Fluorescence Resonance Energy Transfer Research Articles

Single-molecule analysis reveals the phosphorylation of FLS2 governs its spatiotemporal dynamics and immunity.

The Arabidopsis thaliana FLAGELLIN-SENSITIVE2 (FLS2), a typical receptor kinase, recognizes the conserved 22 amino acid sequence in the N-terminal region of flagellin (flg22) to initiate plant defense pathways, which was intensively studied in the past decades. However, the dynamic regulation of FLS2 phosphorylation at the plasma membrane after flg22 recognition needs further elucidation. Through single-particle tracking, we demonstrated that upon flg22 treatment the phosphorylation of Ser-938 in FLS2 impacts its spatiotemporal dynamics and lifetime. Following Förster resonance energy transfer-fluorescence lifetime imaging microscopy and protein proximity indexes assays revealed that flg22 treatment increased the co-localization of GFP-tagged FLS2/FLS2S938D but not FLS2S938A with AtRem1.3-mCherry, a sterol-rich lipid marker, indicating that the phosphorylation of FLS2S938 affects FLS2 sorting efficiency to AtRem1.3-associated nanodomains. Importantly, we found that the phosphorylation of Ser-938 enhanced flg22-induced FLS2 internalization and immune responses, demonstrating that the phosphorylation may activate flg22-triggered immunity through partitioning FLS2 into functional AtRem1.3-associated nanodomains, which fills the gap between the FLS2S938 phosphorylation and FLS2-mediated immunity.

A coumarin-naphthalimide-based ratiometric fluorescent probe for nitroxyl (HNO) based on an ICT-FRET mechanism

Nitroxyl (HNO) is an important reactive nitrogen that is associated with various states in physiology and pathology and plays a unique function in living systems. So, it is important to exploit fluorescent probes with high sensitivity and selectivity for sensing HNO. In this paper, a novel ratiometric fluorescent probe for HNO was developed utilizing intramolecular charge transfer (ICT) and fluorescence resonance energy transfer (FRET) mechanisms. The probe selected coumarin as energy donor, naphthalimide as energy receptor and 2-(diphenylphosphino)benzoate as the sensing site for detecting HNO. When HNO was not present, the 2-(diphenylphosphino)benzoate unit of the probe restricted electron transfer and the ICT process could not occur, leading to the inhibition of FRET process as well. Thus, in the absence of HNO the probe displayed the intrinsic blue fluorescence of coumarin. When HNO was added, the HNO reacted with the 2-(diphenylphosphino)benzoate unit of the probe to yield a hydroxyl group which resulting in the opening of ICT process and the occurring of FRET process. Thus, after providing HNO the probe displayed yellow fluorescence. In addition, the probe showed good linearity in the ratio of fluorescence intensity at 545 nm and 472 nm (I545 nm/I472 nm) with a concentration of HNO (0.1–20 μM). The probe processed a detection limit of 0.014 μM and a response time of 4 min. The probe also specifically identified HNO over a wide pH scope (pH = 4.00–10.00), including physiological conditions. Cellular experiments had shown that this fluorescent probe was virtually non-cytotoxic and could be applied for ratiometric sensing of HNO in A549 cells.

A new insight into the luminescence mechanism of a FRET-ICT-based ratiometric and colorimetric pH probe

Recently, a ratio fluorescent probe molecule BP was designed and synthesized to detect pH in living cells. However, few have conducted in-depth theoretical exploration of the detailed transfer process. In this paper, the luminescence mechanisms of BP and BPH were studied with the results of geometric optimization structures and molecular orbitals at the CAM-B3LYP/TZVP computational level. It was found that a fluorescence resonance energy transfer (FRET) process occurs in the excited state of BP molecules, and the final fluorescence emission is attributed to the intramolecular charge transfer (ICT) of the acceptor styryl pyridine ring. Meanwhile, the fluorescence emission of BPH molecules is due to the ICT process caused by the local excitation process of the acceptor group protonated styryl pyridine ring itself. Therefore, this luminescence is a FRET “ON-OFF” combined ICT process, not like the FRET “OFF-ON” mechanism which the experiment suspected. Our work illustrates a specific FRET combined ICT process of probes BP and BPH from a theoretical perspective which could provide theoretical guidance for the future design of similar fluorescent probes.

