Distance-dependent Phenomenon Research Articles

Gold@Carbon Quantum Dots Nanocomposites Based Two-In-One Sensor: A Novel Approach for Sensitive Detection of Aminoglycosides Antibiotics in Food Samples

Antibiotics are life-saving drugs for humans, but their unwanted use leads to antibacterial resistance (ABR) and causes serious health problems. The excess of these antibiotics entered to the food chain and caused food contamination. Here, Au@CQDs nanocomposites (NCs) was used as a two-in-one sensor to detect two antibiotics. The color change of AuNCs and fluorescence resonance energy transfer are two distance-dependent phenomena used as sensing mechanisms. In the sensing process, Au@CQDs NCs change their color, enhancing the fluorescence intensity of NCs in the presence of Gentamicin (GENTA) and Kanamycin (KMC) antibiotics. The limit of detection of 116 nM and 133 nM for GENTA and 195 nM and 120 nM for KMC have been achieved with colorimetric and fluorimetric readout, respectively. The practicality of the reported sensor was evaluated in real spiked samples and showed excellent recovery efficiency. Therefore this two-in-one sensor can be used for the food monitoring system.

Detecting RNA–Protein Interactions With EGFP‐Cy3 FRET by Acceptor Photobleaching

Förster Resonance Energy Transfer (FRET) is a great tool for cell biologists to investigate molecular interactions in live specimens. FRET is a distance-dependent phenomenon which can detect molecular interactions at distances between 1-10 nm. Several FRET approaches are reported in the literature for live and fixed cells to study protein-protein interactions; this protocol provides details of acceptor photobleaching as a FRET method to study RNA-Protein interactions. Cy3-labeled RNA foci (FRET acceptors) are photobleached at the intra-cellular site of interest (the nuclei) and the intensity of the EGFP-tagged proteins (FRET donors) at that same site are measured pre- and post- photobleaching. In principle, FRET is detected if the intensity of EGFP increases after photobleaching of Cy3. This protocol describes necessary steps and appropriate controls to conduct FRET measurements by the acceptor photobleaching method. Successful applications of this protocol will provide data to support the conclusion that EGFP-labeled proteins directly interact with Cy3-labeled RNA at the site of photobleaching. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: FRET in fixed cells Alternate Protocol: FRET in live cells.

A sensitive dual mode turn-on fluorescence and colorimetric nanosensor for ultrasensitive detection of trace amount of gluten proteins in bread products based on crystalline nano cellulose and gold nanoparticles

In this work, Gold nanoparticles (AuNPs) encapsulated in the surface of crystalline nano cellulose grafted poly citric acid (CNC-g-PCA) and CNC-g-PCA/Au nanocomposite were synthesized successfully that exhibited stable and intense fluorescence property in aqueous buffer. A dual-mode nanosensor is reported with both colorimetric and fluorimetric readout based on citrate-protected AuNPs for discriminative detection of gluten proteins. The proposed sensing system consists of AuNPs and fluorescent CNCs, where CNCs function as a fluorimetric reporter and AuNPs serve a dual function as a colorimetric reporter and fluorescence quencher. The mechanism of the reported dual-mode nanosensor is based on two distance-dependent phenomena, the color change of AuNPs and FRET. The presence of gluten proteins can reverse the process by enlarging the inter-particle distance between AuNPs and CNCs and recovering the fluorescence emission of CNC. The linear range was 0.05 to 0.40 μgmL−1 for UV–vis spectroscopy and 0.017 to 0.298 μgmL−1 for fluorescence spectroscopy, The limit of detection was 4.43 ± 0.019 ngmL−1 for UV–vis spectroscopy and 3.13 ± 0.033 ngmL−1 for fluorescence spectroscopy (n = 6). The fabricated nanosensor was applied to the gluten analysis in gluten-free bread successfully.

