Fluorescence resonance energy transfer (FRET): theory and experiments

Theoretical and experimental investigation of novel quinazoline derivatives: synthesis, photophysical, reactive properties, molecular docking and selective HSA biointeraction

Two new quinazoline derivatives (2a and 2b) were successfully synthesized in this work using the condensation technique in excellent yields. Using spectroscopic techniques and elemental analyses, the compounds were completely characterized. Density functional theory (DFT) computations have been used to examine the title compound's reactive characteristics. Chemical reactivity was predicted using local reactive descriptors and molecule electrostatic potential. Additionally, Time dependent DFT (TD-DFT) simulations were used to examine the impact of solvents on the photophysical characteristics. The affinity of compounds 2a and 2b for human serum albumin (HSA) was further explored using several electronic spectroscopies. Through static mechanisms, both compounds reduce the intrinsic fluorescence of HSA. It is determined that the HSA-2b complex's binding constant is significantly greater than the HSA-2a complex. The fluorescence spectrum measurements proved that the HSA underwent structural changes after interaction with these compounds. It was demonstrated by site marker competitive displacement studies that compounds 2a and 2b preferred to bind to site I in HSA subdomain IIA. Additionally, synchronised fluorescence spectra were utilized to analyze how HSA's conformation changed after interacting with various substances. The molecular docking investigations of these compounds with the three critical HSA binding sites, comprising subdomains IIA, IIIA, and IB, further confirmed the experimental findings. The significant contact between the investigated compounds and HSA was supported by the docking simulations.Communicated by Ramaswamy H. Sarma.

FRET mechanism to enhance the quantum yield of the PCz/gC3N4 nanocomposite, an emissive material for OLED applications

Conjugated polymers such as polycarbazole (PCz) have captivated more attention than other carbazole-based derivatives due to their superior electrical and optical properties. Accordingly, we synthesized PCz/gC3N4 nanocomposites via the in situ polymerization method using FeCl3 as the oxidative reagent. The synthesized nanocomposites were subjected to characterization techniques to examine their optical and electrical parameters and decide whether the materials were suitable as emissive materials. X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR) were carried out to ascertain the crystalline or amorphous nature, surface interactions, and functional groups present in them. The surface microstructural and topographical investigations were conducted using field-emission scanning electron microscopy (FESEM) and transmission electron microscopy (HRTEM) techniques. Optical parameters, such as refractive index ∼2.06, optical absorbance, optical band energy ∼2.77 eV, and the photoluminescence emission range, were studied using UV-Visible and photoluminescence spectrometry. The theoretical relative emission quantum yield of ∼67.9% and 87.7% energy transfer from the donor to the acceptor ion via the Förster energy transfer mechanism are illustrated by the PL data. The Förster energy transfer mechanism has been elaborated. The carrier mobility ∼32.03 m2 V-1 S-1, sheet resistance ∼1.6977 × 102 Ω m, carrier density ∼11.96 × 1014 cm-3 and conductivity ∼5.90 × 10-3 S cm-1 were computed using Hall effect measurements. The dielectric constant, dielectric loss, and IV characteristic curve were estimated by the LCR and Four-probe IV measurement methods. The high PL emission intensity, CIE coordinates in the blue emission region, and the CCT value indicate that it is a suitable emissive layer material for OLED applications.