Lateral flow assay with dual-emission nitrogen-doped carbon dots for ratiometric fluorescent determination of nitrite in food

Nitrite ion (NO2–), renowned for its potent antiseptic properties and color-preserving abilities, potentially leads to carcinogenesis and hypertension if consumed excessively. Herein, a ratiometric fluorescent probe exhibits specific response to NO2– using nitrogen-doped carbon dots (N-CDs) with a low detection limit (LOD) as low as 52 nM and a low quantification limit (LOQ) of 173 nM. Initially, the emission peaks at 495 nm and 415 nm decrease as result of the internal filtration effect (IFE). With further increasing NO2– concentration, the reaction between NO2– and N-CDs forms an azoic compound (N-CDs@NO2–), which promotes the instant quenching of the emission peak at 415 nm through fluorescence resonance energy transfer (FRET). Moreover, portable N-CDs/LFASs devices with smartphone are successfully applied to visually identify NO2– with the exceptional LOD, achieving excellent recoveries and high precision in real sample. Therefore, this newly N-CDs/LFASs offers a reliable means for the NO2– detection, showcasing potential applications.

Synthesis of four coordination polymers with Zn(II), Cd(II), Mn(II), or Co(II) ions and their application for fluorescence sensing toward nitenpyram, imidacloprid, and vitamin B2

Four new Zn(II)-, Cd(II)-, Mn(II)-, and Co(II)-based 1D to 2D coordination polymers (CPs) were synthesized from metal salts and 1,4-di(1-imidazol-1-yl)naphthalene (DIN) ligand via the coordination reaction under hydrothermal conditions with quantitative yields, namely, [Zn(SO4)(DIN)(H2O)] (CP-1), [Cd(NO3)2(DIN)] (CP-2), [Mn(SO4)(DIN)(H2O)3] (CP-3), and [Co(NO3)2(DIN)2(H2O)4] (CP-4). The CPs were analyzed and characterized using FT-IR, Elemental Analysis, TGA, SC-XRD, and PXRD. CP-1 was selected as a model sensor for fluorescence detection, and the sensor exhibited high quenching rates at two excitation wavelengths of λex = 230 and 290 nm, and at a single emission wavelength of λem = 350 nm. At these two different excitation wavelengths, CP-1 behaved differently during the sensing of pesticides, and the highest quenching rate was achieved by the sensor for nitenpyram (λex = 230 nm) and imidacloprid (λex = 290 nm). Furthermore, during the sensing of vitamins, CP-1 encountered a strong quenching effect toward vitamin B2. During the sensing processes, the inner filter effect (for nitenpyram, imidacloprid, and vitamin B2), fluorescence resonance energy transfer (for nitenpyram, imidacloprid, and vitamin B2), and photo-induced electron transfer (for vitamin B2) were the mechanisms responsible for fluorescence quenching.

Mechanistic Innovations in Fluorescent Chemosensors for Detecting Toxic Ions: PET, ICT, ESIPT, FRET and AIE Approaches.

Fluorescent chemosensors have become vital tools for detecting toxic ions due to their exceptional sensitivity, selectivity, and rapid response times. These sensors function through various mechanisms, each providing unique advantages for specific applications. This review offers a comprehensive overview of the mechanistic innovations in fluorescent chemosensors, emphasizing five key approaches: Photoinduced Electron Transfer (PET), Fluorescence Resonance Energy Transfer (FRET), Intramolecular Charge Transfer (ICT), Aggregation-Induced Emission (AIE), and Excited-State Intramolecular Proton Transfer (ESIPT). We highlight the substantial progress made in developing these chemosensors, discussing their design principles, sensing mechanisms, and practical applications, with a particular focus on their use in detecting toxic ions relevant to environmental and biological contexts.

Single-Molecule Imaging of Integral Membrane Protein Dynamics and Function.

Integral membrane proteins (IMPs) play central roles in cellular physiology and represent the majority of known drug targets. Single-molecule fluorescence and fluorescence resonance energy transfer (FRET) methods have recently emerged as valuable tools for investigating structure-function relationships in IMPs. This review focuses on the practical foundations required for examining polytopic IMP function using single-molecule FRET (smFRET) and provides an overview of the technical and conceptual frameworks emerging from this area of investigation. In this context, we highlight the utility of smFRET methods to reveal transient conformational states critical to IMP function and the use of smFRET data to guide structural and drug mechanism-of-action investigations. We also identify frontiers where progress is likely to be paramount to advancing the field.

