YOPRO-1: A Cyanine-Based Molecular Rotor Probe for Amyloid Fibril Detection

The widespread occurrence of amyloidosis in many neurodegenerative diseases, including Alzheimer's, highlights the urgent need for early detection methods. Traditional approaches often fall short in sensitivity, specificity, and the ability to operate within complex biological matrices. Fluorescence spectroscopy, which leverages the unique properties of extrinsic fluorescence sensors, has emerged as a promising avenue for amyloid detection. Thioflavin-T (ThT), while extensively utilized, faces several disadvantages such as poor blood-brain barrier penetration, short emission wavelength, and lack of sensitivity to oligomeric protein aggregates. These limitations necessitate the development of improved amyloid probes with enhanced properties for the better detection and understanding of neurodegenerative diseases. In this context, YOPRO-1, a cyanine-based molecular rotor probe, has been identified as a potent amyloid fibril sensor characterized by its turn-on fluorescence response and specificity for amyloid fibrils over native protein forms. Utilizing a variety of spectroscopic techniques, including steady-state emission, ground-state absorption, time-resolved fluorescence, and molecular docking, we demonstrate the superior selectivity and sensitivity of YOPRO-1 for amyloid fibrils. The probe exhibits a remarkable 245-fold increase in fluorescence intensity upon binding to insulin fibrils, which is a common amyloid model. This capability facilitates its application in complex biological matrices, such as high-percentage human serum, which has rarely been demonstrated by previous amyloid sensing probes. Furthermore, the commercial availability of YOPRO-1 avoids the challenges associated with the synthesis of specific probes, thereby marking a significant advancement in amyloid detection methodologies. Our findings highlight the potential of YOPRO-1 as a versatile and effective tool for the early diagnosis of amyloid-related diseases, offering a foundation for future therapeutic and diagnostic applications.

Allergen-induced DNA release by the airway epithelium amplifies type 2 immunity

BACKGROUND

Alternaria alternata and house dust mite exposure evokes IL-33 secretion from the airway epithelium, which functions as an alarmin to stimulate type 2 immunity. Extracellular DNA (eDNA) is also an alarmin that intensifies inflammation in cystic fibrosis, chronic obstructive pulmonary disease, and asthma.

OBJECTIVE

We investigated the mechanisms underlying allergen-evoked DNA mobilization and release from the airway epithelium and determined the role of eDNA in type 2 immunity.

METHODS

Human bronchial epithelial (hBE) cells were used to characterize allergen-induced DNA mobilization and extracellular release using comet assays to measure DNA fragmentation, Qubit double-stranded DNA assays to measure DNA release, and DNA sequencing to determine eDNA composition. Mice were used to investigate the role of eDNA in type 2 immunity.

RESULTS

Alternaria extract rapidly induces mitochondrial and nuclear DNA release from human bronchial epithelial cells, whereas house dust mite extract induces mitochondrial DNA release. Caspase-3 is responsible for nuclear DNA fragmentation and becomes activated after cleavage by furin. Analysis of secreted nuclear DNA showed disproportionally higher amounts of promotor and exon sequences and lower intron and intergenic regions compared to predictions of random DNA fragmentation. In mice, Alternaria-induced type 2 immune responses were blocked by pretreatment with a DNA scavenger. In caspase-3-deficient mice, Alternaria-induced DNA release was suppressed. Furthermore, intranasal administration of mouse genomic DNA with Alternaria amplified secretion of IL-5 and IL-13 into bronchoalveolar lavage fluid while DNA alone had no effect.

CONCLUSION

These findings highlight a novel, allergen-induced mechanism of rapid DNA release that amplifies type 2 immunity in airways.

Photoinduced Electron Transfer in a Porphyrin-Fullerene Dyad at a Liquid Interface

The excited-state properties of an amphiphilic porphyrin-fullerene dyad and of its porphyrin analogue adsorbed at the dodecane/water interface are investigated by using surface second-harmonic generation. Although the porphyrin is formally centrosymmetric, the second-harmonic spectra of both compounds are dominated by the intense Soret band of the porphyrin. Polarization-selective measurements and molecular dynamics simulations suggest an angle of about 45° between the donor-acceptor axis and the interfacial plane, with the porphyrin interacting mostly with the nonpolar phase. Time-resolved measurements reveal a marked concentration dependence of the dynamics of both compounds upon Q-band excitation, indicating the occurrence of intermolecular quenching processes. The significant differences in dynamics and spectra between the dyad and the porphyrin analogue are explained by a self-quenching of the excited dyad via an intermolecular electron transfer.

