy transfer (FRET) nanosensor for l-tryptophan based on molecularly imprinted quantum dots (QDs) is proposed. The approach combines the advantages of the molecular imprinting technique, the fluorescent characteristics of the QDs and the energy transfer process. Silica-coated CdTe QDs were first synthesized and then molecularly imprinted using a sol–gel process without surfactants. The final composite presents stable fluorescence which increases with the addition of l-tryptophan. This ‘turn-on’ response is due to a FRET mechanism from the l-tryptophan as donor to the imprinted QD as acceptor. QDs are rarely applied as acceptors in FRET systems. The nanosensor shows selectivity towards l-tryptophan in the presence of other amino acids and interfering ions. The l-tryptophan nanosensor exhibits a linear range between 0 and 8 µM concentration, a detection limit of 350 nM and high selectivity. The proposed sensor was successfully applied for the detection of l-tryptophan in saliva. This novel sensor may offer an alternative approach to the design of a new generation of imprinted nanomaterials for the recognition of different analytes.

A homogeneous assay for highly sensitive detection of CaMV35S promoter in transgenic soybean by förster resonance energy transfer between nitrogen-doped graphene quantum dots and Ag nanoparticles

In this work, a novel homogeneous assay for DNA quantitative analysis based on förster resonance energy transfer (FRET) was developed for cauliflwer mosaic virus 35s (CaMV35S) promoter of transgenic soybean detection. The homogenous FRET of fluorescence signal was fabricated by DNA hybridization with probe modified nitrogen-doped graphene quantum dots (NGQDs) and silver nanoparticles (AgNPs), which acted the donor-acceptor pairs for the first time. The highly efficient FRET and unique properties of the NGQDs made the proposed FRET system as a functionalized detection platform for labelling of DNA. Upon the recognition of specific target DNA (tDNA), the FRET between NGQDs and AgNPs was triggered to produce fluorescence quenching, which could be used for tDNA detection. The fabricated homogeneous FRET assay displayed a wide linear range of 0.1–500.0 nM and a low limit of detection 0.03 nM for the detection of CaMV35S (S/N = 3). This proposed biosensor revealed high specificity to detect tDNA, with acceptable intra-assay precision and excellent stability. This method was successfully applied to identify the real sample of 0.5% containing transgenic soybean, which achieved the most of national law regulations. This assay was further validated by polymerase chain reaction as the genetically modified organisms, suggesting that the proposed FRET system is a feasible tool for the further daily genetically modified organism detection.

Failure of the IDA in FRET Systems at Close Inter-Dye Distances Is Moderated by Frequent Low κ(2) Values.

Förster resonance energy transfer (FRET) is analyzed in terms of distance- and orientation-dependent interactions between the transition dipole moments of the involved donor and acceptor molecules. However, the ideal dipole approximation (IDA) is known to fail at short donor-acceptor distances. In this work, we model FRET in a Cy5- and Alexa Fluor 488-labeled double-stranded RNA by means of combined molecular dynamics (MD) simulations and quantum-chemical calculations involving the IDA as well as the more sophisticated monomer transition density (MTD) approach. To this end, the relaxed ground-state geometries of the dyes were fitted to the MD-based structures. Although substantial deviations between IDA and MTD results can be observed for individual snapshots, the statistical impact of the failure on the FRET rates is negligible in the chosen examples. Our results clearly demonstrate that the IDA-based Förster model can still be applied to systems with small donor-acceptor distances, provided that the dyes are not trapped in arrangements with a high IDA failure and that the distribution of the relative transition dipole orientations is fairly isotropic.

Self-Quenching, Dimerization, and Homo-FRET in Hetero-FRET Assemblies with Quantum Dot Donors and Multiple Dye Acceptors

The combination of semiconductor quantum dots (QDs) and Forster resonance energy transfer (FRET) is a powerful tool for bioanalysis and imaging. Through FRET, the dye is able to borrow brightness from the QD, and the FRET efficiency can be tuned through the assembly of multiple acceptor dyes per QD. In principle, the fluorescence intensity from acceptor dyes assembled to a QD donor should always exceed that from the dyes alone, but we observed anomalously low acceptor dye fluorescence intensities in FRET systems with a QD donor and multiple Alexa Fluor 610 (A610) or Alexa Fluor 633 (A633) acceptors. In contrast, fluorescence from Alexa Fluor 555 (A555) or Alexa Fluor 647 (A647) acceptors was well-behaved and agreed with theoretical expectations. The difference between these systems was studied using a combination of UV–visible absorption and fluorescence intensity, lifetime, and anisotropy measurements. Anomalous fluorescence from A610 and A633 arose from the formation of nonfluorescent, H-type dimers of ...