Self-Reporting Conjugated Polymer Nanoparticles for Superoxide Generation and Detection.

Conjugated polymer nanoparticles (CPNs or Pdots) have become increasingly popular fluorophores for multimodal applications that combine imaging with phototherapeutic effects. Reports of CPNs in photodynamic therapy applications typically focus on their ability to generate singlet oxygen. Alternatively, CPN excited states can interact with oxygen to form superoxide radical anion and a CPN-based hole polaron, both of which can have deleterious effects on fluorescence properties. Here, we demonstrate that CPNs prepared from the common conjugated polymer poly[(9,9-dioctylfluorenyl-2,7-diyl)-alt-co-(1,4-benzo-{2,1',3}-thiadiazole)] (PFBT, also known as F8BT) generate superoxide upon irradiation. We use the same CPNs to detect superoxide by doping them with a superoxide-responsive hydrocyanine dye developed by Murthy and co-workers. Superoxide induces off-to-on fluorescence switching by converting quenching hydrocyanine dyes to fluorescent cyanine dyes that act as fluorescence resonance energy transfer (FRET) acceptors for PFBT chromophores. Amplified FRET from the multichromophoric CPNs yields fluorescence signal intensities that are nearly 50 times greater than when the dye is excited directly or over 100 times greater when signal readout is from the CPN channel. The dye loading level governs the maximum amount of superoxide that induces a change in fluorescence properties and also influences the rate of superoxide generation by furnishing competitive excited state deactivation pathways. These results suggest that CPNs can be used to deliver superoxide in applications in which it is desirable and provide a caution for fluorescence-based CPN applications in which superoxide can damage fluorophores.

Synthesis of P, N-dopped carbon nanosheets for highly sensitive fluorescence analysis of nitrofuran antibiotics in fish

The misuse of antibiotics has caused serious impacts on food safety and human health, making it crucial to develop rapidly and highly sensitive methods for detecting trace nitrofuran antibiotics (NFs). In this study, phosphorus, nitride-doped carbon nanosheets (PN/CNs) were synthesized using a simple hydrothermal method based on graphitic carbon nitride. This prepared material showed excellent water solubility and stable optical properties. A new fluorescence sensing platform based on PN/CNs was constructed for the highly sensitive detection of four NFs. This sensitivity was mainly attributed to the fluorescence resonance energy transfer (FRET) mechanism. The limits of detection for nitrofurazone, nitrofurantoin, furazolidone and furaltadone were determined to be 13.41, 15.24, 16.37 and 19.94 nM, respectively. The high sensitivity and selectivity of PN/CNs for these four NFs were thoroughly evaluated by the Stern-Volmer equation and FRET quenching efficiency. This proposed method exhibited high sensitivity and can be successfully applied to detect NFs in fish.

Molecular Insights into the Conformational and Binding Behaviors of Human Serum Albumin Induced by Surface-Active Ionic Liquids.

Extensive research has been carried out to investigate the stability and function of human serum albumin (HSA) when exposed to surface-active ionic liquids (SAILs) with different head groups (imidazolium, morpholinium, and pyridinium) and alkyl chain lengths (ranging from decyl to tetradecyl). Analysis of the protein fluorescence spectra indicates noticeable changes in the secondary structure of HSA with varying concentrations of all SAILs tested. Helicity calculations based on the Fourier transform infrared (FTIR) data show that HSA becomes more organized at the micellar concentration of SAILs, leading to an increased protein activity at this level. Small-angle neutron scattering (SANS) data confirm the formation of a bead-necklace structure between the SAILs and HSA. Atomistic molecular dynamics (MD) simulation results identify several hotspots on the protein surface for interaction with SAIL, which results in the modulation of protein conformational fluctuation and stability. Furthermore, fluorescence resonance energy transfer (FRET) experiments with the intramolecular charge transfer (ICT) probe trans-ethyl p-(dimethylamino) cinnamate (EDAC) demonstrate that higher alkyl chain lengths and SAIL concentrations result in a significantly increased energy transfer efficiency. The findings of this study provide a detailed molecular-level understanding of how the protein structure and function are affected by the presence of SAILs, with potential implications for a wide range of applications involving protein-SAIL composite systems.

