Small Molecule Fluorescent Dyes Research Articles

Two-dimensional black phosphorus/platinum catalase-like nanozyme-based Fenton reaction-mediated dual-mode immunoassays for the detection of enrofloxacin.

Hydrogen peroxide-based Fenton reaction can effectively degrade many small-molecule fluorescent dyes, leading to notable alterations in fluorescence signals. Additionally, the two-dimensional black phosphorus/platinum nanocomposite (BP/Pt) demonstrates exceptional catalase (CAT) characteristics. Based on these, a colorimetric-fluorescence dual-mode signal output pattern based on BP/Pt-Fenton reaction-rhodamine B tandem reaction system isreported. Thephysical adsorption property of the BP/Pt nanozymes was utilized to couple with antibodies, thus constructing a novel dual-mode nanozyme-based immuno-sensing assay (NISA). By using the migratory antibiotic enrofloxacin (ENR) as the target, the NISA providedhighly sensitive detection with the detection limits of 0.058ng/mL for colorimetric-mode and 0.025ng/mL for fluorescence-mode and achieved accurate quantitative detection in environmental water and crucian carp samples. This work provides an innovative design for monitoring antibiotics in the environment and broadens the idea for the application of nanozymes and Fenton systems in immunosensing assays.

Organic Fluorophores with Large Stokes Shift for the Visualization of Rapid Protein and Nucleic Acid Assays.

Organic small-molecule fluorophores, characterized by flexible chemical structure and adjustable optical performance, have shown tremendous potential in biosensing. However, classical organic fluorophore motifs feature large overlap between excitation and emission spectra, leading to the requirement of advanced optical set up to filter desired signal, which limits their application in scenarios with simple settings. Here, a series of wavelength-tunable small-molecule fluorescent dyes (PTs) bearing simple organic moieties have been developed, which exhibit Stokes shift up to 262 nm, molar extinction coefficients ranged 30,000-100,000 M-1 cm-1, with quantum yields up to 54.8 %. Furthermore, these dyes were formulated into fluorescent nanoparticles (PT-NPs), and applied in lateral flow assay (LFA). Consequently, limit of detection for SARS-CoV-2 nucleocapsid protein reached 20 fM with naked eye, a 100-fold improvement in sensitivity compared to the pM detection level for colloidal gold-based LFA. Besides, combined with loop-mediated isothermal amplification (LAMP), the LFA system achieved the visualization of single copy level nucleic acid detection for monkeypox (Mpox).

Molecular engineering and bioimaging applications of C2-alkenyl indole dyes with tunable emission wavelengths covering visible to NIR light

As an important member of dyes, small-molecule fluorescent dyes show indispensable value in biomedical fields. Although various molecular dyes have been developed, full-color dyes covering blue to red region derived from a single chromophore are still in urgent demand. In this work, a series of dyes based on C2-alkenyl indole skeleton were synthesized, namely AI dyes, and their photophysical properties, cytotoxicity, and imaging capacity were verified to be satisfactory. Particularly, the maximal emission wavelengths of these dyes could cover a wide range from visible to NIR light with large Stokes shifts. Besides, the optical and structural discrepancies between the C2- and C3- alkenyl AI dyes were discussed in detail, and the theoretical calculations were conducted to provide insights on such structure–activity relationship. Finally, as a proof-of-concept, a fluorescent probe AI-Py-B capable of imaging endogenous ONOO− was presented, demonstrating the bioimaging potentials of these alkenyl indole dyes. This work is anticipated to open up new possibilities for developing dye engineering and bio-applications of natural indole framework.

Rational construction of long-wavelength emissive AIE molecules and their application for sensitive and visual detection of HClO

Herein, two small-molecule fluorescent dyes, 2-(4-(diethylamino)-2-((4-(4,4,5,5- tetramethyl-1,3,2-dioxaborolan-2-yl)benzyl)oxy)benzylidene)malononitrile (BASM) and ethyl-2-cyano-3-(4-(diethylamino)-2-((4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)benzyl)oxy)phenyl)acrylate (BASE) with aggregation-induced emission characteristics are facilely synthesized and they were applied for the sensitive and selective detection of hypochlorous acid (HClO). For these novel AIE molecules, intricate structure and enormous π-conjugation system are no longer necessary. Due to the enhanced effect of intramolecular charge transfer and restricted intramolecular rotation, BASM and BASE displayed reinforced and long-wavelength emission in solid states and aggregated states. Moreover, the BASM has been rationally designed as a fluorescent probe of HClO based on the selective reaction between the BASM and HClO which generates a fluorescence efficient cyano iminocoumarin. The BASM displays a wide linear range for HClO from 0.5 to 10 μM and the limit of detection is as low as 6.46 nM. Intriguingly, excess amount (10–50 μM) of HClO causes fluorescence quenching due to a unique oxidation process, also explains the sensitivity and selectivity of BASM towards HClO. Furthermore, probe BASM is successfully employed for several practical applications such as detection of HClO in actual samples, fabrication of paper-based sensors, and fluorescence imaging in living bacteria.

Identification of Nonradiative Decay Pathways in Cy3.