Energy transfer from an individual silica nanoparticle to graphene quantum dots and resulting enhancement of photodetector responsivity.

Förster resonance energy transfer (FRET), referred to as the transfer of the photon energy absorbed in donor to acceptor, has received much attention as an important physical phenomenon for its potential applications in optoelectronic devices as well as for the understanding of some biological systems. If one-atom-thick graphene is used for donor or acceptor, it can minimize the separation between donor and acceptor, thereby maximizing the FRET efficiency (EFRET). Here, we report first fabrication of a FRET system composed of silica nanoparticles (SNPs) and graphene quantum dots (GQDs) as donors and acceptors, respectively. The FRET from SNPs to GQDs with an EFRET of ∼78% is demonstrated from excitation-dependent photoluminescence spectra and decay curves. The photodetector (PD) responsivity (R) of the FRET system at 532 nm is enhanced by 100∼101/102∼103 times under forward/reverse biases, respectively, compared to the PD containing solely GQDs. This remarkable enhancement is understood by network-like current paths formed by the GQDs on the SNPs and easy transfer of the carriers generated from the SNPs into the GQDs due to their close attachment. The R is 2∼3 times further enhanced at 325 nm by the FRET effect.

Boronate Affinity Fluorescent Nanoparticles for Förster Resonance Energy Transfer Inhibition Assay of cis-Diol Biomolecules.

Förster resonance energy transfer (FRET) has been essential for many applications, in which an appropriate donor-acceptor pair is the key. Traditional dye-to-dye combinations remain the working horses but are rather nonspecifically susceptive to environmental factors (such as ionic strength, pH, oxygen, etc.). Besides, to obtain desired selectivity, functionalization of the donor or acceptor is essential but usually tedious. Herein, we present fluorescent poly(m-aminophenylboronic acid) nanoparticles (poly(mAPBA) NPs) synthesized via a simple procedure and demonstrate a FRET scheme with suppressed environmental effects for the selective sensing of cis-diol biomolecules. The NPs exhibited stable fluorescence properties, resistance to environmental factors, and a Förster distance comparable size, making them ideal donor for FRET applications. By using poly(mAPBA) NPs and adenosine 5'-monophosphate modified graphene oxide (AMP-GO) as a donor and an acceptor, respectively, an environmental effects-suppressed boronate affinity-mediated FRET system was established. The fluorescence of poly(mAPBA) NPs was quenched by AMP-GO while it was restored when a competing cis-diol compounds was present. The FRET system exhibited excellent selectivity and improved sensitivity toward cis-diol compounds. Quantitative inhibition assay of glucose in human serum was demonstrated. As many cis-diol compounds such as sugars and glycoproteins are biologically and clinically significant, the FRET scheme presented herein could find more promising applications.

Panchromatic and High-efficient Energy Transfer Assembly Based on Type I Core-shell Quantum Dots