(Invited, Digital Presentation) Photovoltaic Applications Using Energy Transfer Characteristics from Quantum Dots

Silicon-related materials are most commonly used in solar cells and become now an invaluable material. However, a reported maximum energy conversion efficiency of Si solar cell is close to reaching its theoretical limits. To further improve the cell performance and create new functions, it will become increasingly important to functionalize Si materials using nanostructures. One- and zero-dimensional Si nanostructures called Si nanowires (SiNWs) and Si quantum dots (Si QDs) are increasingly being used as new solar cell materials. Our group has shown that the conversion efficiency of solar cells can be increased by the non-radiation energy transfer (NRET) from Si QDs [1]. Recently, research has been developed on compound semiconductor QDs and perovskite QDs, and the conversion efficiency has been successfully increased [3-7].n-type SiNW arrays were fabricated by electroless etching and Bosch & nanoimprint lithography followed by CVD process. The CVD process was performed to form p-type Si layer for pn homojunction. Hybrid heterojunction cells of PEDOT:PSS and n-SiNWs were also fabricated. Passivation by ozone and hydrogen were applied to improve the solar cell properties [2]. After the cell fabrications, the solar cells were coated with Si QDs, CdZnS/ZnS QDs, CdZnSe/ZnS QDs and perovskite QDs. The fabrication methods and conditions of QDs have been reported elsewhere [1-7]Energy transfer effects such as NRET are new ways of increasing solar cell efficiency. To effectively use the NRET effect, the surface of Si QDs should be fully passivated by ligand molecules. The NRET process is a highly distance-dependent phenomenon, and its dependence on the length of the passivation ligands clearly showed this. NRET efficiency was increased by shortening the ligand length from 1-octadecene to 1-octene, resulting in higher JSC, ultimately providing higher energy conversion efficiency. The efficiency was increased about 1-2 % by adding SiQDs. We also observed the same effect for CdZnS/ZnS QDs, CdZnSe/ZnS QDs and perovskite CsPbCl3 QDs. In these cases, in addition to the NRET effect, the radiative energy transfer (RET) effect also contributes to the increase in conversion efficiency.

Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET.

To further understand the transcriptome, new tools capable of measuring folding, interactions, and localization of RNA are needed. Although Förster resonance energy transfer (FRET) is an angle- and distance-dependent phenomenon, the majority of FRET measurements have been used to report distances, by assuming rotationally averaged donor–acceptor pairs. Angle-dependent FRET measurements have proven challenging for nucleic acids due to the difficulties in incorporating fluorophores rigidly into local substructures in a biocompatible manner. Fluorescence turn-on RNA aptamers are genetically encodable tags that appear to rigidly confine their cognate fluorophores, and thus have the potential to report angular-resolved FRET. Here, we use the fluorescent aptamers Broccoli and Mango-III as donor and acceptor, respectively, to measure the angular dependence of FRET. Joining the two fluorescent aptamers by a helix of variable length allowed systematic rotation of the acceptor fluorophore relative to the donor. FRET oscillated in a sinusoidal manner as a function of helix length, consistent with simulated data generated from models of oriented fluorophores separated by an inflexible helix. Analysis of the orientation dependence of FRET allowed us to demonstrate structural rigidification of the NiCo riboswitch upon transition metal-ion binding. This application of fluorescence turn-on aptamers opens the way to improved structural interpretation of ensemble and single-molecule FRET measurements of RNA.

Surface-Plasmonic-Field-Induced Photoredox Catalysis and Mediated Electron Transfer for Washing-Free DNA Detection.

Distance-dependent electromagnetic radiation and electron transfer have been commonly employed in washing-free fluorescence and electrochemical bioassays, respectively. In this study, we combined the two distance-dependent phenomena for sensitive washing-free DNA detection. A distance-dependent surface plasmonic field induces rapid photoredox catalysis of surface-bound catalytic labels, and distance-dependent mediated electron transfer allows for rapid electron transfer from the surface-bound labels to the electrode. An optimal system consists of a chemically reversible acceptor (Ru(NH3 )63+ ), a chemically reversible photoredox catalyst (eosin Y), and a chemically irreversible donor (triethanolamine). Side reactions with O2 do not significantly decrease the efficiency of photoredox catalysis. Energy transfer quenching between the electrode and the label can be lowered by increasing the distance between them. Washing-free DNA detection had a detection limit of approximately 0.3 nm in buffer and 0.4 nm in serum without a washing step.