FRET Based Biosensor: Principle Applications Recent Advances and Challenges

Förster resonance energy transfer (FRET)-based biosensors are being fabricated for specific detection of biomolecules or changes in the microenvironment. FRET is a non-radiative transfer of energy from an excited donor fluorophore molecule to a nearby acceptor fluorophore molecule. In a FRET-based biosensor, the donor and acceptor molecules are typically fluorescent proteins or fluorescent nanomaterials such as quantum dots (QDs) or small molecules that are engineered to be in close proximity to each other. When the biomolecule of interest is present, it can cause a change in the distance between the donor and acceptor, leading to a change in the efficiency of FRET and a corresponding change in the fluorescence intensity of the acceptor. This change in fluorescence can be used to detect and quantify the biomolecule of interest. FRET-based biosensors have a wide range of applications, including in the fields of biochemistry, cell biology, and drug discovery. This review article provides a substantial approach on the FRET-based biosensor, principle, applications such as point-of-need diagnosis, wearable, single molecular FRET (smFRET), hard water, ions, pH, tissue-based sensors, immunosensors, and aptasensor. Recent advances such as artificial intelligence (AI) and Internet of Things (IoT) are used for this type of sensor and challenges.

Contribution of smFRET to Chromatin Research

Chromatins are structural components of chromosomes and consist of DNA and histone proteins. The structure, dynamics, and function of chromatins are important in regulating genetic processes. Several different experimental and theoretical tools have been employed to understand chromatins better. In this review, we will focus on the literatures engrossed in understanding of chromatins using single-molecule Förster resonance energy transfer (smFRET). smFRET is a single-molecule fluorescence microscopic technique that can furnish information regarding the distance between two points in space. This has been utilized to efficiently unveil the structural details of chromatins.

Binding ability of roxatidine acetate and roxatidine acetate supported chitosan nanoparticles towards bovine serum albumin: characterization, spectroscopic and molecular docking studies

The RxAc drug loaded on Tween80-chitosan-TPP nanoparticles (NRxAc) has been characterized and probed by UV-Vis, PXRD, FTIR, DLS and SEM technique. The physicochemical characteristics of NRxAc have been employed and evaluated for formulation of drug, particle size, external morphology, drug content and in vitro drug release. Multi-spectroscopic (i.e. fluorescence, UV-Vis, CD spectroscopy) and molecular docking techniques were also used to study the interaction of BSA with RxAc and NRxAc. RxAc and NRxAc quenched the fluorescence emission of BSA via a static quenching mechanism. The experimental data of Fluorescence demonstrated that the binding constant of RxAc and NRxAc were found around 10⁴ L.mol^-1, which suggests moderate binding affinity with BSA via hydrophobic forces. Through the site marker displacement experiments and molecular docking, the probable binding location of RxAc and NRxAc has been suggested in subdomain IB (site III) of BSA. Altogether, the results of present study can provide an important insight and a great deal of helpful information for future design of antiulcer drugs. Hence, The RxAc-loaded chitosan nanoparticles produced might be utilized as a successful tool for developing and using antiulcer drugs.Communicated by Ramaswamy H. Sarma.

Spectroscopic and Molecular Docking Study of the Interaction between Neutral Re(I) Tetrazolate Complexes and Bovine Serum Albumin

Re(I) complexes have potential in biomedical sciences as imaging agents, diagnostics and therapeutics. Thus, it is crucial to understand how Re(I) complexes interact with carrier proteins, like serum albumins. Here, two neutral Re(I) complexes were used (fac-[Re(CO)₃ (1,10-phenanthroline)L], in which L is either 4-cyanophenyltetrazolate (1) or 4-methoxycarbonylphenyltetrazole ester (2), to study the interactions with bovine serum albumin (BSA). Spectroscopic measurements, calculations of thermodynamic and Förster resonance energy transfer parameters, as well as molecular modelling, were performed to study differential binding between BSA and complex 1 and 2. Induced-fit docking combined with quantum-polarised ligand docking were employed in what is believed to be a first for a Re(I) complex as a ligand for BSA. Our findings provide a basis for other molecular interaction studies and suggest that subtle functional group alterations at the terminal region of the Re(I) complex have a significant impact on the ability of this class of compounds to interact with BSA.

