Thioflavin T as a Molecular Rotor: Fluorescent Properties of Thioflavin T in Solvents with Different Viscosity

Interaction analysis of RNA G-quadruplex with ligands and in situ imaging application

RNA G4, as an integral branch of G4 structure, possesses distinct interactions with ligands compared to the common DNA G4, thus the investigation of RNA G4/ligand interactions might be considered as a fresh breakthrough to improve the biosensing performance of G4/ligand system. In this study, we comparatively explored the structural and functional mechanisms of RNA G4 and DNA G4 in the interaction with ligands, hemin and thioflavin T (ThT), utilizing the classical PS2.M sequence as a model. We found that although the catalytic performance of RNA G4/hemin system was lower than DNA G4/hemin, RNA G4/ThT fluorescence system exhibited a significant improvement (2∼3-fold) compared to DNA G4/ThT, and adenine modification could further enhance the signaling. Further, by exploring the interaction between RNA G4 and ThT, we deemed that RNA G4 and ThT were stacked in a bimolecular mode compared to single-molecule binding of DNA G4/ThT, thus more strongly limiting the structural spin in ThT excited state. Further, RNA G4/ThT displayed higher environmental tolerance and lower ion dependence than DNA G4/ThT. Finally, we employed RNA G4/ThT as a highly sensitive label-free fluorescent signal output system for in situ imaging of isoforms BCR-ABL e13a2 and e14a2. Overall, this study successfully screened a high-performance RNA G4 biosensing system through systematic RNA G4/ligands interaction studies, which was expected to provide a promising reference for subsequent G4/ligand research.

Distance-Dependent Tryptophan-Induced Quenching of Thioflavin T Defines the Amyloid Core Architecture

Thioflavin T (ThT) is widely employed as a fluorogenic marker for amyloid formation. ThT fluorescence is utilized to detect amyloid fibrils as well as to follow aggregation kinetics. Here, we make a unique case to demonstrate that site-specific tryptophan-induced fluorescence quenching of ThT bound to the α-synuclein amyloid can define the central amyloid core. We show that distance-dependent quenching of amyloid-bound ThT by site-specifically incorporated tryptophan maps the proximal and distal locations of the polypeptide chain within amyloid fibrils. Our studies indicate that tryptophan-induced fluorescence quenching is dominated by the static quenching mechanism. Our findings underscore the utility of site-specific amino acid-based quenching of ThT fluorescence to characterize the core architecture of amyloid derived from a wide range of proteins.

Organic Dye Molecule Intercalated Prussian Blue for Simultaneously Enhancing Coloration Efficiency and Energy Storage Capacity in Electrochromic Battery

The dual-functional device combining electrochromic properties and energy storage has gained numerous attentions in the field of energy-saving smart electronics. However, achieving simultaneous optimization of coloration efficiency and energy storage capacity of materials poses a significant challenge. This study presents a novel approach by incorporating methyl orange into Prussian blue channels (PB-MO films) to adjust the internal electronic structure of Prussian blue. This modification allows the active layer to simultaneously improve the electrochromic and energy storage performance. The introduction of methyl orange not only alters the ratio of Fe3+/Fe2+ within the framework through the coordination reaction of Fe3+ with methyl orange, but also improves the reaction kinetics after intercalating organic dye molecules, including charge transfer resistance, diffusion capability of ions and capacitive contribution. The PB-MO films demonstrate remarkable properties: high optical contrast (81.4% at 670 nm), excellent coloration efficiency (265 cm2 C-1), and significant specific capacity (84 mAh m-2 at 0.05 A m-2), outperforming pure PB films. The PB-MO films are ideally suited for applications in displays and intelligent energy storage fields, boasting both high coloration efficiency and substantial energy storage capacity, thus advancing promote the development of dual-functional electrochromic devices.

p-Sulfonatocalix[6]arene-Functionalized Gold Nanoparticles: Applications in Drug Delivery and Bioimaging

Surface-functionalized noble metal nanoparticles with macrocyclic hosts have attracted enormous research interest owing to their applications in drug delivery, catalysis, bioimaging, etc. Stable p-sulfonatocalix[6]arene-functionalized gold nanoparticles (SCx6AuNPs) of the sizes ∼7.5 nm have been synthesized and characterized by using UV-vis absorption, transmission electron microscopy, and surface-enhanced Raman spectroscopy measurements. The efficient uptake and stimuli-responsive release of doxorubicin (Dox), an anticancer drug, by the SCx6AuNPs have been established for targeted drug delivery application. The decreased cytotoxicity of Dox loaded on SCx6AuNPs, especially toward normal cell lines, and its multistimuli responsive release validated in both cancerous (A549) and normal (W126) cell lines find promising for selectively targeted drug delivery applications toward cancer cells. At the cellular level, this study also establishes the efficient uptake of the SCx6AuNP nanoconjugates, and its validation has been done by bioimaging measurement by using thioflavin T (ThT) dye loaded on to SCx6AuNPs instead of Dox as the fluorescent tracking probe. The bright fluorescence microscopic image of ThT-SCx6AuNP-stained cancerous cell lines corroborates the uptake of SCx6AuNPs by the cell lines and its projected utility for drug delivery and bioimaging applications.

Bioactive Carbon@CeO2 Composites as Efficient Antioxidants with Antiamyloid and Radioprotective Potentials

Blending carbon particles (CPs) and nanoscale bioactive cerium dioxide is a promising approach for designing composites for biomedical applications, combining the sorption and antioxidant potentials of each individual component. To address this issue, it is crucial to assess the correlation between the components' ratio, physicochemical parameters, and biofunctionality of the composites. Thus, the current research was aimed at fabricating C@CeO2 composites with different molar ratios and the examination of how the parameters of the composites affect their bioactivity. XRD, X-ray photoelectron spectroscopy, and electron microscopy data verified the formation of C@CeO2 composites. CeO2 nanoparticles (NPs) of 4-6 nm are highly dispersed on the surfaces of amorphous CPs. The presence of CeO2 NPs on the carbon surface decreased its adsorption potential in a dose-dependent manner. Besides, the coexistence of carbon and CeO2 in a single composite promotes some redox interactions between O-functionalities and Ce3+/Ce4+ species, resulting in changes in the chemical state of the surface of the composites. These observations suggest the strong connection between these parameters and the biofunctionality of the composites. The presence of CeO2 NPs on the surface of carbon led to a significant increase in the stability of the prepared composites in their aqueous suspensions. The enhancement of bioactivity of the newly prepared C@CeO2 compared to bare carbon and CeO2 was validated by testing their pseudomimetic (catalase/peroxidase-like and superoxide dismutase-like), antiamyloid, and radioprotective activities.

A label-free fluorescence aptamer sensor for point-of-care serotonin detection

Serotonin, a pivotal neurotransmitter regulating various physiological functions, plays a crucial role in disease diagnosis, necessitating precise monitoring of its levels in biological fluids for accurate assessment. Aptamers, known for their high specificity and affinity, have emerged as innovative molecular probes for serotonin analysis. However, existing serotonin aptamer sensing platforms exhibit limitations in terms of portability and rapid detection capabilities. In this study, we introduce a novel, portable, label-free serotonin aptamer sensor utilizing a dye replacement strategy, achieving a short sample-to-result turnaround time and convenient signal readout through a smartphone. The performance of this aptamer sensor was thoroughly assessed across diverse physiological media, demonstrating robust stability in buffer, urine, and serum. Importantly, the detection limit was in the nanomolar range, emphasizing its suitability for the rapid, sensitive, and user-friendly detection of serotonin. This research pioneers an approach for the development of a point-of-care testing (POCT) system for serotonin with practical implications, particularly in resource-limited settings.