Surface‐Plasmonic‐Field‐Induced Photoredox Catalysis and Mediated Electron Transfer for Washing‐Free DNA Detection

AbstractDistance‐dependent electromagnetic radiation and electron transfer have been commonly employed in washing‐free fluorescence and electrochemical bioassays, respectively. In this study, we combined the two distance‐dependent phenomena for sensitive washing‐free DNA detection. A distance‐dependent surface plasmonic field induces rapid photoredox catalysis of surface‐bound catalytic labels, and distance‐dependent mediated electron transfer allows for rapid electron transfer from the surface‐bound labels to the electrode. An optimal system consists of a chemically reversible acceptor (Ru(NH3)63+), a chemically reversible photoredox catalyst (eosin Y), and a chemically irreversible donor (triethanolamine). Side reactions with O2 do not significantly decrease the efficiency of photoredox catalysis. Energy transfer quenching between the electrode and the label can be lowered by increasing the distance between them. Washing‐free DNA detection had a detection limit of approximately 0.3 nm in buffer and 0.4 nm in serum without a washing step.

An innovative approach for performance enhancement of 320 Gbps free space optical communication system over turbulent channel

Free space optical (FSO) communication systems have recently gained huge attention as possible last mile solution in delivering high speed data services for terrestrial applications. However the FSO link performance, particularly the link range is significantly limited by the severity of atmospheric adversities affecting the channel. In this paper we advocate the use of multi-hop relay techniques to transmit wavelength division multiplexed (WDM) signal over the FSO channel. Since weather induced impairments in FSO links are distance dependent phenomena, hence relay transmission allows substantial performance enhancement by alleviating channel losses while, WDM provides cost effective solution in improving the transmission capacity. With aggregate link losses as high as 40 dB/km, the proposed 32 channel—10 Gbps (320 Gbps) FSO link has been evaluated by comparing bit error rate (BER) performances and eye patterns over different turbulent regimes. Gain optimized EDFA amplification and conventional electrical amplification have been employed to realize amplify-and-forward (A–F) multi-hop transmission in the proposed link with the former delivering more inspiring BER performance of over the latter. Our simulation results indicate that for receiver SNR of 35 dB, BER improvement up to five orders of magnitude can achieved using triple relay FSO link in contrast to direct link operating under similar conditions. Additionally, it is also observed during the analysis that for target BER of 10−5, incorporation of triple relay enhances the link range by approximately 1200 m over direct link. However on the flip side, our investigations also revealed that as the number of relay nodes is increased, the SNR gain for specified BER does increase but the magnitude of gain declines. The proposed link was designed and investigated using OptiSystem™ 14.2.

Protein Environment and DNA Orientation Affect Protein-Induced Cy3 Fluorescence Enhancement

The cyanine dye Cy3 is a popular fluorophore used to probe the binding of proteins to nucleic acids as well as their conformational transitions. Nucleic acids labeled only with Cy3 can often be used to monitor interactions with unlabeled proteins because of an enhancement of Cy3 fluorescence intensity that results when the protein contacts Cy3, a property sometimes referred to as protein-induced fluorescence enhancement (PIFE). Although Cy3 fluorescence is enhanced upon contacting most proteins, we show here in studies of human replication protein A and Escherichia coli single-stranded DNA binding protein that the magnitude of the Cy3 enhancement is dependent on both the protein as well as the orientation of the protein with respect to the Cy3 label on the DNA. This difference in PIFE is due entirely to differences in the final protein-DNA complex. We also show that the origin of PIFE is the longer fluorescence lifetime induced by the local protein environment. These results indicate that PIFE is not a through space distance-dependent phenomenon but requires a direct interaction of Cy3 with the protein, and the magnitude of the effect is influenced by the region of the protein contacting Cy3. Hence, use of the Cy3 PIFE effect for quantitative studies may require careful calibration.

A magnetic resonance tuning sensor for the MRI detection of biological targets.

