Clickable rhodamine spirolactam based spontaneously blinking probe for super-resolution imaging

A Bioorthogonal Dual Fluorogenic Probe for the Live-Cell Monitoring of Nutrient Uptake by Mammalian Cells

Cells rely heavily on the uptake of exogenous nutrients for survival, growth, and differentiation. Yet quantifying the uptake of small molecule nutrients at the single cell level is difficult. Here we present a new approach to studying the nutrient uptake in live single cells using Inverse Electron-Demand Diels Alder (IEDDA) chemistry. We have modified carboxyfluorescein-diacetate-succinimidyl esters (CFSE)-a quenched fluorophore that can covalently react with proteins and is only turned on in the cytosol of a cell following esterase activity-with a tetrazine. This tetrazine serves as a second quencher for the pendant fluorophore. Upon reaction with nutrients modified with an electron-rich or strained dienophile in an IEDDA reaction, this quenching group is destroyed, thereby enabling the probe to fluoresce. This has allowed us to monitor the uptake of a variety of dienophile-containing nutrients in live primary immune cell populations using flow cytometry and live-cell microscopy.

Squaraine Dyes Exhibit Spontaneous Fluorescence Blinking That Enables Live-Cell Nanoscopy

Hampered by their susceptibility to nucleophilic attack and chemical bleaching, electron-deficient squaraine dyes have long been considered unsuitable for biological imaging. This study unveils a surprising twist: in aqueous environments, bleaching is not irreversible but rather a reversible spontaneous quenching process. Leveraging this new discovery, we introduce a novel deep-red squaraine probe tailored for live-cell super-resolution imaging. This probe enables single-molecule localization microscopy (SMLM) under physiological conditions without harmful additives or intense lasers and exhibits spontaneous blinking orchestrated by biological nucleophiles, such as glutathione or hydroxide anion. With a low duty cycle (∼0.1%) and high-emission rate (∼6 × 104 photons/s under 400 W/cm2), the squaraine probe surpasses the benchmark Cy5 dye by 4-fold and Si-rhodamine by a factor of 1.7 times. Live-cell SMLM with the probe reveals intricate structural details of cell membranes, which demonstrates the high potential of squaraine dyes for next-generation super-resolution imaging.

Spontaneously Blinking Rhodamine Dyes for Single-Molecule Localization Microscopy

Single-molecule localization microscopy (SMLM) has found extensive applications in various fields of biology and chemistry. As a vital component of SMLM, fluorophores play an essential role in obtaining super-resolution fluorescence images. Recent research on spontaneously blinking fluorophores has greatly simplified the experimental setups and extended the imaging duration of SMLM. To support this crucial development, this review provides a comprehensive overview of the development of spontaneously blinking rhodamines from 2014 to 2023, as well as the key mechanistic aspects of intramolecular spirocyclization reactions. We hope that by offering insightful design guidelines, this review will contribute to accelerating the advancement of super-resolution imaging technologies.

A long-wavelength mitochondria-targeted fluorescent probe for imaging of peroxynitrite during dexamethasone treatment

Peroxynitrite (ONOO^-), as a strong oxidizing reactive nitrogen substance (RNS), is generated endogenously by cells. Its visualization research is crucial to understand relevant disease processes. Herein, we reported a long-wavelength mitochondria-targeted fluorescence "turn on" probe TL. The probe TL could react with ONOO^- by using 4-(Bromomethyl)benzeneboronic as a reactive site, which exhibited outstanding characteristics for detection of ONOO^-, thus improving response time (about 50 s), sensitivity (DL, 10.1 nM), and emission wavelength (667 nm). Besides, TL displayed well mitochondria targeting and biological visualizing of exogenous and endogenous ONOO^- in biological systems. Finally, TL was used to monitor high concentration of dexamethasone-induced an up-regulation of ONOO^-. This indicated that TL has excellent potential to study the fluctuation of ONOO^- in the physiological and pathological system.

