Investigation of the weak binding of a tetrahistidine‐tagged peptide to quantum dots by using capillary electrophoresis with fluorescence detection

Capillary electrophoresis with fluorescence detection was utilized to probe the self‐assembly between cyanine group dye labeled tetrahistidine containing peptide and CdSe/ZnS quantum dots, inside the capillary. Quantum dots and cyanine group dye labeled tetrahistidine containing peptide were injected into the capillary one after the other and allowed to self‐assemble. Their self‐assembly resulted into a measurable Förster resonance energy transfer signal between quantum dots and cyanine group dye labeled tetrahistidine containing peptide. The Förster resonance energy transfer signal increased upon increasing the cyanine group dye labeled tetrahistidine containing peptide/quantum dot molar ratio and reached a plateau at the 32/1 molar ratio. Additionally, the Förster resonance energy transfer signal was also affected by the increment of the interval time of injection and the sampling time. Online ligand exchange experiments were used to assess, the potential of a monovalent ligand of imidazole and a hexavalent ligand peptide, to displace surface bound cyanine group dye labeled peptide ligands from the quantum dots surface. Under optimal conditions, a linear relationship between the integrated peak areas and hexavalent ligand peptide was obtained at a hexavalent ligand concentration range of 0−0.5 mM. Therefore, the present assay has the potential to be applied in the online ligands detection.     

In‐capillary probing of quantum dots and fluorescent protein self‐assembly and displacement using Förster resonance energy transfer

Herein, a Förster resonance energy transfer system was designed, which consisted of CdSe/ZnS quantum dots donor and mCherry fluorescent protein acceptor. The quantum dots and the mCherry proteins were conjugated to permit Förster resonance energy transfer. Capillary electrophoresis with fluorescence detection was used for the analyses for the described system. The quantum dots and mCherry were sequentially injected into the capillary, while the real‐time fluorescence signal of donor and acceptor was simultaneously monitored by two channels with fixed wavelength detectors. An effective separation of complexes from free donor and acceptor was achieved. Results showed quantum dots and hexahistidine tagged mCherry had high affinity and the assembly was affected by His₆‐mCherry/quantum dot molar ratio. The kinetics of the self‐assembly was calculated using the Hill equation. The microscopic dissociation constant values for out of‐ and in‐capillary assays were 10.49 and 23.39 μM, respectively. The capillary electrophoresis with fluorescence detection that monitored ligands competition assay further delineated the different binding capacities of histidine containing peptide ligands for binding sites on quantum dots. This work demonstrated a novel approach for the improvement of Förster resonance energy transfer for higher efficiency, increased sensitivity, intuitionistic observation, and low sample requirements of the in‐capillary probing system.     

Characterization of the Self-Assembly of Glutathione Stabilized Cadmium Selenide–Zinc Sulfide Quantum Dots with a Cyanine5-Labeled Peptide by Capillary Electrophoresis and Fluorescence

Capillary electrophoresis with fluorescence detection was used to characterize the self-assembly of cadmium selenide–zinc sulfide quantum dots and a cyanine5-labeled peptide (cyanine5-EAAAAAHHHHHH). The self-assembly was driven by metal-affinity forces to allow characterization by Förster resonance energy transfer. The Förster resonance energy transfer signal increased with the ratio of cyanine5-EAAAAAHHHHHH to quantum dots and reached a plateau at a ratio of 32:1. This method illustrates the application of quantum dot-based bioanalysis.     

On the possibility of nonradiative energy transfer between hydrophobic quantum dots in solutions

The Förster resonance energy transfer between CdSe quantum dots with two different sizes has been studied in an organic solvent upon the formation of close-packed aggregates of quantum dots, with the aggregation being both spontaneous and induced by a precipitating solvent. The addition of a precipitant has been established to noticeably increase the efficiency of the energy transfer. It has been shown that the sizes and numbers of resulting aggregates may be controlled by varying the experimental conditions.     