The role of twisting in driving excited-state symmetry breaking and enhanced two-photon absorption in quadrupolar cationic pyridinium derivatives

Two symmetric quadrupolar cationic push-pull compounds with a central electron-acceptor (N+-methylpyrydinium, A+) and different lateral electron-donors, (N,N-dimethylamino and N,N-diphenylamino, D) in a D-π-A+-π-D arrangement, were investigated together with their dipolar counterparts (D-π-A+) for their excited-state dynamics and NLO properties. As for the quadrupolar compounds, attention was focused on excited-state symmetry breaking (ESSB), which leads to a relaxed dipolar excited state. Both electron charge displacements and structural rearrangements were recognized in the excited-state dynamics of these molecules by resorting to femtosecond-resolved broadband fluorescence up-conversion experiments and advanced data analysis, used as a valuable alternative approach for fluorescent molecules compared to time-resolved IR spectroscopy, only suitable for compounds bearing IR markers. Specifically, intramolecular charge transfer (ICT) was found to be guided by ultrafast inertial solvation, while diffusive solvation can drive the twisting of lateral groups to originate twisted-ICT (TICT) states on a picosecond time scale. Yet still, only the bis-N,N-diphenylamino-substituted compound undergoes ESSB, in both highly and sparingly polar solvents, provided that it can experience large amplitude motions to a fully symmetry-broken TICT state. Besides well-known solvation effects, this structural requirement proved to be a necessary condition for these quadrupolar cations to undergo ESSB. In fact, a more efficient uncoupling between the out-of-plane D and A+ groups in the TICT state allows a greater stabilization gained through solvation, relative to the bis-N,N-dimethylamino-substituted derivative, which instead maintains its symmetry. This different behavior parallels the two-photon absorption (TPA) ability, which is greatly enhanced in the case of the bis-N,N-diphenylamino-substituted compound, paving the way for cutting-edge bio-imaging applications.

Probing Liquid Interfaces with Room-Temperature Ionic Liquids Using the Excited-State Dynamics of a Cationic Dye

Interfaces with room-temperature ionic liquids (ILs) play key roles in many applications of these solvents, but our understanding of their properties is still limited. We investigate how the addition of ILs in the aqueous subphase affects the adsorption of the cationic dye malachite green at the dodecane/water interface using stationary and time-resolved surface second harmonic generation. We find that the interfacial concentration of malachite green depends crucially on the nature of both anionic and cationic constituents. This concentration reports on the overall charge of the interface, which itself depends on the relative interfacial affinity of the ions. Our results reveal that the addition of ILs to the aqueous subphase has similar effects to the addition of conventional salts. However, the IL cations have a significantly higher propensity to adsorb than small inorganic cations. Furthermore, the IL constituents show a synergistic effect, as the interfacial concentration of each of them also depends on the interfacial affinity of the other.

Fabrication of Supramolecular Chirality from Achiral Molecules at the Liquid/Liquid Interface Studied by Second Harmonic Generation

We present the investigation into the supramolecular chirality of 5-octadecyloxy-2-(2-pyridylazo)phenol (PARC18) at water/1,2-dichloroethane interface by second harmonic generation (SHG). We observe that PARC18 molecules form supramolecular chirality through self-assembly at the liquid/liquid interface although they are achiral molecules. The bulk concentration of PARC18 in the organic phase has profound effects on the supramolecular chirality. By increasing bulk concentration, the enantiomeric excess at the interface first grows and then decreases until it eventually vanishes. Further analysis reveals that the enantiomeric excess is determined by the twist angle of PARC18 molecules at the interface rather than their orientational angle. At lower and higher bulk concentrations, the average twist angle of PARC18 molecules approaches zero, and the assemblies are achiral; whereas at medium bulk concentrations, the average twist angle is nonzero, so that the assemblies show supramolecular chirality. We also estimate the coverage of PARC18 molecules at the interface versus the bulk concentration and fit it to Langmuir adsorption model. The result indicates that PARC18 assemblies show strongest supramolecular chirality in a half-full monolayer. These findings highlight the opportunities for precise control of supramolecular chirality at liquid/liquid interfaces by manipulating the bulk concentration.

Detecting order and lateral pressure at biomimetic interfaces using a mechanosensitive second-harmonic-generation probe

A mechanosensitive harmonophore is used to probe the order and lateral pressure in phospholipid monolayers by surface-second harmonic generation.