In Silico and Glioblastoma Cell Line Evaluation of Thioflavin-Derived Zinc Nanoparticles Targeting Beclin Protein

INTRODUCTION

This study explores the anticancer potential of Thioflavin-derived zinc nanoparticles (Th-ZnNPs) using both in vitro and in silico methods. Thioflavin, known for its specific binding properties, faces challenges such as bioavailability, rapid metabolism, and solubility. To overcome these limitations and enhance therapeutic efficacy, nanotechnology was utilized to synthesize Th-ZnNPs. These nanoparticles (NPs) are designed to improve drug delivery and effectiveness. The Beclin protein, which plays a critical role in regulating autophagy in cancer cells, was identified as a potential target for these NPs. The study aims to evaluate the interaction between Th-ZnNPs and Beclin protein in glioblastoma cell lines and assess the potential of these NPs as novel anticancer agents.

METHODS

 Th-ZnNPs were synthesized using advanced nanotechnology techniques to improve the bioavailability and solubility of Thioflavin. To explore their anticancer potential, in silico analyses were performed, including molecular docking studies to evaluate the binding affinity between the ZnNPs and Beclin protein, which is integral to autophagy regulation. This computational approach identified the Beclin protein as a promising target for the ZnNPs. Complementary in vitro assays were then conducted, where glioblastoma cell lines (procured from the National Centre for Cell Science, Pune, India) were treated with ZnNPs to assess their cytotoxic effects. The assays also included mechanistic studies to validate the interaction between ZnNPs and Beclin protein and to understand their influence on autophagy pathways.

RESULTS

The synthesis of Th-ZnNPs successfully enhanced their solubility and bioavailability compared to Thioflavin alone. In silico findings showed a strong binding affinity between the Th-ZnNPs and the Beclin protein, suggesting that these NPs may effectively target cancer cells through this interaction. Beclin protein was validated as a relevant target due to its critical role in autophagy regulation. In vitro assays further confirmed the anticancer potential of the Th-ZnNPs, as they exhibited significant cytotoxic effects on glioblastoma cells. Additionally, mechanistic studies revealed that Th-ZnNPs impact Beclin protein and modulate autophagy pathways, supporting their proposed role as effective anticancer agents.

CONCLUSIONS

The study highlights the promising anticancer potential of Th-ZnNPs. By overcoming the limitations of Thioflavin through nanotechnology, these NPs show significant therapeutic promise in targeting glioblastoma cells. The strong binding affinity between Th-ZnNPs and the Beclin protein, coupled with confirmed cytotoxic effects, underscores their potential as novel anticancer agents. This integrated approach not only enhances the delivery and efficacy of Thioflavin but also opens new avenues for targeted therapy in glioblastoma treatment.

Natural compound plumbagin based inhibition of hIAPP revealed by Markov state models based on MD data along with experimental validations

Human islet amyloid polypeptide (amylin or hIAPP) is a 37 residue hormone co-secreted with insulin from β cells of the pancreas. In patients suffering from type-2 diabetes, amylin self-assembles into amyloid fibrils, ultimately leading to the death of the pancreatic cells. However, a research gap exists in preventing and treating such amyloidosis. Plumbagin, a natural compound, has previously been demonstrated to have inhibitory potential against insulin amyloidosis. Our investigation unveils collapsible regions within hIAPP that, upon collapse, facilitates hydrophobic and pi-pi interactions, ultimately leading to aggregation. Intriguingly plumbagin exhibits the ability to bind these specific collapsible regions, thereby impeding the aforementioned interactions that would otherwise drive hIAPP aggregation. We have used atomistic molecular dynamics approach to determine secondary structural changes. MSM shows metastable states forming native like hIAPP structure in presence of PGN. Our in silico results concur with in vitro results. The ThT assay revealed a striking 50% decrease in fluorescence intensity at a 1:1 ratio of hIAPP to Plumbagin. This finding suggests a significant inhibition of amyloid fibril formation by plumbagin, as ThT fluorescence directly correlates with the presence of these fibrils. Further TEM images revealed disappearance of hIAPP fibrils in plumbagin pre-treated hIAPP samples. Also, we have shown that plumbagin disrupts the intermolecular hydrogen bonding in hIAPP fibrils leading to an increase in the average beta strand spacing, thereby causing disaggregation of pre-formed fibrils demonstrating overall disruption of the aggregation machinery of hIAPP. Our work is the first to report a detailed atomistic simulation of 22 μs for hIAPP. Overall, our studies put plumbagin as a potential candidate for both preventive and therapeutic candidate for hIAPP amyloidosis.

Efficiency of Encapsulation of Thioflavin T (ThT) into Polar and Nonpolar Environments of Different Bile Salt Aggregates: A Femtosecond Fluorescence Study

The binding of Thioflavin T (ThT) with various bile salts, a potential host molecule, has been analyzed by steady-state and time-resolved fluorescence spectroscopy. A comparative study has been executed to investigate the influence of confinement of different bile salts, namely, sodium cholate (NaCh), sodium taurocholate (NaTC), and sodium deoxycholate (NaDC) on binding and excited state torsional motion of ThT molecules. The changes in absorption and emission properties of probe molecules were found to be sensitive to increasing bile salt concentration in aqueous 0.2 (M) NaCl solutions. The photophysics of ThT mainly depends on hydrophobicity, morphology, and size of bile salt aggregates in solution. In the presence of bile salts, the emission intensity and emission lifetime of ThT increase significantly, indicating encapsulation of dye. Moreover, we have also investigated the effect of the ionic strength of the medium by sodium chloride (NaCl) on the spectroscopic properties of ThT in the restricted surroundings of aqueous bile salts. It is observed that the fluorescence lifetime of ThT in bile salts increases significantly in the presence of NaCl. The encapsulation efficiency of ThT in bile salt aggregates has been assessed by iodide (I-) as an external ionic quencher. We found that NaDC aggregates are more efficient in the modulation of photophysical properties of ThT and also provide better protection efficiency to decrease the nonradiative deactivation processes.

Effects of amyloid-β-mimicking peptide hydrogel matrix on neuronal progenitor cell phenotype

Self-assembling peptide-based hydrogels have become a highly attractive scaffold for three-dimensional (3D) in vitro disease modeling as they provide a way to create tunable matrices that can resemble the extracellular matrix (ECM) of various microenvironments. Alzheimer's disease (AD) is an exceptionally complex neurodegenerative condition; however, our understanding has advanced due to the transition from two-dimensional (2D) to 3D in vitro modeling. Nonetheless, there is a current gap in knowledge regarding the role of amyloid structures, and previously developed models found long-term difficulty in creating an appropriate model involving the ECM and amyloid aggregates. In this report, we propose a multi-component self-assembling peptide-based hydrogel scaffold to mimic the amyloid-beta (β) containing microenvironment. Characterization of the amyloid-β-mimicking hydrogel (Col-HAMA-FF) reveals the formation of β-sheet structures as a result of the self-assembling properties of phenylalanine (Phe, F) through π-π stacking of the residues, thus mimicking the amyloid-β protein nanostructures. We investigated the effect of the amyloid-β-mimicking microenvironment on healthy neuronal progenitor cells (NPCs) compared to a natural-mimicking matrix (Col-HAMA). Our results demonstrated higher levels of neuroinflammation and apoptosis markers when NPCs were cultured in the amyloid-like matrix compared to a natural brain matrix. Here, we provided insights into the impact of amyloid-like structures on NPC phenotypes and behaviors. This foundational work, before progressing to more complex plaque models, provides a promising scaffold for future investigations on AD mechanisms and drug testing. STATEMENT OF SIGNIFICANCE: In this study, we engineered two multi-component hydrogels: one to mimic the natural extracellular matrix (ECM) of the brain and one to resemble an amyloid-like microenvironment using a self-assembling peptide hydrogel. The self-assembling peptide mimics β-amyloid fibrils seen in amyloid-β protein aggregates. We report on the culture of neuronal progenitor cells within the amyloid-mimicking ECM scaffold to study the impact through marker expressions related to inflammation and DNA damage. This foundational work, before progressing to more complex plaque models, offers a promising scaffold for future investigations on AD mechanisms and drug testing.