Unique dynamic mode between Artepillin C and human serum albumin implies the characteristics of Brazilian green propolis representative bioactive component

As a representative bioactive component in Brazil green propolis, Artepillin C (ArtC; 3, 5-diprenyl-4-hydroxycinnamic acid) has been reported a wide variety of physiological activities including anti-tumor, anti-inflammatory, and antimicrobial activity etc. However, it seems incompatible that ArtC in vivo was characterized as low absorption efficiency and low bioavailability. In order to obtain the elucidation, we further investigated the physicochemical basis of ArtC interacting with human serum albumin (HSA) in vitro. We found a unique dynamic mode interaction between ArtC and HSA, which is completely different from other reported propolis bioactive components. Thermodynamic analysis showed that hydrophobic interactions and electrostatic forces are the main driving force. The competitive assay indicates that the binding site of ArtC with HSA is close to the Sudlow’s site I. The findings of this study reveal the unique physicochemical transport mechanism of ArtC in the human body, which helps to further understand the uniqueness of the representative functional components of Brazilian green propolis in the human body.

Strategic reconstruction of macrophage-derived extracellular vesicles as a magnetic resonance imaging contrast agent

Reconstruction of extracellular vesicles with imaging agents allows precise downstream analysis using clinical imaging modalities, for example, MRI. This will further improve the biocompatibility of agents thereby enhancing clinical investigations.

Ligand free surface of CdS nanoparticles enhances the energy transfer efficiency on interacting with Eosin Y dye - Helping in the sensing of very low level of chlorpyrifos in water

With an aim to sense the presence of chlorpyrifos (CP) pesticide in water, fluorescence resonance energy transfer (FRET) between the chemically synthesized ligand free CdS nanocrystals (donor) and Eosin Y dye (acceptor) has been studied in presence and absence of CP in the FRET pair system. This prepared water soluble CdS nanocrystals have been characterized by Transmission Electron microscopy (TEM), which shows that CdS nanocrystals are spherical in shape with an average size of 5 nm approximately. Further, Fourier Transform Infrared Spectroscopic (FTIR) study confirms that these CdS nanocrystals are ligand free stable nanocrystals. It has been observed that this CdS nanocrystals and Eosin Y FRET pair can strongly sense the presence of chlorpyrifos (CP) pesticide in water up to a very low concentration of 10 ppb, which is the sensitivity of detection or detection limit. This FRET pair is found to be very simple and cost effective for the sensing of toxic pesticide CP.

Chemical cross-linking of a variety of green fluorescent proteins as Förster resonance energy transfer donors for Yukon orange fluorescent protein: A project-based undergraduate laboratory experience

Förster resonance energy transfer (FRET) is the basis for many techniques used in biomedical research. Due to its wide use in molecular sensing, FRET is commonly introduced in many biology, chemistry, and physics courses. While FRET is of great importance in the biophysical sciences, the complexity and difficulty of constructing FRET experiments has resulted in limited usage in undergraduate laboratory settings. Here, we present a practical undergraduate laboratory experiment for teaching FRET using a diverse set of green-emitting fluorescent proteins (FPs) as donors for a cross-linked Yukon orange FP. This laboratory experiment enables students to make the connection of basic lab procedures to real world applications and can be applied to molecular biology, biochemistry, physical chemistry, and biophysical laboratory courses. Published 2018. This article is a U.S. Government work and is in the public domain in the USA., 46(5):516-522, 2018.