Förster resonance energy transfer in nanoclusters of InP@ZnS colloidal quantum dots with dodecylamine ligand shells

Förster resonance energy transfer between InP@ZnS hydrophobic colloidal quantum dots of two different sizes has been studied in the closely packed nanoclusters formed spontaneously in an organic solvent upon the addition of a precipitating solvent. The quantum dots had a core@shell structure and were stabilized by dodecylamine ligands.     

Specifics of luminescence of nanoclusters consisting of InP@ZnS colloidal quantum dots stabilized by oleylamine

Spectral, luminescent, and kinetic characteristics of nanoclusters of hydrophobic colloidal quantum dots (CQDs) of the core@shell type InP@ZnS stabilized by oleylamine have been studied, with the nanoclusters consisting of CQDs of two average sizes: with core diameters of 2.1 and 3.0 nm. For the nanoclusters consisting of the particles of any of these kinds, the experimental data indicate the occurrence of Förster resonance energy transfer with an efficiency of about 50%. For the mixed nanoclusters, energy transfer has not been observed within the experimental error.     

Fluorescence and Sensing Applications of Graphene Oxide and Graphene Quantum Dots: A Review

Graphene oxide and graphene quantum dots are attractive fluorophores that are inexpensive, nontoxic, photostable, water‐soluble, biocompatible, and environmentally friendly. They find extensive applications in fluorescent biosensors and chemosensors, in which they serve as either fluorophores or quenchers. As fluorophores, they display tunable photoluminescence emission and the “giant red‐edge effect”. As quenchers, they exhibit a remarkable quenching efficiency through either electron transfer or Förster resonance energy transfer (FRET) process. In this review, the origin of fluorescence and the mechanism of excitation wavelength‐dependent fluorescence of graphene oxide and graphene quantum dots are discussed. Sensor design strategies based on graphene oxide and graphene quantum dots are presented. The applications of these sensors in health care, the environment, agriculture, and food safety are highlighted.     

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.     

Nonradiative energy transfer in mixed Langmuir monolayers and Langmuir–Blodgett films of compounds of different chemical composition and structure

Russian Chemical Bulletin - The efficiency of the Förster resonance energy transfer (FRET) in a monolayer film containing the energy donor and energy acceptor fluorophores is low since the...     

THE DISTANCE BETWEEN THE PHYTOCHROME CHROMOPHORE AND THE N-TERMINAL CHAIN DECREASES DURING PHOTOTRANSFORMATION. A NOVEL FLUORESCENCE ENERGY TRANSFER METHOD USING LABELED ANTIBODY FRAGMENTS

A novel antibody-fluorescence method has been developed to elucidate the chromophore topography in phytochrome as it undergoes a photochromic transformation. Förster energy transfer from N-terminal bound, fluorescently labeled Oat-25 Fab antibody fragments to the phytochrome chromophore was measured. The results suggest that the chromophore moves relative to the N-terminus upon the Pr → Pfr phototransformation. This conclusion is consistent with previous models which have proposed a reorientation and an interaction of the Pfr chromophore with the N-terminus. The method described appears to be the first study of a Forster energy transfer measurement using a donor-label attached to a Fab fragment of a photosensor protein.     

Through‐Space Conjugated Molecular Wire Comprising Three π‐Electron Systems

A [2.2]paracyclophane‐based through‐space conjugated oligomer comprising three π‐electron systems was designed and synthesized. The arrangement of three π‐conjugated systems in an appropriate order according to the energy band gap resulted in efficient unidirectional photoexcited energy transfer by the Förster mechanism. The energy transfer efficiency and rate constants were estimated to be >0.999 and >10¹² s^?1, respectively. The key point for the efficient energy transfer is the orientation of the transition dipole moments. The time‐dependent density functional theory (TD‐DFT) studies revealed the transition dipole moments of each stacked π‐electron system; each dipole moment was located on the long axis of each stacked π‐electron system. This alignment of the dipole moments is favorable for fluorescence resonance energy transfer (FRET).     

Direct conjugation of semiconductor nanocrystals to a globular protein to study protein-folding intermediates

In this Article, we study the development of semiconductor nanocrystals (quantum dots of average diameter less than 2 nm) directly conjugated to a transporter protein human serum albumin (HSA) as fluorescent biological labels. F?rster resonance energy transfer (FRET) from the amino acid tryptophan (Trp214) to quantum dot in HSA is monitored to follow the local and global changes in the protein structure during thermal unfolding and refolding processes. This study is likely to attract widespread attention as a powerful tool for the study of protein folding.     