Thioflavin T─a Reporter of Microviscosity in Protein Aggregation Process: The Study Case of α-Synuclein

Thioflavin T (ThT) informed microviscosity changes can be used to monitor protein aggregation. Steady-state, time-resolved and lasing spectroscopy were used to detect transient states in α-synuclein - a protein associated with Parkinson's disease. The major focus was on the nucleation phase, where conventional ThT fluorescence assay lacks appropriate sensitivity to detect early stage oligomers. Instead, lasing spectroscopy and lasing threshold parameters, in particular, were sensitive to detecting protein oligomers. Through lasing spectroscopy, a change in microviscosity correlating with the stages of protein aggregation was observed at two wavelengths 405 and 440 nm. The two wavelengths are associated with free dye molecules and β-sheet bound ThT molecules. This provides a perspective on elucidating the early formed protein aggregation, a critical aspect in understanding the pathogenesis of neurodegenerative diseases. The insights from the presented study shows the potential of using lasing spectroscopy as a sensitive tool in studying protein aggregation dynamics.

Redesign of a thioflavin-T-binding protein with a flat β-sheet to evaluate a thioflavin-T-derived photocatalyst with enhanced affinity

Amyloids, proteinous aggregates with β-sheet-rich fibrils, are involved in several neurodegenerative diseases such as Alzheimer's disease; thus, their detection is critically important. The most common fluorescent dye for amyloid detection is thioflavin-T (ThT), which shows on/off fluorescence upon amyloid binding. We previously reported that an engineered globular protein with a flat β-sheet, peptide self-assembly mimic (PSAM), can be used as an amyloid binding model. In this study, we further explored the residue-specific properties of ThT-binding to the flat β-sheet by introducing systematic mutations. We found that site-specific mutations at the ThT-binding channel enhanced affinity. We also evaluated the binding of a ThT-based photocatalyst, which showed the photooxygenation activity on the amyloid fibril upon light radiation. Upon binding of the photocatalyst to the PSAM variant, singlet oxygen-generating activity was observed. The results of this study expand our understanding of the detailed binding mechanism of amyloid-specific molecules.

Fluorescence saturation imaging microscopy: molecular fingerprinting with a standard confocal microscope

Molecular specificity in fluorescence imaging of cells and tissues can be increased by measuring parameters other than intensity. For instance, fluorescence lifetime imaging became a widespread modality for biomedical optics. Previously, we suggested using the fluorescence saturation effect at pulsed laser excitation to map the absorption cross-section as an additional molecular contrast in two-photon microscopy [Opt. Lett.47(17), 4455 (2022).10.1364/OL.465605]. Here, it is shown that, somewhat counterintuitive, fluorescence saturation can be observed under cw excitation in a standard confocal microscopy setup. Mapping the fluorescence saturation parameter allows obtaining additional information about the fluorophores in the system, as demonstrated by the example of peptide hydrogel, stained cells and unstained thyroid gland. The suggested technique does not require additional equipment and can be implemented on confocal systems as is.

Dual Functional Microcapsule based on Monodisperse Short PEG Amphiphile for Drug Encapsulation and Protein Affinity Controlled Release

A short monodisperse poly(ethylene glycol) (PEG) and a neutral organic rotamer conjugate TEG-BTA-2 amphiphile was designed for the construction of a stimuli-responsive switchable self-assembled structure for drug encapsulation by noncovalent interaction and targeted controlled delivery. A short PEG, tetraethylene glycol (TEG) was covalently attached with a neutral organic rotamer benzothiazole dye (BTA-2) affording the neutral TEG-BTA-2 (<500 D). The TEG-BTA-2 is self-assembled into a microsphere in an aqueous medium, but remarkably undergoes morphology change switching to a rice-like microcapsule for curcumin encapsulation. Curcumin-loaded microcapsules were stable in an aqueous solution, however, were noticed disintegrating upon the addition of BSA protein. This is possibly due to an interaction with BSA protein leading to a protein affinity-controlled curcumin release in a neutral PBS buffer. Moreover, cell internalization of the neutral amphiphile TEG-BTA-2 into A549 cells was observed by fluorescence microscopy, providing an opportunity for application as a molecular vehicle for targeted drug delivery and monitoring.

Excited State Rotational Freedom Impacts Viscosity Sensitivity in Arylcyanoamide Fluorescent Molecular Rotor Dyes

The microviscosity of intracellular environments plays an important role in monitoring cellular function. Thus, the capability of detecting changes in viscosity can be utilized for the detection of different disease states. Viscosity-sensitive fluorescent molecular rotors are potentially excellent probes for these applications; however, the predictable relationships between chemical structural features and viscosity sensitivity are poorly understood. Here, we investigate a set of arylcyanoamide-based fluorescent probes and the effect of small aliphatic substituents on their viscosity sensitivity. We found that the location of the substituents and the type of π-network of the fluorophore can significantly affect the viscosity sensitivity of these fluorophores. Computational analysis supported the notion that the excited state rotational energy barrier plays a dominant role in the relative viscosity sensitivity of these fluorophores. These findings provide valuable insight into the design of molecular rotor-based fluorophores for viscosity measurement.

Topological effect of an intramolecular split G-quadruplex on thioflavin T binding and fluorescence light-up

In this work, the topological effect on binding interaction between a G-quadruplex and thioflavin T (ThT) ligand was systematically investigated on a platform of an intramolecular split G-quadruplex (Intra-SG). Distinct fluorescence changes from ThT were presented in the presence of distinct split modes of Intra-SG structures and an intriguing phenomenon of target-induced fluorescence light-up occurred for split modes 2 : 10, 5 : 7 and 8 : 4. It was validated that hybridization between the Intra-SG spacer and target did not unfold the G-quadruplex, but facilitated the ThT binding. Moreover, the 3' guanine-rich fragment of Intra-SG was very susceptible to topology variation produced by the bound target strand. Additionally, a bioanalytical method was developed for ultrasensitive gene detection, confirming the utility of the ThT/Intra-SG complex as a universal signal transducer. It is believed that the results and disclosed rules will inspire researchers to develop many new DNA-based signal transducers in the future.

Deciphering amyloid fibril molecular maturation through FLIM-phasor analysis of thioflavin T

The investigation of amyloid fibril formation is paramount for advancing our understanding of neurodegenerative diseases and for exploring potential correlated therapeutic strategies. Moreover, the self-assembling properties of amyloid fibrils show promise for the development of advanced protein-based biomaterials. Among the methods employed to monitor protein aggregation processes, fluorescence has emerged as a powerful tool. Its exceptional sensitivity enables the detection of early-stage aggregation events that are otherwise challenging to observe. This research underscores the pivotal role of fluorescence analysis, particularly in investigating the aggregation processes of hen egg white lysozyme, a model protein extensively studied for insights into amyloid fibril formation. By combining classical spectroscopies with fluorescence microscopy and by exploiting the fluorescence properties (intensity and lifetime) of the thioflavin T, we were able to noninvasively monitor key and complex molecular aspects of the process. Intriguingly, the fluorescence lifetime imaging-phasor analysis of thioflavin T fluorescence lifetime on structures at different stages of aggregation allowed to decipher the complex fluorescence decay behavior, highlighting that their changes rise from the combination of specific binding to amyloid typical cross-β structures and of the rigidity of the molecular environment.