Superlarge, Rigidified DNA Tetrahedron with a Y-Shaped Backbone for Organizing Biomolecules Spatially and Maintaining Their Full Bioactivity.

A major impediment to the clinical translation of DNA tiling nanostructures is a technical bottleneck for the programmable assembly of DNA architectures with well-defined local geometry due to the inability to achieve both sufficient structural rigidity and a large framework. In this work, a Y-backbone was inserted into each face to construct a superlarge, sufficiently rigidified tetrahedral DNA nanostructure (called RDT) with extremely high efficiency. In RDT, the spatial size increased by 6.86-fold, and the structural rigidity was enhanced at least 4-fold, contributing to an ∼350-fold improvement in the resistance to nucleolytic degradation even without a protective coating. RDT can be mounted onto an artificial lipid-bilayer membrane with molecular-level precision and well-defined spatial orientation that can be validated using the fluorescence resonance energy transfer (FRET) assay. The spatial orientation of Y-shaped backbone-rigidified RDT is unachievable for conventional DNA polyhedrons and ensures a high level of precision in the geometric positioning of diverse biomolecules with an approximately homogeneous environment. In tests of RDT, surface-confined horseradish peroxidase (HRP) exhibited nearly 100% catalytic activity and targeting aptamer-immobilized gold nanoparticles showed 5.3-fold enhanced cellular internalization. Significantly, RDT exhibited a 27.5-fold enhanced structural stability in a bodily environment and did not induce detectable systemic toxicity.

Split Luciferase Molecular Tension Sensors for Bioluminescent Readout of Mechanical Forces in Biological Systems.

The ability of proteins to sense and transmit mechanical forces underlies many biological processes, but characterizing these forces in biological systems remains a challenge. Existing genetically encoded force sensors typically rely on fluorescence or bioluminescence resonance energy transfer (FRET or BRET) to visualize tension. However, these force sensing modules are relatively large, and interpreting measurements requires specialized image analysis and careful control experiments. Here, we report a compact molecular tension sensor that generates a bioluminescent signal in response to tension. This sensor (termed PILATeS) makes use of the split NanoLuc luciferase and consists of the H. sapiens titin I10 domain with the insertion of a 10-15 amino acid tag derived from the C-terminal β-strand of NanoLuc. Mechanical load across PILATeS mediates exposure of this tag to recruit the complementary split NanoLuc fragment, resulting in force-dependent bioluminescence. We demonstrate the ability of PILATeS to report biologically meaningful forces by visualizing forces at the interface between integrins and extracellular matrix substrates. We further use PILATeS as a genetically encoded sensor of tension experienced by the mechanosensing protein vinculin. We anticipate that PILATeS will provide an accessible means of visualizing molecular-scale forces in biological systems.

Rhodamine B functionalized Titanium dioxide and Silver sulfide adorned Bismuth Ferrite Oxide as a Turn-Off fluorescent sensing probe to organochlorine pesticides

Rhodamine B(RhB) functionalized Bismuth Ferrite Oxide(BFO)/Titanium dioxide(TiO2)/Silver disulfide(AgS)nanoparticles were used to build a fluorescent turn-off sensor for the detection of Chlorpyrifos(CLP). The fluorescence was drastically quenched by the RhB fluorescence resonance energy transfer to the surface of BFO/TiO2/AgS NCs via electrostatic interactions. Then the addition of CLP to RhB@BFO/TiO2/AgSNCs initiates the loss of fluorescence by the adsorption of CLP molecules to the turn-off sensor probe. Under favorable conditions, the linearity between the fluorescence quenching and the concentrations was monitored and the limit of detection was estimated to be 0.006 ppm, 0.004 ppm for 2:1 and 3:1 ratio, with the fluorescence quenching efficiency ranges from 92.9 to 94 %.