Membrane bound COMT isoform is an interfacial enzyme: general mechanism and new drug design paradigm

We have determined the substrate differentiation mechanism between the membrane bound and water soluble isoforms of important drug target catechol-O-methyltransferase.

Exploring Fluorescent Dyes at Biomimetic Interfaces with Second Harmonic Generation and Molecular Dynamics

The adsorption of a DNA fluorescent probe belonging to the thiazole orange family at the dodecane/water and dodecane/phospholipid/water interfaces has been investigated using a combination of surface second harmonic generation (SSHG) and all-atomistic molecular dynamics (MD) simulations. Both approaches point to a high affinity of the cationic dye for the dodecane/water interface with a Gibbs free energy of adsorption on the order of -45 kJ/mol. Similar affinity was observed with a monolayer of negatively charged DPPG (1,2-dipalmitoyl-sn-glycero-3-phospho-rac-(1-glycerol)) lipids. On the other hand, no significant adsorption could be found with the zwitterionic DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) lipids. This was rationalized in terms of Coulombic interactions between the monolayer surface and the cationic dye. The similar affinity for the interface with and without DPPG, despite the favorable Coulombic attraction in the latter case, could be explained after investigating the interfacial orientation of the dye. In the absence of a monolayer, the dye adsorbs with its molecular plane almost flat at the interface, whereas in the presence of DPPG it has to intercalate into the monolayer and adopt a significantly different orientation to benefit from the electrostatic stabilization.

Ionic hydration-induced evolution of decane–water interfacial tension

We show that ionic hydration is responsible for the non-monotonic variation of the interfacial tension with increasing ionic concentration.

Second harmonic generation from an individual amorphous selenium nanosphere

Among the numerous nonlinear optics effects, second harmonic generation (SHG) is always a hotspot and it is extensively used for optical frequency conversion, biomedical imaging, etc. However, SHG is forbidden in a medium with inversion symmetry under the electric-dipole approximation. Here, we demonstrated SHG from a single amorphous selenium (a-Se) nanosphere under near-infrared femtosecond pulse excitation. It was found that SH spectra are tunable with the size of a-Se nanospheres and the SHG efficiency of a single a-Se sphere with a diameter over 300 nm is estimated at 10(-8). We also established two physical mechanisms of SHG from the amorphous nanospheres. There is an electric-dipole contribution to the second-order nonlinearity in view of the inevitable structural discontinuity at the surface. The discontinuity of the normal component of the electric field strength leads to the quadrupole-type contributions arising from the large electric field gradient. The SHG process can be enhanced by resonance near the fundamental wavelength, giving rise to the detectable second harmonic (SH) spectra of a single a-Se nanosphere (d > 300 nm) or two small a-Se nanospheres (d = 200 nm) aggregated into a dimer, while the single nanosphere with smaller size (d > 300 nm) is undetectable. As an essential trace element for animals, a-Se features unique biological compatibility and has specific properties of optical nonlinearity within the optical window in biological tissue. This discovery makes a-Se nanospheres promising both in nonlinear optics and biomedicine.

Detection of Ligand-Induced Conformational Changes in Oligonucleotides by Second-Harmonic Generation at a Supported Lipid Bilayer Interface

There is a high demand for characterizing oligonucleotide structural changes associated with binding interactions as well as identifying novel binders that modulate their structure and function. In this study, second-harmonic generation (SHG) was used to study RNA and DNA oligonucleotide conformational changes associated with ligand binding. For this purpose, we developed an avidin-based biotin capture surface based on a supported lipid bilayer membrane. The technique was applied to two well-characterized aptamers, both of which undergo conformational changes upon binding either a protein or a small molecule ligand. In both cases, SHG was able to resolve conformational changes in these oligonucleotides sensitively and specifically, in solution and in real time, using nanogram amounts of material. In addition, we developed a competition assay for the oligonucleotides between the specific ligands and known, nonspecific binders, and we demonstrated that intercalators and minor groove binders affect the conformation of the DNA and RNA oligonucleotides in different ways upon binding and subsequently block specific ligand binding in all cases. Our work demonstrates the broad potential of SHG for studying oligonucleotides and their conformational changes upon interaction with ligands. As SHG offers a powerful, high-throughput screening approach, our results here also open an important new avenue for identifying novel chemical probes or sequence-targeted drugs that disrupt or modulate DNA or RNA structure and function.