Poly(dimethylsiloxane) as a room-temperature solid solvent for photophysics and photochemistry

Medium viscosity strongly affects the dynamics of solvated species and can drastically alter the deactivation pathways of their excited states. This study demonstrates the utility of poly(dimethylsiloxane) (PDMS) as a room-temperature solid-state medium for optical spectroscopy. As a thermoset elastic polymer, PDMS is transparent in the near ultraviolet, visible, and near infrared spectral regions. It is easy to mould into any shape, forming surfaces with a pronounced smoothness. While PDMS is broadly used for the fabrication of microfluidic devices, it swells in organic solvents, presenting severe limitations for the utility of such devices for applications employing non-aqueous fluids. Nevertheless, this swelling is reversible, which proves immensely beneficial for loading samples into the PDMS solid matrix. Transferring molecular-rotor dyes (used for staining prokaryotic cells and amyloid proteins) from non-viscous solvents into PDMS induces orders-of-magnitude enhancement of their fluorescence quantum yield and excited-state lifetimes, providing mechanistic insights about their deactivation pathways. These findings demonstrate the unexplored potential of PDMS as a solid solvent for optical applications.

DNA Quadruplex Structure with a Unique Cation Dependency

DNA quadruplex structures provide an additional layer of regulatory control in genome maintenance and gene expression and are widely used in nanotechnology. We report the discovery of an unprecedented tetrastranded structure formed from a native G-rich DNA sequence originating from the telomeric region of Caenorhabditis elegans. The structure is defined by multiple properties that distinguish it from all other known DNA quadruplexes. Most notably, the formation of a stable so-called KNa-quadruplex (KNaQ) requires concurrent coordination of K+ and Na+ ions at two distinct binding sites. This structure provides novel insight into G-rich DNA folding under ionic conditions relevant to eukaryotic cell physiology and the structural evolution of telomeric DNA. It highlights the differences between the structural organization of human and nematode telomeric DNA, which should be considered when using C. elegans as a model in telomere biology, particularly in drug screening applications. Additionally, the absence/presence of KNaQ motifs in the host/parasite introduces an intriguing possibility of exploiting the KNaQ fold as a plausible antiparasitic drug target. The structure's unique shape and ion dependency and the possibility of controlling its folding by using low-molecular-weight ligands can be used for the design or discovery of novel recognition DNA elements and sensors.

Molecular Rotors: Fluorescent Sensors for Microviscosity and Conformation of Biomolecules

The viscosity and crowding of biological environment are considered vital for the correct cellular function, and alterations in these parameters are known to underly a number of pathologies including diabetes, malaria, cancer and neurodegenerative diseases, to name a few. Over the last decades, fluorescent molecular probes termed molecular rotors proved extremely useful for exploring viscosity, crowding, and underlying molecular interactions in biologically relevant settings. In this review, we will discuss the basic principles underpinning the functionality of these probes and will review advances in their use as sensors for lipid order, protein crowding and conformation, temperature and non-canonical nucleic acid structures in live cells and other relevant biological settings.

Measuring Solvent Exchange in Silica Nanoparticles with Rotor-Based Fluorophore

Measuring the diffusivity of molecules is the first step toward understanding their dependence and controlling diffusion, but the challenge increases with the decrease of molecular size, particularly for non-fluorescent and non-reactive molecules such as solvents. Here, the capability to monitor the solvent exchange process within the micropores of silica with millisecond time resolution is demonstrated, by simply embedding a rotor-based fluorophore (thioflavin T) in colloidal silica nanoparticles. Basically, the silica provides an extreme case of viscous microenvironment, which is affected by the polarity of the solvents. The fluorescence intensity traces can be well fitted to the Fickian diffusion model, allowing analytical solution of the diffusion process, and revealing the diffusion coefficients. The validation experiments, involving the water-to-ethanol and ethanol-to-water solvent exchange, the comparison of different drying conditions, and the variation in the degree of cross-linking in silica, confirmed the effectiveness and sensitivity of this method for characterizing diffusion in silica micropores. This work focuses on the method development of measuring diffusivity and the high temporal resolution in tracking solvent exchange dynamics over a short distance (within 165 nm) opens enormous possibilities for further studies.

Recent Advances in Fluorescent Probes for G-quadruplex DNAs / RNAs

Guanine-quadruplexes (G4s) are high-level structures formed by the folding of guaninerich nucleic acid sequences. G4s play important roles in various physiological processes, such as gene transcription, replication, recombination, and maintenance of chromosomal stability. Specific and sensitive monitoring of G4s lays the foundation for further understanding the structure, content, distribution, and function of G4s in organisms, which is important for the treatment and diagnosis of diseases. Moreover, visualization of G4s will provide new ideas for developing antitumor strategies targeting G4s. The design and development of G4-specific ligands are challenging due to the subtle differences in the structure of G4s. This review focuses on the progress of research on G4 fluorescent probes and their binding mechanisms to G4s. Finally, the challenges and future prospects for better detection and targeting of G4s in different organisms are discussed. This paper provides ideas for the development of novel G4 fluorescent probes.

Cavity Lasing Characteristics of Thioflavin T and Thioflavin X in Different Solvents and Their Interaction with DNA for the Controlled Reduction of a Light Amplification Threshold in Solid-State Biofilms

The lasing characteristics of Thioflavin T (ThT) and Thioflavin X (ThX) dyes were investigated in solvents with increasing viscosity: water, ethanol, butanol, ethylene glycol, and glycerol and three forms of DNA (double-helix natural, fragmented, and aggregated). The results identified that lasing thresholds and photostability depend on three critical factors: the solvation shell surrounding dye molecules, the organization of their dipole moments, which is driven by the DNA structure, and the molecules diffusion coefficient in the excitation focal spot. The research highlights that dye doped to DNA accumulated in binding sites fosters long-range dye orientation, facilitating a marked reduction of lasing thresholds in the liquid phase as well as amplified spontaneous emission (ASE) thresholds in the solid state. Leveraging insights from lasing characteristics obtained in liquid, ASE in the solid state was optimized in a controlled way by changing the parameters influencing the DNA structure, i.e., magnesium salt addition, heating, and sonication. The modifications led to a large decrease in the ASE thresholds in the dye-doped DNA films. It was shown that the examination of lasing in cavities can be useful for preparing optical materials with improved architectures and functionalities for solid-state lasers.

The presence of a G-quadruplex prone sequence upstream of a minimal promoter increases transcriptional activity in the yeast Saccharomyces cerevisiae

Non-canonical secondary structures in DNA are increasingly being revealed as critical players in DNA metabolism, including modulating the accessibility and activity of promoters. These structures comprise the so-called G-quadruplexes (G4s) that are formed from sequences rich in guanine bases. Using a well-defined transcriptional reporter system, we sought to systematically investigate the impact of the presence of G4 structures on transcription in yeast Saccharomyces cerevisiae. To this aim, different G4 prone sequences were modeled to vary the chance of intramolecular G4 formation, analyzed in vitro by Thioflavin T binding test and circular dichroism and then placed at the yeast ADE2 locus on chromosome XV, downstream and adjacent to a P53 response element (RE) and upstream from a minimal CYC1 promoter and Luciferase 1 (LUC1) reporter gene in isogenic strains. While the minimal CYC1 promoter provides basal reporter activity, the P53 RE enables LUC1 transactivation under the control of P53 family proteins expressed under the inducible GAL1 promoter. Thus, the impact of the different G4 prone sequences on both basal and P53 family protein-dependent expression was measured after shifting cells onto galactose containing medium. The results showed that the presence of G4 prone sequences upstream of a yeast minimal promoter increased its basal activity proportionally to their potential to form intramolecular G4 structures; consequently, this feature, when present near the target binding site of P53 family transcription factors, can be exploited to regulate the transcriptional activity of P53, P63 and P73 proteins.