In order to overcome the low energy transfer efficiency of the conventional FRET (Forster resonance energy transfer) system, a novel spectra-matching and distance-controllable CIS@ZnS-SQ FRET assembly has been prepared via ultrasonic self-assembly method, by using the synthesized visible CIS@ZnS type I core-shell quantum dots as energy donor and the near infrared SQ dyes as acceptor. Through controllable synthesis of quantum dots, the absorption and fluorescence performance of FRET system were adjusted by the size of CIS@ZnS, while the distance of energy donor-acceptor and the non-valid charge recombination in the FRET system were controlled by the wide-band shell of quantum dots. The excitons transfer and recombination kinetics in CIS@ZnS-SQ assembly were investigated by the pump-probe femtosecond ultrafast transient absorption measurements, with which results in the FRET-type energy transfer mechanism: CIS*+SQ→CIS+SQ* has been proven and a high energy transfer rate of about 5.0×10 s has been gained between CIS@ZnS and SQ. The excitons’ lifetime and FRET energy transfer efficiency were calculated from the fluorescence decay kinetic curves tested by time-resolved fluorescence measurements. The results show that the energy transfer in CIS@ZnS-SQ depends on the size of CIS@ZnS quantum dots. As the size of CIS@ZnS (mainly refers to the ZnS shell thickness) increases from 2.1±0.4 nm to 2.9±0.4 nm, 4.1±0.3 nm, 5.4±0.5 nm and 7.2±0.5 nm, the fluorescence quantum yield of CIS@ZnS improves from 5.4% to 26%, 33%, 38% and 43.3% as well as the distance between CIS@ZnS and SQ (energy donor and acceptor) increases gradually, which makes the FRET energy transfer efficiency (ηFRET) first rise and then decline. As a result, an optimal ηFRET value of 62.8% was gained in the FRET assembly when the reaction time of ZnS shell was 20 min. This research will have a promising theoretical and practical value for the development of the panchromatic and high-efficiency solar cells.

A flexible approach to assess fluorescence decay functions in complex energy transfer systems.

BackgroundTime-correlated Förster resonance energy transfer (FRET) probes molecular distances with greater accuracy than intensity-based calculation of FRET efficiency and provides a powerful tool to study biomolecular structure and dynamics. Moreover, time-correlated photon count measurements bear additional information on the variety of donor surroundings allowing more detailed differentiation between distinct structural geometries which are typically inaccessible to general fitting solutions.ResultsHere we develop a new approach based on Monte Carlo simulations of time-correlated FRET events to estimate the time-correlated single photon counts (TCSPC) histograms in complex systems. This simulation solution assesses the full statistics of time-correlated photon counts and distance distributions of fluorescently labeled biomolecules. The simulations are consistent with the theoretical predictions of the dye behavior in FRET systems with defined dye distances and measurements of randomly distributed dye solutions. We validate the simulation results using a highly heterogeneous aggregation system and explore the conditions to use this tool in complex systems.ConclusionThis approach is powerful in distinguishing distance distributions in a wide variety of experimental setups, thus providing a versatile tool to accurately distinguish between different structural assemblies in highly complex systems.Electronic supplementary materialThe online version of this article (doi:10.1186/s13628-015-0020-z) contains supplementary material, which is available to authorized users.

Single-step bioassays in serum and whole blood with a smartphone, quantum dots and paper-in-PDMS chips.

The development of nanoparticle-based bioassays is an active and promising area of research, where point-of-care (POC) diagnostics are one of many prospective applications. Unfortunately, the majority of nanoparticle-based assays that have been developed to date have failed to address two important considerations for POC applications: use of instrumentation amenable to POC settings, and measurement of analytes in biological sample matrices such as serum and whole blood. To address these considerations, we present design criteria and demonstrate proof-of-concept for a semiconductor quantum dot (QD)-based assay format that utilizes smartphone readout for the single-step, Förster resonance energy transfer (FRET)-based detection of hydrolase activity in serum and whole blood, using thrombin as a model analyte. Important design criteria for assay development included (i) the size and emission wavelength of the QDs, which had to balance brightness for smartphone imaging, optical transmission through blood samples, and FRET efficiency for signaling; (ii) the wavelength of a light-emitting diode (LED) excitation source, which had to balance transmission through blood and the efficiency of excitation of QDs; and (iii) the use of an array of paper-in-polydimethylsiloxane (PDMS)-on-glass sample chips to reproducibly limit the optical path length through blood to ca. 250 μm and permit multiplexing. Ultimately, CdSe/CdS/ZnS QDs with peak emission at 630 nm were conjugated with Alexa Fluor 647-labeled peptide substrates for thrombin and immobilized on paper test strips inside the sample cells. This FRET system was sensitive to thrombin activity, where the recovery of QD emission with hydrolytic loss of FRET permitted kinetic assays in buffer, serum and whole blood. Quantitative results were obtained in less than 30 min with a limit of detection 18 NIH units mL(-1) of activity in 12 μL of whole blood. Proof-of-concept for a competitive binding assay was also demonstrated with the same platform. Overall, this work demonstrates that the integration of QDs with smartphones and other consumer electronics can potentiate bioassays that are highly amenable to future point-of-care diagnostic applications.