Ratiometric fluorescence and smartphone-assisted sensing platform based on dual-emission carbon dots for brilliant blue detection

In this study, an innovative ratiometric fluorescence and smartphone-assisted visual sensing platform based on blue-yellow dual-emission carbon dots (BY-CDs) was constructed for the first time to determine brilliant blue. The BY-CDs was synthesized via a facile one-step hydrothermal process involving propyl gallate and o-phenylenediamine. The synthesized BY-CDs exhibit favorable water solubility and exceptional fluorescence stability. Under excitation at 370 nm, BY-CDs show two distinguishable fluorescence emission bands (458 and 558 nm). Upon addition of brilliant blue, the fluorescence intensity at 558 nm exhibited a significant quenching effect attributed to fluorescence resonance energy transfer (FRET), while the fluorescence intensity at 458 nm was basically unchanged. The prepared BY-CDs can effectively serve as a ratiometric nanosensor for determining brilliant blue with the ratio of fluorescence intensities at 458 and 558 nm (F458/F558) as response signal. In addition, the developed ratiometric fluorescence sensor exhibits a noticeable alteration in color from yellow to green under UV light with a wavelength of 365 nm upon addition of varying concentrations of brilliant blue, which provides the possibility of visual detection of brilliant blue by a smartphone application. Finally, the BY-CDs based dual-mode sensing platform successfully detected brilliant blue in actual food samples and achieved a desirable recovery rate. This study highlights the merits of fast, convenient, economical, real-time, visual, high accuracy, excellent precision, good selectivity and high sensitivity for brilliant blue detection, and paves new paths for the monitoring of brilliant blue in real samples.

A ratiometric fluorescence sensor for detection of organophosphorus pesticides based on enzyme-regulated multifunctional Fe-based metal-organic framework

The residues of organophosphorus pesticides (OPs) are increasing environmental pollution and public health concerns. Thus, the development of simple, convenient and sensitive method for detection of OPs is crucial. Herein, a multifunctional Fe-based MOF with fluorescence, catalytic and adsorption, is synthesized by a simple one-pot hydrothermal method. The ratiometric fluorescence sensor for detection of OPs is constructed by using only one multifunctional sensing material. The NH2-MIL-101(Fe) is able catalyze the o-phenylenediamine (OPD) into 2,3-diaminophenazine (DAP) in the presence of H2O2. The generated DAP can significantly quench the intrinsic fluorescence of NH2-MIL-101(Fe) by the fluorescence resonance energy transfer (FRET) and internal filtration effect (IFE), while producing a new measurable fluorescence. Without immobilization or molecular imprinting, pyrophosphate ion (PPi) can inhibit the peroxidase-like activity of the NH2-MIL-101(Fe) by chelating with Fe3+/Fe2+ redox couple. Moreover, PPi can also be hydrolyzed by alkaline phosphatase (ALP), the presence of OPs inhibits the activity of ALP, resulting in the increase of extra PPi preservation and signal changes of ratiometric fluorescence, the interactions of ALP with different OPs are explored by molecular docking, the OPs (e.g., glyphosate) interact with crucial amino acid residues (Asp, Ser, Ala, Lys and Arg) are indicated. The proposed sensor exhibits excellent detection performance for OPs with the detection limit of 18.7 nM, which provides a promising strategy for detection of OPs.

In-Vitro Study of the Binding of Atorvastatin with Adenine using Multi-Spectroscopic Approaches.

Atorvastatin-an oral lipid regulating drug is a competitive inhibitor of 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMG-CoA reductase), which is the rate determining enzyme for cholesterol synthesis. Adenine is a purine nucleobase that is found in deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) to generate genetic information. The binding mechanism of atorvastatin and adenine was studied for the first time utilizing various techniques, including UV-visible spectrophotometry, spectrofluorimetry, synchronous fluorescence spectroscopy (SF), Fourier transform infrared (FTIR), fluorescence resonance energy transfer (FRET), and metal ion complexation. The fluorescence spectra of the complex indicated that atorvastatin is bound to adenine via hydrophobic interaction through a spontaneous binding process, and the fluorescence quenching mechanism was found to be static quenching with a binding constant of 1.4893 × 104 Lmol-1 at 298 K. Various temperature settings were used to investigate thermodynamic characteristics, such as binding forces, binding constants, and the number of binding sites. The interaction parameters, including the standard enthalpy change (ΔHο) and standard entropy change (ΔSο) were calculated using Van't Hoff's equation to be 42.82 kJmol-1 and 208.9 Jmol-1K-1, respectively. The findings demonstrated that the adenine- atorvastatin binding was endothermic. Furthermore, the results of the experiments revealed that some metal ions (K+, Ca+2, Co+2, Cu+2, and Al+3) facilitate the binding interaction between atorvastatin and adenine. Slight changes are observed in the FTIR spectra of adenine, indicating the binding interaction between adenine and atorvastatin.