BF2-Functionalized Benzothiazole Amyloid Markers: Effect of Donor Substituents on One- and Two-Photon Properties

Investigation of amyloids with the aid of fluorescence microscopy provides crucial insights into the development of numerous diseases associated with the formation of aggregates. Here, we present a series of BF2-functionalized benzothiazoles with electron-donating methoxy group(s), which are tested as amyloid fluorescent markers. We evaluate how the position of donor functional group(s) influences optical properties (fluorescence lifetime (τ) and fluorescence quantum yield (FQY)) in a solution and upon binding to amyloids. We elucidate the importance of surrounding environmental factors (hydrogen-bonding network, polarity, and viscosity) on the observed changes in FQY and evaluate how the localization of a donor influences radiative and nonradiative decay pathways. We conclude that a donor attached to the benzothiazole ring contributes to the increment of radiative decay pathways upon binding to amyloids (kr), while the donor attached to the flexible part of a molecule (with rotational freedom) contributes to a decrease in nonradiative decay pathways (knr). We find that the donor-acceptor-donor architecture allows us to obtain 58 times higher FQY of the dye upon binding to bovine insulin amyloids. Finally, we measure two-photon absorption (2PA) cross sections (σ2) of the dyes and their change upon binding by the two-photon excited fluorescence (2PEF) technique. Measurements reveal that dyes that exhibit the increase/decrease of σ2 values when transferred from highly polar solvents to CHCl3 present a similar behavior upon amyloid binding. Our 2PA experimental values are supported by quantum mechanics/molecular mechanics (QM/MM) simulations. Despite this trend, the values of σ2 are not the same, which points out the importance of two-photon absorption measurements of amyloid-dye complexes in order to understand the performance of 2P probes upon binding.

Matrix Dynamics and Their Crucial Role in Non-radiative Decay during Thermally Activated Delayed Fluorescence

We investigated the interplay of matrix dynamics with the molecular dynamics of a thermally activated delayed fluorescence (TADF) emitter, NAI-DMAC, to identify factors that influence the photophysical processes leading to TADF. The matrix dynamics surrounding NAI-DMAC molecules were varied continuously from the liquid to the solid state by depositing toluene solutions containing poly(methyl methacrylate) (PMMA) and NAI-DMAC onto optical substrates. We monitored changes of the NAI-DMAC emission as the liquid films dried to form solid PMMA films using temperature- and time-resolved photoluminescence spectroscopy. We observed that, in low-viscosity solutions, the proportion of delayed fluorescence from NAI-DMAC was much smaller than that of prompt fluorescence, indicating that negligible TADF occurred in the low-viscosity environment. However, as the viscosity of the environment diverged at the final stages of dry-down to form solid PMMA films, the delayed fluorescence component of NAI-DMAC emission was extended to longer time scales and increased in amplitude relative to prompt emission as the temperature increased─signatures that TADF occurred in the solid state as expected. Our findings reveal the influence that matrix dynamics have on the competition between conformational motion needed to access emissive states and undergo TADF versus larger amplitude structural fluctuations that lead to non-radiative decay. Insights from these studies will inform ongoing work to understand and predict how host matrices used in organic light-emitting devices can be designed to maximize the radiative properties of TADF emitters by allowing molecular motion needed to undergo TADF while restricting larger amplitude motion leading to non-radiative decay.

Amphiphilic Molecules Exhibiting Zwitterionic Excited-State Intramolecular Proton Transfer and Near-Infrared Emission for the Detection of Amyloid β Aggregates in Alzheimer's Disease

Chromophores with zwitterionic excited-state intramolecular proton transfer (ESIPT) have been shown to have larger Stock shifts and red-shifted emission wavelengths compared to the conventional π-delocalized ESIPT molecules. However, there is still a dearth of design strategies to expand the current library of zwitterionic ESIPT compounds. Herein, a novel zwitterionic excited-state intramolecular proton transfer system is reported, enabled by addition of 1,4,7-triazacyclononane (TACN) fragments on a dicyanomethylene-4H-pyran (DCM) scaffold. The solvent-dependent steady-state photophysical studies, pKa measurements, and computational analysis strongly support that the ESIPT process is more efficient with two TACN groups attached to the DCM scaffold and not affected by polar protic solvents. Impressively, compound DCM-OH-2-DT exhibits a near-infrared (NIR) emission at 740 nm along with an uncommonly large Stokes shift. Moreover, DCM-OH-2-DT shows high affinity towards soluble amyloid β (Aβ) oligomers in vitro and in 5xFAD mouse brain sections, and we have successfully applied DCM-OH-2-DT for the in vivo imaging of Aβ aggregates and demonstrated its potential use as an early diagnostic agent for AD. Overall, this study can provide a general molecular design strategy for developing new zwitterionic ESIPT compounds with NIR emission in vivo imaging applications.

Thioflavin-T: A Quantum Yield-Based Molecular Viscometer for Glycerol-Monohydroxy Alcohol Mixtures

Molecular rotor dye thioflavin T (ThT) is almost nonfluorescent in low-viscosity solvents but highly fluorescent when bound to amyloid fibrils. This unique property arises from the rotation of the dimethylaniline moiety relative to the benzothiazole moiety in the excited state, which drives the dye from an emissive locally excited state to a twisted intramolecular charge-transfer state. This process is viscosity-controlled, and therefore, we can use the quantum yield of ThT to assess the viscosity of the environment. In this study, we have investigated the quantum yield of ThT (φThT) in various compositions of six alcoholic solvent mixtures of glycerol with methanol, ethanol, n-propanol, iso-propanol, n-butanol, and tert-butanol. We have proposed an empirical model using φThT as a function of the mole fraction of glycerol to estimate the interaction parameters between the components of the solvent mixtures. This analysis allowed us to predict the extent of nonideality of the solvent mixtures. The Förster-Hoffmann- and Loutfy-Arnold-type power law relationship was established between the quantum yield of ThT and bulk viscosity for solvent mixtures of methanol, ethanol, n-butanol, and tert-butanol with glycerol, and it was found to be similar in nature in all the four mixtures. Applying this knowledge, we proposed a methodology to quantify and predict the bulk viscosity coefficient values of several compositions of n-propanol-glycerol and iso-propanol-glycerol mixtures which have not been previously documented.

An unnatural amino acid modified human insulin derivative for visual monitoring of insulin aggregation

Insulin often forms toxic fibrils during production and transportation, which are deposited as amyloids at repeated injection sites in diabetic patients. Distinguishing early fibrils from non-fibrillated insulin is difficult. Herein, we introduce a chemically modified human insulin derivative with a distinct visual colour transition upon aggregation, facilitating insulin quality assessment.