Terbium-based time-gated Förster resonance energy transfer imaging for evaluating protein-protein interactions on cell membranes.

Fluorescence imaging of cells and subcellular compartments is an essential tool to investigate biological processes and to evaluate the development and progression of diseases. In particular, protein-protein interactions can be monitored by Förster resonance energy transfer (FRET) between two proximal fluorophores that are attached to specific recognition biomolecules such as antibodies. We investigated the membrane expression of E- and N-cadherins in three different cell lines used as model systems to study epithelial to mesenchymal transition (EMT) and a possible detection of circulating tumour cells (CTCs). EMT is a key process in cancer metastasis, during which epithelial markers (such as E-cadherin) are down-regulated in the primary tumour whereas mesenchymal markers (such as N-cadherin) are up-regulated, leading to enhanced cell motility, intravasation, and appearance of CTCs. Various FRET donor-acceptor pairs and protein recognition strategies were utilized, in which Lumi4-Tb terbium complexes (Tb) and different organic dyes were conjugated to several distinct E- and N-cadherin-specific antibodies. Pulsed excitation of Tb at low repetition rates (100 Hz) and time-gated (TG) imaging of both the Tb-donor and the dye-acceptor photoluminescence (PL) allowed efficient detection of the EMT markers as well as FRET in the case of sufficient donor-acceptor proximity. Efficient FRET was observed only between two E-cadherin-specific antibodies and further experiments indicated that these antibodies recognized the same E-cadherin molecule, suggesting a limited accessibility of cadherins when they are clustered at adherens junctions. The investigated Tb-to-dye FRET systems provided reduced photobleaching compared to the AlexaFluor 488-568 donor-acceptor pair. Our results demonstrate the applicability and advantages of Tb-based TG FRET for efficient and stable imaging of antibody-antibody interactions on different cell lines. They also reveal the limitations of interpreting colocalization on cell membranes in the case of lacking FRET signals.

Re-evaluation of biotin-streptavidin conjugation in Förster resonance energy transfer applications.

Bioaffinity conjugation between streptavidin (SA) and biotin has been widely used to link donors and acceptors for investigating the distance-dependent Förster resonance energy transfer (FRET). When studying a commonly used FRET system of (QD-SA)-(biotin-DNA-dye) [donor: quantum dot (QD); acceptor: small organic fluorescent dye; and linker: deoxyribose nucleic acid (DNA) molecule via SA-biotin conjugation], however, a contradictory finding was recently reported in the literature. It was found that the FRET lost its dependence on the number of DNA base pairs when using a phosphate-buffered saline (PBS) solution. We found that the conflicted results were caused by the ionic strength of the adopted buffer solutions. Our results suggest that the dependent FRET on the number of DNA bases is favorable in a low-ionic-strength buffer, whereas in relatively high-ionic-strength buffers, the FRET loses the DNA length dependence. We propose that the independence is mainly caused by the conformational change of DNA molecules from a stretched to a coiled mode when the cations in the high-ionic-strength buffer neutralize the negatively charged backbone of DNA molecules, thereby bringing the acceptors close to the donors.

Revolutionizing the FRET-based light emission in core-shell nanostructures via comprehensive activity of surface plasmons.

We demonstrate the surface-plasmon-induced enhancement of Förster resonance energy transfer (FRET)using a model multilayer core-shell nanostructure consisting of an Au core and surrounding FRET pairs, i.e., CdSe quantum dot donors and S101 dye acceptors. The multilayer configuration was demonstrated to exhibit synergistic effects of surface plasmon energy transfer from the metal to the CdSe and plasmon-enhanced FRET from the quantum dots to the dye. With precise control over the distance between the components in the nanostructure, significant improvement in the emission of CdSe was achieved by combined resonance energy transfer and near-field enhancement by the metal, as well as subsequent improvement in the emission of dye induced by the enhanced emission of CdSe. Consequently, the Förster radius was increased to 7.92 nm and the FRET efficiency was improved to 86.57% in the tailored plasmonic FRET nanostructure compared to the conventional FRET system (22.46%) without plasmonic metals.