Antiviral activity of luteolin against porcine epidemic diarrhea virus in silico and in vitro

BackgroundPorcine epidemic diarrhea virus (PEDV) mainly causes acute and severe porcine epidemic diarrhea (PED), and is highly fatal in neonatal piglets. No reliable therapeutics against the infection exist, which poses a major global health issue for piglets. Luteolin is a flavonoid with anti-viral activity toward several viruses.ResultsWe evaluated anti-viral effects of luteolin in PEDV-infected Vero and IPEC-J2 cells, and identified IC50 values of 23.87 µM and 68.5 µM, respectively. And found PEDV internalization, replication and release were significantly reduced upon luteolin treatment. As luteolin could bind to human ACE2 and SARS-CoV-2 main protease (Mpro) to contribute viral entry, we first identified that luteolin shares the same core binding site on pACE2 with PEDV-S by molecular docking and exhibited positive pACE2 binding with an affinity constant of 71.6 µM at dose-dependent increases by surface plasmon resonance (SPR) assay. However, pACE2 was incapable of binding to PEDV-S1. Therefore, luteolin inhibited PEDV internalization independent of PEDV-S binding to pACE2. Moreover, luteolin was firmly embedded in the groove of active pocket of Mpro in a three-dimensional docking model, and fluorescence resonance energy transfer (FRET) assays confirmed that luteolin inhibited PEDV Mpro activity. In addition, we also observed PEDV-induced pro-inflammatory cytokine inhibition and Nrf2-induced HO-1 expression. Finally, a drug resistant mutant was isolated after 10 cell culture passages concomitant with increasing luteolin concentrations, with reduced PEDV susceptibility to luteolin identified at passage 10.ConclusionsOur results push forward that anti-PEDV mechanisms and resistant-PEDV properties for luteolin, which may be used to combat PED.

Highly efficient and sensitive detection of tetracycline in environmental water: Insights into the synergistic mechanism of biomass-derived carbon dots and N-methyl pyrrolidone solvent

The tetracycline (TC) residue in water environment has caused serious public safety issue. Thus, efficient sensing of TC is highly desirable for environmental protection. Herein, biomass-derived nitrogen-doped carbon dots (N-CDs) synthesized from natural Ophiopogon japonicus f. nanus (O. japonicus) were used for TC detection. The unique solvent synergism efficiently enhanced detection sensitivity, and the detailed sensing mechanism was deeply investigated. The blue fluorescence of N-CDs was quenched by TC via static quenching and inner filter effect. Moreover, the enhancement of green fluorescence from deprotonated TC was firstly proposed and sufficiently verified. The solvent effect of N-methyl pyrrolidone (NMP) and the fluorescence resonance energy transfer (FRET) with N-CDs achieved an instantaneous enhancement of the green emission by 64-fold. Accordingly, a ratiometric fluorescence method was constructed for rapid and sensitive sensing of TC with a low detection limit of 6.3 nM within 60 s. The synergistic effect of N-CDs and solvent assistance significantly improved the sensitivity by 7-fold compared to that in water. Remarkably, the biomass-derived N-CDs displayed low cost, good solubility, and desired stability. The deep insights into the synergism with solvent can provide prospects for the utilization of biomass-based materials and broaden the development of advanced sensors with promising applications.