Toward a solid-phase nucleic acid hybridization assay within microfluidic channels using immobilized quantum dots as donors in fluorescence resonance energy transfer

The optical properties and surface area of quantum dots (QDs) have made them an attractive platform for the development of nucleic acid biosensors based on fluorescence resonance energy transfer (FRET). Solid-phase assays based on FRET using mixtures of immobilized QD–oligonucleotide conjugates (QD biosensors) have been developed. The typical challenges associated with solid-phase detection strategies include non-specific adsorption, slow kinetics of hybridization, and sample manipulation. The new work herein has considered the immobilization of QD biosensors onto the surfaces of microfluidic channels in order to address these challenges. Microfluidic flow can be used to dynamically control stringency by adjustment of the potential in an electrokinetic-based microfluidics environment. The shearing force, Joule heating, and the competition between electroosmotic and electrophoretic mobilities allow the optimization of hybridization conditions, convective delivery of target to the channel surface to speed hybridization, amelioration of adsorption, and regeneration of the sensing surface. Microfluidic flow can also be used to deliver (for immobilization) and remove QD biosensors. QDs that were conjugated with two different oligonucleotide sequences were used to demonstrate feasibility. One oligonucleotide sequence on the QD was available as a linker for immobilization via hybridization with complementary oligonucleotides located on a glass surface within a microfluidic channel. A second oligonucleotide sequence on the QD served as a probe to transduce hybridization with target nucleic acid in a sample solution. A Cy3 label on the target was excited by FRET using green-emitting CdSe/ZnS QD donors and provided an analytical signal to explore this detection strategy. The immobilized QDs could be removed under denaturing conditions by disrupting the duplex that was used as the surface linker and thus allowed a new layer of QD biosensors to be re-coated within the channel for re-use of the microfluidic chip.     

Perylene-Cy3 FRET System to Analyze Photoactive DNA Structures

We report a new Förster resonance energy transfer (FRET) system for structural analyses of DNA duplexes using perylene and Cy3 as donor and acceptor, respectively, linked at the termini of a DNA duplex via D-threoninol. Experimentally obtained FRET efficiencies were in good agreement with theoretical values calculated based on canonical B-form DNA. Due to the relatively long Förster radius, this system can be used to analyze large DNA structures, and duplexes containing photo-reactive molecules can be analyzed since perylene can be excited with visible light. The system was used to analyze a DNA duplex containing stilbene, demonstrating that in the region of the stilbene cluster the duplex adopts a ladder-like structure rather than helical one. Upon photodimerization between stilbene residues, FRET efficiencies indicated the reaction does not disturb DNA duplex. This FRET system will be useful for analysis of photoreactions of nucleobases as well as a wide range of nucleic acid structures.     

Rapid,single-step nucleic acid detection

A rapid detection method for nucleic acid based on bioluminescence resonance energy transfer (BRET) from the luminescence donor Renilla luciferase to an acceptor quantum dot upon oligonucleotide probe hybridization has been developed. Utilizing a competitive assay, we detected the target nucleic acid by correlating the BRET signal with the amount of target present in the sample. This method allows for the detection of as little as 4 pmol (20 nM) of nucleic acid in a single-step, homogeneous format both in vitro in a buffer matrix as well as in a cellular matrix. Using this method, one may perform nucleic acid detection in as little as 30 min, showing much improvement over time-consuming blotting methods and solid-phase methods which require multiple wash steps to remove unbound probe. This is the first report on the use of quantum dots as a BRET acceptor in the development of a nucleic acid hybridization assay. An erratum to this article can be found at     

ROFRET: A Molecular‐Scale Fluorescent Probe Displaying Viscosity‐Enhanced Intramolecular Förster Energy Transfer

The fluorescent probe ROFRET contains a Bodipy molecular rotor connected through a short triazole‐based spacer to a fully alkylated Bodipy. Förster resonance energy transfer takes place from the rotor to the other Bodipy, and is enhanced to a limiting value as the viscosity of the solvent increases. Time‐resolved spectroscopy and steady‐state studies are consistent with both forward and reverse energy transfer, and delayed fluorescence.     