Experimental and Theoretical Investigation of the Distance Dependence of Localized Surface Plasmon Coupled Förster Resonance Energy Transfer

The distance dependence of localized surface plasmon (LSP) coupled Förster resonance energy transfer (FRET) is experimentally and theoretically investigated using a trilayer structure composed of separated monolayers of donor and acceptor quantum dots with an intermediate Au nanoparticle layer. The dependence of the energy transfer efficiency, rate, and characteristic distance, as well as the enhancement of the acceptor emission, on the separations between the three constituent layers is examined. A d(-4) dependence of the energy transfer rate is observed for LSP-coupled FRET between the donor and acceptor planes with the increased energy transfer range described by an enhanced Förster radius. The conventional FRET rate also follows a d(-4) dependence in this geometry. The conditions under which this distance dependence is valid for LSP-coupled FRET are theoretically investigated. The influence of the placement of the intermediate Au NP is investigated, and it is shown that donor-plasmon coupling has a greater influence on the characteristic energy transfer range in this LSP-coupled FRET system. The LSP-enhanced Förster radius is dependent on the Au nanoparticle concentration. The potential to tune the characteristic energy transfer distance has implications for applications in nanophotonic devices or sensors.

Enhanced Photocurrent Generation by Förster Resonance Energy Transfer between Phospholipid-Assembled Conjugated Oligoelectrolytes and Nile Red

We show that Förster resonance energy transfer (FRET) between a conjugated oligoelectrolyte based on distyrylstilbene (DSSN+) and Nile red can enhance photocurrent generation when the photoagents are assembled vertically on gold electrodes. DSSN+ and Nile red intercalated into phospholipid membranes of unilamellar vesicles were found to form a useful FRET system because of the solvatochromic properties of DSSN+, and the accompanying photophysical properties were suitable for FRET with Nile red. As a result, a FRET efficiency of 93–94% was achieved, as shown by steady-state and time-resolved spectra in vesicle solutions. When Nile red was tethered in a self-assembled monolayer of 11-mercaptoundecanoic acid (MUA) on gold electrodes and phospholipid-assembled DSSN+ was sequentially organized on the MUA layer, the anodic photocurrent increased notably, reaching about 815 nA/cm2 by virtue of FRET between the vertically aligned dyes.

Development of a Robust Model System of FRET using Base Surrogates Tethering Fluorophores for Strict Control of Their Position and Orientation within DNA Duplex

Although distance dependence of Förster resonance energy transfer (FRET) is well-studied and FRET has been extensively applied as "molecular ruler", only limited examples of orientation-dependent FRET have been reported. To create a robust FRET system that precisely reflects the orientation between donor and acceptor, donor and acceptor fluorophores were introduced into a DNA via a D-threoninol scaffold. Strong stacking interactions among intercalated dyes and natural base-pairs suppress free movement of the dyes, clamping them in the duplex in a fixed orientation. Pyrene and perylene were used as donor and acceptor, respectively, and both the distance and orientation between these dyes were systematically controlled by varying the number of intervening AT pairs from 1 to 21 (corresponding to two turns of helix). FRET efficiency determined from static fluorescence measurement did not decrease linearly with the number (n) of inserted AT pairs but dropped significantly every 5 base pairs (i.e., n = 8, 13, and 18), corresponding to a half-turn of the B-type helix. This clearly demonstrates that FRET efficiency reflects the orientation between pyrene and perylene. We also measured time-resolved fluorescence spectroscopy with a streak camera and successfully observed the time-course of the energy transfer directly. As expected, the FRET efficiencies determined from the lifetime of pyrene emission were in good agreement with static measurements. Theoretical calculation of FRET efficiency assuming that the DNA duplex is a rigid cylinder with B-type geometry coincided with the experimental results. We believe that our method of using d-threoninol will contribute to further development of FRET-based measurement techniques.

Nanophotonic Control of the Förster Resonance Energy Transfer Efficiency

We have studied the influence of the local density of optical states (LDOS) on the rate and efficiency of Förster resonance energy transfer (FRET) from a donor to an acceptor. The donors and acceptors are dye molecules that are separated by a short strand of double-stranded DNA. The LDOS is controlled by carefully positioning the FRET pairs near a mirror. We find that the energy transfer efficiency changes with LDOS, and that, in agreement with theory, the energy transfer rate is independent of the LDOS, which allows one to quantitatively control FRET systems in a new way. Our results imply a change in the characteristic Förster distance, in contrast to common lore that this distance is fixed for a given FRET pair.