Visualizing Tension and Growth in Model Membranes Using Optical Dyes

Cells dynamically regulate their membrane surface area during a variety of processes critical to their survival. Recent studies with model membranes have pointed to a general mechanism for surface area regulation under tension in which cell membranes unfold or take up lipid to accommodate membrane strain. Yet we lack robust methods to simultaneously measure membrane tension and surface area changes in real time. Using lipid vesicles that contain two dyes isolated to spatially distinct parts of the membrane, we introduce, to our knowledge, a new method to monitor the processes of membrane stretching and lipid uptake in model membranes. Laurdan, located within the bilayer membrane, and Förster resonance energy transfer dyes, localized to the membrane exterior, act in concert to report changes in membrane tension and lipid uptake during osmotic stress. We use these dyes to show that membranes under tension take up lipid more quickly and in greater amounts compared to their nontensed counterparts. Finally, we show that this technique is compatible with microscopy, enabling real-time analysis of membrane dynamics on a single vesicle level. Ultimately, the combinatorial use of these probes offers a more complete picture of changing membrane morphology. Our optical method allows us to remotely track changes in membrane tension and surface area with model membranes, offering new opportunities to track morphological changes in artificial and biological membranes and providing new opportunities in fields ranging from mechanobiology to drug delivery.

Engineering of Optically Encoded Microbeads with FRET-Free Spatially Separated Quantum-Dot Layers for Multiplexed Assays

Quantum dot (QD) encoded microbeads are emerging for multiplexed analysis of biological markers. The quantitative encoding of microbeads prepared with different concentrations of QDs of different colors suffers from resonance energy transfer from the QDs fluorescing at shorter wavelengths to the QDs fluorescing at longer wavelengths. Here, we used the layer-by-layer deposition technique to spatially separate QDs of different colors with several polymer layers so that the distance between them would be larger than the Förster energy transfer radius. We performed fluorescence lifetime measurements to investigate and determine the conditions excluding significant resonance energy transfer between QDs within QD-encoded microbeads. Additionally, the number of QDs adsorbed onto microbeads was systematically established and multilayer structures of the QD-encoded microbead shells were characterized by scanning probe nanotomography. Finally, we prepared eight populations of FRET-free microbeads encoded with QDs of three colors at two intensity levels and demonstrated that all the optical codes are excitable at a single wavelength and may be clearly identified in three channels of a flow cytometer. The developed approach for engineering QD-encoded microbeads that are free from optical artefacts related to inter-QD resonance energy transfer paves the way to quantitative QD-based multiplexed assays.

Proteasome Subunit Selective Activity-Based Probes Report on Proteasome Core Particle Composition in a Native Polyacrylamide Gel Electrophoresis Fluorescence-Resonance Energy Transfer Assay

Most mammalian tissues contain a single proteasome species: constitutive proteasomes. Tissues able to express, next to the constitutive proteasome catalytic activities (β1c, β2c, β5c), the three homologous activities, β1i, β2i and β5i, may contain numerous distinct proteasome particles: immunoproteasomes (composed of β1i, β2i and β5i) and mixed proteasomes containing a mix of these activities. This work describes the development of new subunit-selective activity-based probes and their use in an activity-based protein profiling assay that allows the detection of various proteasome particles. Tissue extracts are treated with subunit-specific probes bearing distinct fluorophores and subunit-specific inhibitors. The samples are resolved by native polyacrylamide gel electrophoresis, after which fluorescence-resonance energy transfer (FRET) reports on the nature of proteasomes present.

Persistent luminescence nanoprobe for biosensing and lifetime imaging of cell apoptosis via time-resolved fluorescence resonance energy transfer

Time-resolved fluorescence technique can reduce the short-lived background luminescence and auto-fluorescence interference from cells and tissues by exerting the delay time between pulsed excitation light and signal acquisition. Here, we prepared persistent luminescence nanoparticles (PLNPs) to design a universal time-resolved fluorescence resonance energy transfer (TR-FRET) platform for biosensing, lifetime imaging of cell apoptosis and in situ lifetime quantification of intracellular caspase-3. Three kinds of PLNPs-based nanoprobes are assembled by covalently binding dye-labeled peptides or DNA to carboxyl-functionalized PLNPs for the efficient detection of caspase-3, microRNA and protein. The peptides-functionalized nanoprobe is also employed for fluorescence lifetime imaging to monitor cell apoptosis, which shows a dependence of cellular fluorescence lifetime on caspase-3 activity and thus leads to an in situ quantification method. This work provides a proof-of-concept for PLNPs-based TR-FRET analysis and demonstrates its potential in exploring dynamical information of life process.