A quantum-dot based protein module for in vivo monitoring of protease activity through fluorescence resonance energy transfer

Here, we present a new generation of nanoscale probes for in vivo monitoring of protease activity by fluorescence resonance energy transfer (FRET). The approach is based on a genetically programmable protein module carrying a fluorescently labeled, protease-specific sequence that can self-assemble onto quantum dots. The protein module was used for real-time detection of human immunodeficiency virus type-1 protease (HIV-1 Pr) activity as well as quantitative assessment of inhibitor efficiency.     

Compact,Polyvalent Mannose Quantum Dots as Sensitive,Ratiometric FRET Probes for Multivalent Protein–Ligand Interactions

A highly efficient cap‐exchange approach for preparing compact, dense polyvalent mannose‐capped quantum dots (QDs) has been developed. The resulting QDs have been successfully used to probe multivalent interactions of HIV/Ebola receptors DC‐SIGN and DC‐SIGNR (collectively termed as DC‐SIGN/R) using a sensitive, ratiometric Förster resonance energy transfer (FRET) assay. The QD probes specifically bind DC‐SIGN, but not its closely related receptor DC‐SIGNR, which is further confirmed by its specific blocking of DC‐SIGN engagement with the Ebola virus glycoprotein. Tuning the QD surface mannose valency reveals that DC‐SIGN binds more efficiently to densely packed mannosides. A FRET‐based thermodynamic study reveals that the binding is enthalpy‐driven. This work establishes QD FRET as a rapid, sensitive technique for probing structure and thermodynamics of multivalent protein–ligand interactions.     

Compact,Polyvalent Mannose Quantum Dots as Sensitive,Ratiometric FRET Probes for Multivalent Protein–Ligand Interactions

A highly efficient cap‐exchange approach for preparing compact, dense polyvalent mannose‐capped quantum dots (QDs) has been developed. The resulting QDs have been successfully used to probe multivalent interactions of HIV/Ebola receptors DC‐SIGN and DC‐SIGNR (collectively termed as DC‐SIGN/R) using a sensitive, ratiometric Förster resonance energy transfer (FRET) assay. The QD probes specifically bind DC‐SIGN, but not its closely related receptor DC‐SIGNR, which is further confirmed by its specific blocking of DC‐SIGN engagement with the Ebola virus glycoprotein. Tuning the QD surface mannose valency reveals that DC‐SIGN binds more efficiently to densely packed mannosides. A FRET‐based thermodynamic study reveals that the binding is enthalpy‐driven. This work establishes QD FRET as a rapid, sensitive technique for probing structure and thermodynamics of multivalent protein–ligand interactions.     

A Potential Carcinogenic Pyrene Derivative under Förster Resonance Energy Transfer to Various Energy Acceptors in Nanoscopic Environments

Picosecond‐resolved Förster resonance energy transfer (FRET) from various vibronic bands in benzo[a]pyrene (BP) shows a strong dependency on the spectral overlap of an energy acceptor in a confined environment. Our study on the dipolar interactions between BP and different acceptors, including ethidium (Et), acridine orange (AO), and crystal violet (CV), at the surface of a model anionic micelle revealed that the Förster distance (R₀) and the rate of energy transfer is dependent on the individual spectral overlap of the vibronic bands of BP with the absorption spectra of the different energy acceptors. The differential behavior of the vibronic bands is compared with that of different dyes [quantum dots (QDs)] in a “dye‐blend” (mixture) under FRET to an energy acceptor. Comparison of the FRET of the QDs with that of BP confirmed the independent nature of the dipolar interaction of the vibronic bands with other organic molecules, and the use of deconvolution techniques in the interpretation of the donor–acceptor (D –A) distance was also justified. We also showed that the consideration of differential FRET from the vibronic bands of BP and from the QDs in the dye‐blend is equally acceptable in theoretical frameworks including the Infelta–Tachiya model and D –A distribution analysis in nanoenvironments.