Photoexcited fluorescent markers are extensively used in spectroscopy, imaging, and analysis of biological systems. The performance of fluorescent markers depends on high levels of emission, which are limited by competing nonradiative decay pathways. Small-molecule fluorescent dyes have been increasingly used as markers due to their high and stable emission. Despite their prevalence, the nonradiative decay pathways of these dyes have not been determined. Here, we investigate these pathways for a widely used indocarbocyanine dye, Cy3, using transient grating spectroscopy. We identify a nonradiative decay pathway via a previously unknown dark state formed within ∼1 ps of photoexcitation. Our experiments, in combination with electronic structure calculations, suggest that the generation of the dark state is mediated by picosecond vibrational mode coupling, likely via a conical intersection. We further identify the vibrational modes, and thus structural elements, responsible for the formation and dynamics of the dark state, providing insight into suppressing nonradiative decay pathways in fluorescent markers such as Cy3.

Small-molecule fluorescent dyes based on benzothiazole derivatives for targeting endoplasmic reticulum and tissue imaging

Small-molecule fluorescent dyes with excellent biocompatibility and deep tissue permeability are playing an important part in biological development. Herein, a series of D-A typesmall-molecules L1, L2 and L3 containing different terminal groups have been designed and synthesized, of which the structures were confirmed by single crystal X-ray diffraction analysis. Interestingly, it was found that different end groups within the molecules gave an obvious effect on the fluorescent emission properties while unconspicuous influence on the absorption properties. Moreover, these compounds were successfully applied to fluorescent imaging for staining cellular endoplasmic reticulum (ER) and tissue slice from mouse exhibiting negligible cytotoxicity as well as favourable permeability. These compounds may act as probes for ER targeting and alternative bio-imaging reagents.

Surface-adaptive nanoparticles with near-infrared aggregation-induced emission for image-guided tumor resection.

Aggregation-induced emission (AIE) nanoparticles (NPs) are widely used for image-guided tumor resection because of their high signal-to-noise ratios and long systemic circulation time. These NPs are derived by encapsulating small-molecule fluorescent dyes with AIE property inside the cores of NPs assembled by amphiphilic polymers. Although the systemic circulation of AIE NPs is prolonged, hydrophilic polymer coatings simultaneously decrease the binding and uptake of AIE NPs by tumor cells. To overcome this problem, surface-adaptive AIE dye-encapsulated mixed-shell micelles (MSMs) with polyethylene glycol/poly (β-amino ester) (PEG/PAE) surfaces were prepared. Due to the charge conversion ability of PAE, MSMs demonstrated enhanced cellular uptake by tumor cells in acidic conditions. In addition, compared with single-PEG-shelled micelles (PEGSMs), MSMs exhibited prolonged systemic circulation due to the presence of micro-phase separated surfaces. Moreover, due to the co-ordination effect of enhanced cancer cell uptake and prolonged systemic circulation time, MSMs were more enriched than PEGSMs in the tumor cells and exhibited excellent performance during image-guided tumor resection.

Genetically Encoded Calcium Indicators as Probes to Assess the Role of Calcium Channels in Disease and for High-Throughput Drug Discovery.

The calcium ion (Ca2+) is an important signaling molecule implicated in many cellular processes, and the remodeling of Ca2+ homeostasis is a feature of a variety of pathologies. Typical methods to assess Ca2+ signaling in cells often employ small molecule fluorescent dyes, which are sometimes poorly suited to certain applications such as assessment of cellular processes, which occur over long periods (hours or days) or in vivo experiments. Genetically encoded calcium indicators are a set of tools available for the measurement of Ca2+ changes in the cytosol and subcellular compartments, which circumvent some of the inherent limitations of small molecule Ca2+ probes. Recent advances in genetically encoded calcium sensors have greatly increased their ability to provide reliable monitoring of Ca2+ changes in mammalian cells. New genetically encoded calcium indicators have diverse options in terms of targeting, Ca2+ affinity and fluorescence spectra, and this will further enhance their potential use in high-throughput drug discovery and other assays. This review will outline the methods available for Ca2+ measurement in cells, with a focus on genetically encoded calcium sensors. How these sensors will improve our understanding of the deregulation of Ca2+ handling in disease and their application to high-throughput identification of drug leads will also be discussed.

Detection of amyloid-β fibrils using the DNA-intercalating dye YOYO-1: Binding mode and fibril formation kinetics

Identification of the chemical and biological properties of amyloid fibrils is important for understanding their roles in human diseases and to clarify the mechanisms that govern their formation. In pursuit of these goals, small molecule fluorescent dyes have received increasing attention as probes of amyloid conformations. In this study, we report on the ability of YOYO-1, a homodimeric derivative of oxazole yellow, to detect fibrils formed by the Alzheimer's disease related Aβ(1–42) peptide. We find that YOYO-1 binds to Aβ(1–42) fibrils with the long axes of its oxazole yellow moieties parallel to the fibril axis, resulting in a 200x emission enhancement; a result that shows that YOYO-1 is a sensitive amyloid probe. Further, YOYO-1 exhibits characteristic absorption shifts upon binding to the Aβ(1–42) fibrils that we attribute to a self-stacking to non-stacking transition in its homodimer configuration; herein we show how this phenomenon can be exploited to estimate the degree of dye binding. Furthermore, we show that YOYO-1 can be used to monitor the kinetics of amyloid formation reactions. Taken together, our results show that YOYO-1 is a sensitive amyloid probe that can operate with both absorption and fluorescence read-outs, and this suggests that this commercially available dye could become a useful complement to thioflavin-T for in vitro amyloid-sensing applications.