Sensors that detect specific molecules of interest in a living organism can be useful tools for studying biological functions and diseases. Here, we provide a protocol for the construction of nanosensors that can noninvasively detect biologically important targets with magnetic resonance imaging (MRI). The key operating principle of these sensors is magnetic resonance tuning (MRET), a distance-dependent phenomenon occurring between a superparamagnetic quencher and a paramagnetic enhancer. The change in distance between the two magnetic components modulates the longitudinal (T1) relaxivity of the enhancer. In this MRET sensor, distance variation is achieved by interactive linkers that undergo binding, cleavage, or folding/unfolding upon their interaction with target molecules. By the modular incorporation of suitable linkers, the MRET sensor can be applied to a wide range of targets. We showcase three examples of MRET sensors for enzymes, nucleic acid sequences, and pH. This protocol comprises three stages: (i) chemical synthesis and surface modification of the quencher, (ii) conjugation with interactive linkers and enhancers, and (iii) MRI sensing of biological targets. The entire procedure takes up to 3 d.

A real-time in vitro assay to evaluate the release of macromolecules from liposomes.

The availability of a real-time assay to experimentally investigate the release of encapsulated proteins would be beneficial given the interest in the use of liposomes as a drug delivery vehicle. Although simple assays for small molecular weight substances exist, assays to evaluate macromolecules do not. Here we describe a method that detects the release of model macromolecules from liposomes in real time. The assay employs the intermolecular distance-dependent phenomenon of fluorescence resonance energy transfer (FRET) between the fluorophore donor, fluorescein (FITC), and fluorescent quencher, QSY® 9. The macromolecular species were conjugated to the markers fluorescein (44kDa dextran) and QSY® 9 (67kDa bovine serum albumin, BSA). Following confirmation of quenching between FITC-Dex and QSY® 9-BSA, liposomes were loaded with the macromolecular markers and subjected to various treatments (high-pressure extrusion and Triton X solubilisation) to cause release from liposomes. An increase in FITC fluorescence was observed when liposomes were subjected to extrusion cycles. Surprisingly, the addition of Triton X did not cause an increase in fluorescence probably because the FRET pair became associated with mixed micelles. This assay method should be useful in studies to investigate the mechanisms by which macromolecules are released from liposomes, particularly when liposomes are exposed to release-triggers (eg, temperature change, pH change, ultrasound). Such understanding will underpin the formulation of triggered liposomal delivery systems for macromolecules.

Platinum atomic contacts: From tunneling to contact

We present a theoretical study of the electronic transport through Pt nanocontacts. We show that the analysis of the tunneling regime requires a very careful treatment of the technical details. For instance, an insufficient size of the system can cause unphysical charge oscillations to arise along the transport direction; moreover, the use of an inappropriate basis set can deviate the distance dependence of the conductance from the expected exponential trend. While the conductance decay can be either corrected by employing ghost atoms or a large-cutoff-radius basis set, the same does not apply to the corrugation, for which only the second option is recommended. Interestingly, these details were not found to have a remarkable impact in the contact regime. These findings are important for theoretical studies of distance-dependent phenomena in scanning-probe and break-junction experiments.

Distance-dependent magnetic resonance tuning as a versatile MRI sensing platform for biologicaltargets.

Nanoscale distance-dependent phenomena, such as Förster resonance energy transfer, are important interactions for use in sensing and imaging, but their versatility for bioimaging can be limited by undesirable photon interactions with the surrounding biological matrix, especially in in vivo systems. Here, we report a new type of magnetism-based nanoscale distance-dependent phenomenon that can quantitatively and reversibly sense and image intra-/intermolecular interactions of biologically important targets. We introduce distance-dependent magnetic resonance tuning (MRET), which occurs between a paramagnetic 'enhancer' and a superparamagnetic 'quencher', where the T1 magnetic resonance imaging (MRI) signal is tuned ON or OFF depending on the separation distance between the quencher and the enhancer. With MRET, we demonstrate the principle of an MRI-based ruler for nanometre-scale distance measurement and the successful detection of both molecular interactions (for example, cleavage, binding, folding and unfolding) and biological targets in in vitro and in vivo systems. MRET can serve as a novel sensing principle to augment the exploration of a wide range of biological systems.

How Far Can We Probe by SERS?