Quantitation of Tissue Amyloid via Fluorescence Spectroscopy Using Controlled Concentrations of Thioflavin-S

Amyloids are misfolded proteins that aggregate into fibrillar structures, the accumulation of which is associated with the pathogenesis of many neurodegenerative diseases, such as Alzheimer's disease (AD). Early, sensitive detection of these misfolded aggregates is of great interest to the field, as amyloid deposition begins well before the presentation of clinical symptoms. Thioflavin-S (ThS) is a fluorescent probe commonly used to detect amyloid pathology. Protocols for ThS staining vary, but they often use high staining concentrations followed by differentiation, which causes varying levels of non-specific staining and potentially leaves more subtle amyloid deposition unidentified. In this study, we developed an optimized ThS staining protocol for the sensitive detection of β-amyloids in the widely used 5xFAD Alzheimer's mouse model. Controlled dye concentrations together with fluorescence spectroscopy and advanced analytical methods enabled not only the visualization of plaque pathology, but also the detection of subtle and widespread protein misfolding throughout the 5xFAD white matter and greater parenchyma. Together, these findings demonstrate the efficacy of a controlled ThS staining protocol and highlight the potential use of ThS for the detection of protein misfolding that precedes clinical manifestation of disease.

Insights into the Strong Emission Enhancement of Molecular Rotor Thioflavin T in Aqueous Cellulose Nanocrystal Dispersion: White Light Generation in Protein and Micellar Media

Thioflavin t (THT) is a well-known molecular rotor extensively used to detect amyloid-like structures. But THT shows very weak emission in water. In this article, we have found that THT shows very strong emission in the presence of cellulose nanocrystals (CNCs). Steady-state and time-resolved emission techniques have been used to study the strong emission of THT in aqueous CNC dispersion. The time-resolved study showed that in the presence of CNCs, the lifetime increased by ∼1500 fold compared to pure water (<1 ps). To know the nature of interaction and also the reason for this increase in emission zeta potential, stimuli-dependent and temperature-dependent studies have been carried out. These studies proposed that electrostatic interaction is the main factor for this binding of THT with CNCs. Further, the addition of another anionic lipophilic dye, merocyanine 540 (MC540), with CNCs-THT in both BSA protein (CIE: 0.33, 0.32) and TX-100 micellar (4.5 mM) (CIE: 0.32, 0.30) solutions produced excellent white light emission. Lifetime decay and absorption studies proposed a possible fluorescence resonance energy transfer mechanism in this generation of white light emission.

Monitoring amyloid aggregation via a twisted intramolecular charge transfer (TICT)-based fluorescent sensor array

Imaging amyloid-beta (Aβ) aggregation is critical for understanding the pathology and aiding the pre-symptomatic intervention of Alzheimer's disease (AD). Amyloid aggregation consists of multiple phases with increasing viscosities and demands probes with broad dynamic ranges and gradient sensitivities for continuous monitoring. Yet, existing probes designed based on the twisted intramolecular charge transfer (TICT) mechanism mainly focused on donor engineering, limiting the sensitivities and/or dynamic ranges of these fluorophores to a narrow window. Herein, using quantum chemical calculations, we investigated multiple factors affecting the TICT process of fluorophores. It includes the conjugation length, the net charge of the fluorophore scaffold, the donor strength, and the geometric pre-twisting. We have established an integrative framework for tuning TICT tendencies. Based on this framework, a platter of hemicyanines with varied sensitivities and dynamic ranges is synthesized, forming a sensor array and enabling the observation of various stages of Aβ aggregations. This approach will significantly facilitate the development of TICT-based fluorescent probes with tailored environmental sensitivities for numerous applications.

Modulatory role of copper on hIAPP aggregation and toxicity in presence of insulin

Aggregation of the human islets amyloid polypeptide, or hIAPP, is linked to β-cell death in type II diabetes mellitus (T2DM). Different pancreatic β-cell environmental variables such as pH, insulin and metal ions play a key role in controlling the hIAPP aggregation. Since insulin and hIAPP are co-secreted, it is known from numerous studies that insulin suppresses hIAPP fibrillation by preventing the initial dimerization process. On the other hand, zinc and copper each have an inhibitory impact on hIAPP fibrillation, but copper promotes the production of toxic oligomers. Interestingly, the insulin oligomeric equilibrium is controlled by the concentration of zinc ions when the effect of insulin and zinc has been tested together. Lower zinc concentrations cause the equilibrium to shift towards the monomer and dimer states of insulin, which bind to monomeric hIAPP and stop it from developing into a fibril. On the other hand, the combined effects of copper and insulin have not yet been done. In this study, we have demonstrated how the presence of copper affects hIAPP aggregation and the toxicity of the resultant conformers with or without insulin. For this purpose, we have used a set of biophysical techniques, including NMR, fluorescence, CD etc., in combination with AFM and cell cytotoxicity assay. In the presence and/or absence of insulin, copper induces hIAPP to form structurally distinct stable toxic oligomers, deterring the fibrillation process. More specifically, the oligomers generated in the presence of insulin have slightly higher toxicity than those formed in the absence of insulin. This research will increase our understanding of the combined modulatory effect of two β-cell environmental factors on hIAPP aggregation.

Selective recognition of the amyloid marker single thioflavin T using DNA origami-based gold nanobipyramid nanoantennas

The development of effective methods for the detection of protein misfolding is highly beneficial for early stage medical diagnosis and the prevention of many neurodegenerative diseases. Self-assembled plasmonic nanoantennas with precisely tunable nanogaps show extraordinary electromagnetic enhancement, generating extreme signal amplification imperative for the design of ultrasensitive biosensors for point of care applications. Herein, we report the custom arrangement of Au nanobipyramid (Au NBP) monomer and dimer nanoantennas engineered precisely based on the DNA origami technique. Furthermore, we demonstrate the SERS based detection of thioflavin T (ThT), a well-established marker for the detection of amyloid fibril formation, where G-Quadruplexes govern the site-specific attachment of ThT in the plasmonic hotspot. This is the first study for the SERS based detection of the ThT dye attached specifically using a G-Quadruplex complex. The spectroscopic signals of ThT were greatly enhanced due to the designed nanoantennas demonstrating their potential as superior SERS substrates. This study paves the way for boosting the design of next-generation diagnostic tools for the specific and precise detection of various target disease biomarkers using molecular probes.

Mechanistic Insight into the Amyloid Fibrillation Inhibition of Hen Egg White Lysozyme by Three Different Bile Acids

Amyloid aggregation of protein is linked to many neurodegenerative diseases. Identification of small molecules capable of targeting amyloidogenic proteins has gained significant importance. Introduction of hydrophobic and hydrogen bonding interactions through site-specific binding of small molecular ligand to protein can effectively modulate the protein aggregation pathway. Here, we investigate the possible roles of three different bile acids, cholic acid (CA), taurocholic acid (TCA), and lithocholic acid (LCA) with varying hydrophobic and hydrogen bonding properties in inhibiting protein fibrillation. Bile acids are an important class of steroid compounds that are synthesized in the liver from cholesterol. Increasing evidence suggests that altered taurine transport, cholesterol metabolism, and bile acid synthesis have strong implications in Alzheimer's disease. We find that the hydrophilic bile acids, CA and TCA (taurine conjugated form of CA), are substantially more efficient inhibitors of lysozyme fibrillation than the most hydrophobic secondary bile acid LCA. Although LCA binds more strongly with the protein and masks the Trp residues more prominently through hydrophobic interactions, the lesser extent of hydrogen bonding interactions at the active site has made LCA a relatively weaker inhibitor of HEWL aggregation than CA and TCA. The introduction of a greater number of hydrogen bonding channels by CA and TCA with several key amino acid residues which are prone to form oligomers and fibrils has weakened the protein's internal hydrogen bonding capabilities for undergoing amyloid aggregation.