Intermolecular FRET Pairs as An Approach to Visualize Specific Enzyme Activity in Model Biomembranes and Living Cells

Herein, we propose an analytical approach based on intermolecular fluorescent resonant energy transfer (FRET) pairs for the visualization of specific enzyme activity in model biomembranes and in living cells. Cell visualizations with fluorescent confocal laser microscopy usually rely on fluorescent probes, such as Fluorescein isothiocyanate (FITC), Alexa488, Tetramethylrhodamine isothiocyanate (TRITC) and many others. However, for more specific tasks, such as the detection of certain enzymatic activity inside the living cell, the toolbox is quite limited. In the case of enzyme-hydrolases for example, the choice is limited to organic molecules comprising a fluorescent dye (typically, 4-methylumbelliferone (MUmb) or 7-amino-4-methylcoumarin (AMC) derivatives) and a fluorescence quencher, bound via an enzyme-sensitive linker—so that when the linker is degraded, the fluorescent signal increases. Unfortunately, both MUmb and AMC are quenched and have a relatively low quantum yield in cells, and their excitation and emission ranges overlap with that of intracellular fluorophores, often producing a strong background noise. R6G, on the other hand, has excellent quantum yield apart from intracellular fluorophores, but there are no efficient quenchers that could be chemically linked to R6G. Herein, we show that R6G is able to form intermolecular FRET pairs with MUmb or AMC, with the latter serving as fluorescence donors. This yields a combination of R6G’s excellent fluorescence properties with a possibility to use an enzyme-sensitive linker in MUTMAC or AMC derivatives. This phenomenon was initially discovered in a model system, reversed micelles, where the donor, the acceptor, and the enzyme are forced to be in close proximity to each other, so that proximity could serve as an explanation for the intermolecular FRET effect. Surprisingly enough, the phenomenon has been reproduced in living cells. Moreover, we were able to create working intermolecular donor–acceptor FRET pairs for several different enzymes, including chymotrypsin, phosphatase, and asparaginase. This appears counterintuitive, as besides the overlap of the emission spectra of the donor and the absorption spectra of the acceptor, there are other criteria for the FRET effect, including the convergence of two fluorophores at a distance of about 1–10 nm, and the orientation of their dipoles at a certain angle, which is difficult to imagine in a bulk system like a living cell. We hypothesize that FRET-enabling donor–acceptor interaction may be taking place at the inner surface of the lipid bilayer, to which both donor and acceptor molecules would likely have an affinity. This hypothesis would require a more detailed investigation. Therefore, we have shown that the method suggested has good potential in the visualization of enzyme functioning inside living cells, which is often a challenging task. Shifting of the fluorescence signal to the long-wavelength region would increase the signal selectivity, making it easily distinguishable from autofluorescence.

Thermodynamic compensation to temperature extremes in B. subtilis vs T. maritima lysine riboswitches

T. maritima and B. subtilis are bacteria that inhabit significantly different thermal environments, ∼80 vs. ∼40°C, yet employ similar lysine riboswitches to aid in the transcriptional regulation of the genes involved in the synthesis and transport of amino acids. Despite notable differences in G-C basepair frequency and primary sequence, the aptamer moieties of each riboswitch have striking similarities in tertiary structure, with several conserved motifs and long-range interactions. To explore genetic adaptation in extreme thermal environments, we compare the kinetic and thermodynamic behaviors in T. maritima and B. subtilis lysine riboswitches via single-molecule fluorescence resonance energy transfer analysis. Kinetic studies reveal that riboswitch folding rates increase with lysine concentration while the unfolding rates are independent of lysine. This indicates that both riboswitches bind lysine through an induced-fit (“bind-then-fold”) mechanism, with lysine binding necessarily preceding conformational changes. Temperature-dependent van’t Hoff studies reveal qualitative similarities in the thermodynamic landscapes for both riboswitches in which progression from the open, lysine-unbound state to both transition states (‡) and closed, lysine-bound conformations is enthalpically favored yet entropically penalized, with comparisons of enthalpic and entropic contributions extrapolated to a common [K+] = 100 mM in quantitative agreement. Finally, temperature-dependent Eyring analysis reveals the TMA and BSU riboswitches to have remarkably similar folding/unfolding rate constants when extrapolated to their respective (40 and 80°C) environmental temperatures. Such behavior suggests a shared strategy for ligand binding and aptamer conformational change in the two riboswitches, based on thermodynamic adaptations in number of G-C basepairs and/or modifications in tertiary structure that stabilize the ligand-unbound conformation to achieve biocompetence under both hyperthermophilic and mesothermophilic conditions.