Surface-enhanced Raman spectroscopy (SERS) has gained paramount importance in the recent past due to its widespread applications in biodetection, monitoring chemical reactions, small molecule protein interactions, etc. It is believed that SERS is a distance-dependent phenomenon and is effective within 1 nm from the nanoparticle surface. In this work, we have investigated this distance dependence of SERS as a function of nanoparticle size. Earlier attempts have made use of flexible separators, like DNA and chemical molecules, between nanoparticle and analyte to vary the distance. We have used silica coating to vary the distance, without ambiguity, of the analyte from the silver nanoparticle surface. Our results suggest that SERS is observed up to a distance of 1 nm for 20 nm silver nanoparticles juxtaposed to 5 nm in the case of 90 nm silver nanoparticles. This is due to large scattering cross sections and increased radiative damping in the case of the larger nanoparticles. This study gives direct correlat...

Real-Time Monitoring Distance Changes in Surfactant-Coated Au Nanoparticle Films upon Volatile Organic Compounds (VOCs)

We explore into the role of the organic ligands composition surrounding Au nanoparticles (NPs) toward internanoparticles distance changes and film structure during vapor sensing by the use of in situ grazing-incidence small-angle X-ray scattering (GISAXS) and other relevant techniques. We observed distinct changes in core-to-core distance and film structure upon measured concentrations of polar ethanol (EtOH) and nonpolar toluene (Tol) vapors. As-formed tetraoctylammonium bromide (TOABr)-coated Au NPs (SNPs) film exhibited ∼0.4 nm core-to-core increase in distance and improved SNPs correlation upon 80% Tol. In the presence of EtOH, SNPs distance seems not to change and correlation critically diminishes, leading to an amorphous film. As-formed films were exchanged with nonanedithiol (NDT) and exposed to 100% Tol vapor. Interestingly, the incorporation of NDT increased distance between NPs and rendered film flexibility. It is determine that just a small number of S, from NDT ligands, binds to Au NPs, and those exchanged alkanedithiol chains adopted a loop conformation around the Au NPs as evidenced by X-ray absorption near-edge structure (XANES) and kink defects by Fourier transformed infrared (FT-IR) experiments, respectively. These findings may solve some fundamental questions about internanoparticle distance-dependent phenomena such as electron transport in chemiresistors and coupling effects in localized surface plasmon resonance (LSPR) solid-state sensors.

Improving Lanthanide-Based Resonance Energy Transfer Detection by Increasing Donor-Acceptor Distances

Lanthanide-based resonance energy transfer (LRET) is an established method for measuring or detecting proximity between a luminescent lanthanide (energy donor) and an organic fluorophore (energy acceptor). Because resonance energy transfer is a distance-dependent phenomenon that increases in efficiency to the 6th power of the distance between the donor and the acceptor, assay systems are often designed to minimize donor-acceptor distances. However, the authors show that because of the R(6) relationship between transfer efficiency and sensitized emission lifetime, energy transfer can be difficult to measure in a time-gated manner when the donor-acceptor distance is small relative to the Förster radius. In such systems, the advantages inherent in time-resolved, ratiometric measurements are lost but can be regained by designing the system such that the average donor-acceptor distance is increased.

Involvement of phosphodiesterase I in mineralization: histochemical studies using antler from red deer (Cervus elaphus) as a model.

The growing antler of 1-year-old red deer is an excellent system in which to study processes involved in "cartilage model" endochondral-type bone growth. Antlers grow from the tip, permitting the developmental sequences of bone formation to be studied as distance-dependent phenomena, in which early processes can be observed at the distal end, and later events are sequentially more proximal. Quantitative light microscope histochemical assays for alkaline phosphatase (ALP) and phosphodiesterase I (PDE I) were used to determine the activities of these two phosphohydrolases in relation to antler mineralization and remodeling. Both enzymes were absent in proliferating young cartilage near the end, but progressively increased in activity in a proximal direction. ALP levels were maximal when mineralization was just beginning, whereas PDE I activity was greatest more proximally, where mineralization was more complete. This study provides strong indirect evidence that each of these enzymes has a function in mineralization, but that their roles are not identical.