Construction of a controllable Förster resonance energy transfer system based on G-quadruplex for DNA sensing

Conjugations of oligonucleotides, chromophores, and gold nanoparticles (GNPs) can be used for energy transfer assays to detect DNA. Herein, a homogenous Förster resonance energy transfer (FRET) system employing two-step modification of oligonucleotide on GNPs was reported. The distance between the donor (fluorescein attached onto DNA) and the acceptor (GNPs) was controlled by using the G-rich DNA. In the presence of porphyrin or berberine, which can act as ligands of G-quadruplexes, the G-rich DNA spacer can result into G-quadruplex structure. Therefore, the intimate contact between the fluorophore and the GNP results in efficient energy transfer and fluorescence quenching. After hybridization with target DNA, the G-quadruplex stretched and resulted in an enhancement of fluorescence. So the present FRET system can be used for target DNA sensing with detection limit as low as 40pM (S/N=3). In this study, a relation between the fluorescence quenching efficiency and GNP sizes was found and bigger GNPs had higher fluorescence enhancement after hybridization with target DNA.

Verification and Biophysical Characterization of a New Three‐Color Förster Resonance‐Energy‐Transfer (FRET) System in DNA

AbstractWe report on a new three‐color FRET system consisting of three fluorescent dyes, i.e., of a carbostyril (=quinolin‐2(1H)‐one)‐derived donor D, a (bathophenanthroline)ruthenium complex as a relay chromophore A1, and a Cy dye as A2 (FRET=Förster resonance‐energy‐transfer) (cf. Fig. 1). With their widely matching spectroscopic properties (cf. Fig. 2), the combination of these dyes yielded excellent FRET efficiencies. Furthermore, fluorescence lifetime measurements revealed that the long fluorescence lifetime of the Ru complex was transferred to the Cy dye offering the possibility to measure the whole system in a time‐resolved mode. The FRET system was established on double‐stranded DNA (cf. Fig. 3) but it should also be generally applicable to other biomolecules.

Understanding Nonviral Nucleic Acid Delivery with Quantum Dot-FRET Nanosensors

Nonviral delivery of nucleic acids is a potentially safe and viable therapeutic modality for inherited and acquired diseases. However, current systems have proven too inefficient for widespread clinical translation. The rational design of improved carriers depends on a quantitative, mechanistic understanding of the rate-limiting barriers to efficient intracellular delivery. Separation of the nucleic acid from the carrier is one of the barriers, which may be analyzed by Förster resonance energy transfer (FRET), a mechanism used to detect interactions between fluorescently labeled molecules. When applied to the molecular components of polymer or lipid-based nanocomplexes, FRET provides information on their complexation status, uptake, release and degradation. Recently, the design of FRET systems incorporating quantum dots as energy donors has led to improved signal stability, allowing prolonged measurements, as well as increased sensitivity, enabling direct detection and the potential for multiplexing. The union of quantum dots and FRET is providing new insights into the mechanisms of nonviral nucleic acid delivery through convergent characterization of delivery barriers, and has the potential to accelerate the design of improved carriers to realize the potential of nucleic acid therapeutics and gene medicine.

Construction of a Supramolecular Förster Resonance Energy Transfer System and Its Application Based on the Interaction between Cy3-Labeled Melittin and Phosphocholine Encapsulated Quantum Dots

Due to possessing unique optical properties, semiconductor quantum dots (QDs) have been applied to construct bioconjugates. Using QDs as donors, the Förster resonance energy transfer (FRET) system can be developed and applied to biological imaging and sensing, and various construction strategies have been reported. To provide a new practicable method, we introduce a protocol with two routes to construct a supramolecular FRET system based on the high-affinity interaction between melittin and phosphocholine. Melittin exists with a random coil structure in aqueous environments but will adopt a bent helix when inserted into natural or artificial membranes. Such specific and high affinity protein-membrane interaction makes it possible to construct a QDs-based FRET system. The strategy applying protein-membrane interaction to construct a QDs-based FRET system can be applied to the investigation on the protein-membrane interaction through distance-depended FRET and further proteolysis of trypsin. Because of the existence of various protein-membrane interactions in real life, the system has the potential to be expanded to other related systems.