Synthesis of benzylidene-benzofuranone derivatives as probes for detection of amyloid fibrils in cells

Aggregated protein is the common cause of a wide variety of neurodegenerative diseases, such as Alzheimer's disease (AD), Parkinson's disease, etc. It is proven that protein aggregation like amyloid β (Aβ) is one of the critical factors causing AD and, its diagnosis in the early stages of the disease is important for the treatment or prevention of AD. To have a better understanding of protein aggregation and its pathologies, there is a huge need to design and develop new and more trustworthy probe molecules for in vitro amyloid quantification and in vivo amyloid imaging. In this study, 17 new biomarker compounds, have been synthesized from benzofuranone derivatives, to detect and identify amyloid in vitro (dye-binding assay) as well as in the cell by staining method. According to the results, some of these synthetic derivatives can be considered suitable identifiers and quantifiers to detect amyloid fibrils in vitro. Compared to thioflavin T, 4 probes out of 17 probes have shown good results in selectivity and detectability of Aβ depositions, and their binding properties were also confirmed with in silico analysis. The drug-likeness prediction results for selected compounds by the Swiss ADME server show a satisfactory percentage of blood-brain barrier (BBB) permeability and gastrointestinal (GI) absorption. Among all of them, compound 10 was able to show better binding properties than others, and in vivo study showed that this compound was capable of detecting intracellular amyloid.Communicated by Ramaswamy H. Sarma.

Electroabsorption and Stark Fluorescence Spectroscopies of Thioflavin T

Thioflavin T (ThT) is a typical fluorescent marker for detecting the formation of amyloid fibrils, because its fluorescence intensity increases by more than 2 orders of magnitude upon complexation with the fibrils. Strong electrostatic fields on protein surfaces are known to be a significant factor in chemical reactions and biological functions. Therefore, ThT bound to amyloid fibrils must experience strong electric fields. This study employed electroabsorption and Stark fluorescence spectroscopies to clarify the effects of external electric fields on the photophysics of ThT. The absorption spectrum shows two bands ascribed to locally excited (LE) and charge transfer (CT) states. Coupling between the LE and CT states is enhanced in the presence of an external electric field, resulting in fluorescence quenching. The electric field strength of the amyloid fibril surface was inferred from the fluorescence quenching efficiency of ThT.

Tunable Self-Assembled Peptide Hydrogel Sensor for Pharma Cold Supply Chain

Defrost sensors are a crucial element for proper functioning of the pharmaceutical cold chain. In this paper, the self-assembled peptide-based hydrogels were used to construct a sensitive defrost sensor for the transportation and storage of medications and biomaterials. The turbidity of the peptide hydrogel was employed as a marker of the temperature regime. The gelation kinetics under different conditions was studied to detect various stages of hydrogel structural transitions aimed at tuning the system properties. The developed sensor can be stored at room temperature for a long period, irreversibly indicates whether the product has been thawed, and can be adjusted to a specific temperature range and detection time.

Effects of Mutations and Post-Translational Modifications on α-Synuclein In Vitro Aggregation

Fibrillar aggregates of the α-synuclein (αS) protein are the hallmark of Parkinson's Disease and related neurodegenerative disorders. Characterization of the effects of mutations and post-translational modifications (PTMs) on the αS aggregation rate can provide insight into the mechanism of fibril formation, which remains elusive in spite of intense study. A comprehensive collection (375 examples) of mutant and PTM aggregation rate data measured using the fluorescent probe thioflavin T is presented, as well as a summary of the effects of fluorescent labeling on αS aggregation (20 examples). A curated set of 131 single mutant de novo aggregation experiments are normalized to wild type controls and analyzed in terms of structural data for the monomer and fibrillar forms of αS. These tabulated data serve as a resource to the community to help in interpretation of aggregation experiments and to potentially be used as inputs for computational models of aggregation.

Chemical tools for study and modulation of biomolecular phase transitions

Biomolecular phase transitions play an important role in organizing cellular processes in space and time. Methods and tools for studying these transitions, and the intrinsically disordered proteins (IDPs) that often drive them, are typically less developed than tools for studying their folded protein counterparts. In this perspective, we assess the current landscape of chemical tools for studying IDPs, with a specific focus on protein liquid-liquid phase separation (LLPS). We highlight methodologies that enable imaging and spectroscopic studies of these systems, including site-specific labeling with small molecules and the diverse range of capabilities offered by inteins and protein semisynthesis. We discuss strategies for introducing post-translational modifications that are central to IDP and LLPS function and regulation. We also investigate the nascent field of noncovalent small-molecule modulators of LLPS. We hope that this review of the state-of-the-art in chemical tools for interrogating IDPs and LLPS, along with an associated perspective on areas of unmet need, can serve as a valuable and timely resource for these rapidly expanding fields of study.

Paper-Based Distance Sensor for the Detection of Lipase via a Phase Separation-Induced Viscosity Change

Human pancreatic lipase is a symbolic biomarker for the diagnosis of acute pancreatitis, which has profound significance for clinical detection and disease treatment. Herein, we first demonstrate a paper-based lipase sensor via a phase separation-induced viscosity change. Lipase catalyzes triolein to produce oleic acid and glycerol. Adding an excess of Ca²⁺ produces calcium oleate. The remaining Ca²⁺ binds with sodium alginate, triggering hydrogelation with an "egg-box" structure. The viscosity change of the aqueous solution induced by the phase separation process can be quantified by measuring the solution flow distance on a pH test paper. The paper-based lipase sensor has high sensitivity with a detection limit of 0.052 U/mL and also shows excellent specificity. Additionally, it is also utilized for quantitative lipase analysis in human serum samples to exhibit its potency in acute pancreatitis detection. This method overcomes the drawbacks of low sensitivity, slow response, and poor reproducibility caused by the nonuniform distribution of the highly viscous hydrogel on the sensing interface in existing approaches. In conclusion, thanks to the prominent characteristics of high portability, low cost, and easy operation, it is prospective for simple quantitative detection of lipase and has great potential for commercialization.

Controlling the fluorescence quantum yields of benzothiazole-difluoroborates by optimal substitution

Precise tuning of the fluorescence quantum yield, vital for countless applications of fluorophores, remains exceptionally challenging due to numerous factors affecting energy dissipation phenomena often leading to its counterintuitive behavior. In contrast to the absorption and emission wavelength which can be precisely shifted to the desired range by simple structural changes, no general strategy exists for controllable modification of the fluorescence quantum yield. The rigidification of the molecular skeleton is known to usually enhance the emission and can be practically realized via the limiting molecular vibrations by aggregation. However, the subtle balance between the abundant possible radiative and non-radiative decay pathways makes the final picture exceptionally sophisticated. In the present study, a series of nine fluorophores obtained by peripheral substitution with two relatively mild electron donating and electron withdrawing groups are reported. The obtained fluorescence quantum yields range from dark to ultra-bright and the extreme values are obtained for the isomeric molecules. These severe changes in emission efficiency have been shown to arise from the complex relationship between the Franck-Condon excited state and conical intersection position. The experimental findings are rationalized by the advanced quantum chemical calculations delivering good correlation between the measured emission parameters and theoretical radiative and internal conversion rate constants. Therefore, the described substituent exchange provides a method to rigorously adjust the properties of molecular probes structurally similar to thioflavin T.