Influence of secondary structure on kinetics and reaction mechanism of DNA hybridization

Hybridization of nucleic acids with secondary structure is involved in many biological processes and technological applications. To gain more insight into its mechanism, we have investigated the kinetics of DNA hybridization/denaturation via fluorescence resonance energy transfer (FRET) on perfectly matched and single-base-mismatched DNA strands. DNA hybridization shows non-Arrhenius behavior. At high temperature, the apparent activation energies of DNA hybridization are negative and independent of secondary structure. In contrast, when temperature decreases, the apparent activation energies of DNA hybridization change to positive and become structure dependent. The large unfavorable enthalpy of secondary structure melting is compensated for by concomitant duplex formation. Based on our results, we propose a reaction mechanism about how the melting of secondary structure influences the hybridization process. A significant point in the mechanism is that the rate-limiting step switches along with temperature variation in the hybridization process of structured DNA, because the free energy profile of hybridization in structured DNA varies with the variation in temperature.

Homogeneous, Competitive Fluorescence Quenching Immunoassay Based on Gold Nanoparticle/Polyelectrolyte Coated Latex Particles

This study reports a homogeneous and competitive fluorescence quenching immunoassay based on gold nanoparticle/polyelectrolyte (Au(NP)/PE) coated latex particles prepared by the layer-by-layer (LbL) technique. First, the resonant energy transfer from a layer of fluorescent PEs to Au(NP) in LbL assembled films on planar substrates was investigated. The quenching efficiency (QE) for the planar films depended on the cube of the distance between the two layers. A QE of 50% was achieved at a distance of ca. 15 nm, indicating that the Au(NP)/PE system is suitable for detecting binding/release events for antibodies. A homogeneous, competitive binding immunoassay for biotin was designed based on Au(NP)/PE-coated polystyrene particles of 488 nm diameter as quenching agents for a fluorescein isothiocyanate labeled anti-biotin immunoglobulin (FITC-anti-biotin IgG). Biotin molecules were localized on the Au(NP)/PE-coated latexes by depositing a layer of biotinylated poly(allylamine hydrochloride) (B-PAH), and FITC-anti-biotin IgGs were subsequently bound to the particles through interaction with the biotin on B-PAH. Transmission electron microscopy and quartz crystal microgravimetry confirmed the multilayer formation on latex particles and planar gold surfaces, respectively. The biotin-functionalized Au(NP)/PE-coated latexes terminated by FITC-anti-biotin IgG exhibited a dynamic sensing range of 1-50 nmol. These results indicate that Au(NP)/PE-coated latexes can be readily used as dynamic range tunable sensors.

Development of dual receptor biosensors: an analysis of FRET pairs

The development of a dual receptor detection method for enhanced biosensor monitoring was investigated by analyzing potential fluorescent resonance energy transfer (FRET) pairs. The dual receptor scheme requires the integration of a chemical transducer system with two unique protein receptors that bind to a single biological agent. The two receptors are tagged with special molecular groups (donors and acceptors fluorophores) while the chemical transduction system relies on the well-known mechanisms of FRET. During the binding event, the two FRET labeled receptors dock at the binding sites on the surface of the biological agent. The resulting close proximity of the two fluorophores upon binding will initiate the energy transfer resulting in fluorescence. The paper focuses on the analysis and optimization of the chemical transduction system. A variety of FRET fluorophore pairs were tested in a spectrofluorimeter and promising FRET pairs were then tagged to the protein, avidin and its ligand, biotin. Due to their affinities, the FRET-tagged biomolecules combine in solution, resulting in a stable, fluorescent signal from the acceptor FRET dye with a simultaneous decrease in fluorescent signal from the donor FRET dye. The results indicate that the selected FRET pairs can be utilized in the development of dual receptor sensors.