Mechanistic insight into functionally different human islet polypeptide (hIAPP) amyloid: the intrinsic role of the C-terminal structural motifs

Targeting amyloidosis requires high-resolution insight into the underlying mechanisms of amyloid aggregation. The sequence-specific intrinsic properties of a peptide or protein largely govern the amyloidogenic propensity. Thus, it is essential to delineate the structural motifs that define the subsequent downstream amyloidogenic cascade of events. Additionally, it is important to understand the role played by extrinsic factors, such as temperature or sample agitation, in modulating the overall energy barrier that prompts divergent nucleation events. Consequently, these changes can affect the fibrillation kinetics, resulting in structurally and functionally distinct amyloidogenic conformers associated with disease pathogenesis. Here, we have focused on human Islet Polypeptide (hIAPP) amyloidogenesis for the full-length peptide along with its N- and C-terminal fragments, under different temperatures and sample agitation conditions. This helped us to gain a comprehensive understanding of the intrinsic role of specific functional epitopes in the primary structure of the peptide that regulates amyloidogenesis and subsequent cytotoxicity. Intriguingly, our study involving an array of biophysical experiments and ex vivo data suggests a direct influence of external changes on the C-terminal fibrillating sequence. Furthermore, the observations indicate a possible collaborative role of this segment in nucleating hIAPP amyloidogenesis in a physiological scenario, thus making it a potential target for future therapeutic interventions.

Impact of the Flavonoid Quercetin on β-Amyloid Aggregation Revealed by Intrinsic Fluorescence

We report the effects of quercetin, a flavonoid present in the human diet, on early stage beta-amyloid (Aβ) aggregation, a seminal event in Alzheimer's disease. Molecular level changes in Aβ arrangements are monitored by time-resolved emission spectral (TRES) measurements of the fluorescence of Aβ's single tyrosine intrinsic fluorophore (Tyr). The results suggest that quercetin binds β-amyloid oligomers at early stages of their aggregation, which leads to the formation of modified oligomers and hinders the creation of β-sheet structures, potentially preventing the onset of Alzheimer's disease.

The intriguing dose-dependent effect of selected amphiphilic compounds on insulin amyloid aggregation: Focus on a cholesterol-based detergent, Chobimalt

The amyloidogenic self-assembly of many peptides and proteins largely depends on external conditions. Among amyloid-prone proteins, insulin attracts attention because of its physiological and therapeutic importance. In the present work, the amyloid aggregation of insulin is studied in the presence of cholesterol-based detergent, Chobimalt. The strategy to elucidate the Chobimalt-induced effect on insulin fibrillogenesis is based on performing the concentration- and time-dependent analysis using a combination of different experimental techniques, such as ThT fluorescence assay, CD, AFM, SANS, and SAXS. While at the lowest Chobimalt concentration (0.1 µM; insulin to Chobimalt molar ratio of 1:0.004) the formation of insulin fibrils was not affected, the gradual increase of Chobimalt concentration (up to 100 µM; molar ratio of 1:4) led to a significant increase in ThT fluorescence, and the maximal ThT fluorescence was 3-4-fold higher than the control insulin fibril's ThT fluorescence intensity. Kinetic studies confirm the dose-dependent experimental results. Depending on the concentration of Chobimalt, either (i) no effect is observed, or (ii) significantly, ∼10-times prolonged lag-phases accompanied by the substantial, ∼ 3-fold higher relative ThT fluorescence intensities at the steady-state phase are recorded. In addition, at certain concentrations of Chobimalt, changes in the elongation-phase are noticed. An increase in the Chobimalt concentrations also triggers the formation of insulin fibrils with sharply altered morphological appearance. The fibrils appear to be more flexible and wavy-like with a tendency to form circles. SANS and SAXS data also revealed the morphology changes of amyloid fibrils in the presence of Chobimalt. Amyloid aggregation requires the formation of unfolded intermediates, which subsequently generate amyloidogenic nuclei. We hypothesize that the different morphology of the formed insulin fibrils is the result of the gradual binding of Chobimalt to different binding sites on unfolded insulin. A similar explanation and the existence of such binding sites with different binding energies was shown previously for the nonionic detergent. Thus, the data also emphasize the importance of a protein partially-unfolded state which undergoes the process of fibrils formation; i.e., certain experimental conditions or the presence of additives may dramatically change not only kinetics but also the morphology of fibrillar aggregates.

Solution structure of recombinant Pvfp-5β reveals insights into mussel adhesion

Some marine organisms can resist to aqueous tidal environments and adhere tightly on wet surface. This behavior has raised increasing attention for potential applications in medicine, biomaterials, and tissue engineering. In mussels, adhesive forces to the rock are the resultant of proteinic fibrous formations called byssus. We present the solution structure of Pvfp-5β, one of the three byssal plaque proteins secreted by the Asian green mussel Perna viridis, and the component responsible for initiating interactions with the substrate. We demonstrate that Pvfp-5β has a stably folded structure in agreement with the presence in the sequence of two EGF motifs. The structure is highly rigid except for a few residues affected by slow local motions in the µs-ms time scale, and differs from the model calculated by artificial intelligence methods for the relative orientation of the EGF modules, which is something where computational methods still underperform. We also show that Pvfp-5β is able to coacervate even with no DOPA modification, giving thus insights both for understanding the adhesion mechanism of adhesive mussel proteins, and developing of biomaterials.

Twisted intramolecular charge transfer of nitroaromatic push-pull chromophores

The structural changes during the intramolecular charge transfer (ICT) of nitroaromatic chromophores, 4-dimethylamino-4′-nitrobiphenyl (DNBP) and 4-dimethylamino-4′-nitrostilbene (DNS) were investigated by femtosecond stimulated Raman spectroscopy (FSRS) with both high spectral and temporal resolutions. The kinetically resolved Raman spectra of DNBP and DNS in the locally-excited and charge-transferred states of the S₁ state appear distinct, especially in the skeletal vibrational modes of biphenyl and stilbene including ν_8a and ν_C=C. The ν_8a of two phenyls and the ν_C=C of the central ethylene group (only for stilbene), which are strongly coupled in the planar geometries, are broken with the twist of nitrophenyl group with the ICT. Time-resolved vibrational spectroscopy measurements and the time-dependent density functional theory simulations support the ultrafast ICT dynamics of 220–480 fs with the twist of nitrophenyl group occurring in the S₁ state of the nitroaromatic chromophores. While the ICT of DNBP occurs via a barrier-less pathway, the ICT coordinates of DNS are strongly coupled to several low-frequency out-of-phase deformation modes relevant to the twist of the nitrophenyl group.

Effect of pH on the structure and function of cyclin-dependent kinase 6

Cyclin-dependent kinase 6 (CDK6) is an important protein kinase that regulates cell growth, development, cell metabolism, inflammation, and apoptosis. Its overexpression is associated with reprogramming glucose metabolism through alternative pathways and apoptosis, which ultimately plays a significant role in cancer development. In the present study, we have investigated the structural and conformational changes in CDK6 at varying pH employing a multi-spectroscopic approach. Circular dichroism (CD) spectroscopy revealed at extremely acidic conditions (pH 2.0–4.0), the secondary structure of CDK6 got significantly disrupted, leading to aggregates formation. These aggregates were further characterized by employing Thioflavin T (ThT) fluorescence. No significant secondary structural changes were observed over the alkaline pH range (pH 7.0–11.0). Further, fluorescence and UV spectroscopy revealed that the tertiary structure of CDK6 was disrupted under extremely acidic conditions, with slight alteration occurring in mild acidic conditions. The tertiary structure remains intact over the entire alkaline range. Additionally, enzyme assay provided an insight into the functional aspect of CDK at varying pH; CDK6 activity was optimal in the pH range of 7.0–8.0. This study will provide a platform that provides newer insights into the pH-dependent dynamics and functional behavior of CDK6 in different CDK6 directed diseased conditions, viz. different types of cancers where changes in pH contribute to cancer development.