Recruiting Rate Determines the Blinking Propensity of Rhodamine Fluorophores for Super-Resolution Imaging

Live-cell single-molecule localization microscopy has advanced with the development of self-blinking rhodamines. A pK_cycling of <6 is recognized as the criterion for self-blinking, yet a few rhodamines matching the standard fail for super-resolution reconstruction. To resolve this controversy, we constructed two classic rhodamines (pK_cycling < 6) and four sulfonamide rhodamines with three exhibited exceptional larger pK_cycling characteristics (6.91-7.34). A kinetic study uncovered slow equilibrium rates, and limited switch numbers resulted in the reconstruction failure of some rhodamines. From the kinetic disparity, a recruiting rate was first abstracted to reveal the natural switching frequency of spirocycling equilibrium. The new parameter independent from applying a laser satisfactorily explained the imaging failure, efficacious for determining the propensity of self-blinking from a kinetic perspective. Following the prediction from this parameter, the sulfonamide rhodamines enabled live-cell super-resolution imaging of various organelles through Halo-tag technology. It is determined that the recruiting rate would be a practical indicator of self-blinking and imaging performance.

Subtle Structural Translation Magically Modulates the Super-Resolution Imaging of Self-Blinking Rhodamines

The evolution of super-resolution imaging techniques is benefited from the ongoing competition for optimal rhodamine fluorophores. Yet, it seems blind to construct the desired rhodamine molecule matching the imaging need without the knowledge on imaging impact of even the minimum structural translation. Herein, we have designed a pair of self-blinking sulforhodamines (STMR and SRhB) with the bare distinction of methyl or ethyl substituents and engineered them with Halo protein ligands. Although the two possess similar spectral properties (λ_ab, λ_fl, ϕ, etc.), they demonstrated unique single-molecule characteristics preferring to individual imaging applications. Experimentally, STMR with high emissive rates was qualified for imaging structures with rapid dynamics (endoplasmic reticulum, and mitochondria), and SRhB with prolonged on-times and photostability was suited for relatively "static" nuclei and microtubules. Using this new knowledge, the mitochondrial morphology during apoptosis and ferroptosis was first super-resolved by STMR. Our study highlights the significance of even the smallest structural modification to the modulation of super-resolution imaging performance and would provide insights for future fluorophore design.

Dual-Mode Multiple Ion Sensing via Analyte-Specific Modulation of Keto-Enol Tautomerization of an ESIPT Active Pyrene Derivative: Experimental Findings and Computational Rationalization

A pyrene-based e xcited - state intramolecular proton transfer (ESIPT) active probe PMHMP was synthesized, characterized, and employed for the ppb-level, dual-mode, and high-fidelity detection of Cu²⁺ (LOD: 7.8 ppb) and Zn²⁺ ions (LOD: 4.2 ppb) in acetonitrile medium. The colorless solution of PMHMP turned yellow upon the addition of Cu²⁺, suggesting its ratiometric, naked-eye sensing. On the contrary, Zn²⁺ ions displayed concentration-dependent fluorescence rise till a 0.5 mole fraction and subsequent quenching. Mechanistic investigations indicated the formation of a 1:2 exciplex (Zn²⁺:PMHMP) at a lower concentration of Zn²⁺, which eventually turned into a more stable 1:1 (Zn²⁺:PMHMP) complex with an additional amount of Zn²⁺ ions. However, in both cases, it was observed that the hydroxyl group and the nitrogen atom of the azomethine unit were involved in the metal ion coordination, which eventually altered the ESIPT emission. Furthermore, a green-fluorescent 2:1 PMHMP-Zn²⁺ complex was developed and additionally employed for the fluorimetric analysis of both Cu²⁺ and H₂PO₄ ^- ions. The Cu²⁺ ion, owing to its higher binding affinity for PMHMP, could replace the Zn²⁺ ion from the preformed complex. On the other hand, H₂PO₄ ^- formed a tertiary adduct with the Zn²⁺-complex, leading to a distinguishable optical signal. Furthermore, extensive and organized density functional theory calculations were performed to explore the ESIPT behavior of PMHMP and the geometrical and electronic properties of the metal complexes.

Dual-Mode Optical Sensor Array for Detecting and Identifying Perillaldehyde in Solution Phase and Plant Leaf with Smartphone

Promising techniques for detecting and quantifying active components in the plants and foods have received global concern in smart agriculture. Dual-mode optical assays are becoming more attractive and popular thanks to robust and reliable analysis parameters. We herein unveil a novel turn-on and dual-mode sensor array comprising three kinds of reactive indicators including ring-closed rhodamine-hydrazine, squaraine-hydrazine, and 2,4-dinitrophenylhydrazine for evaluating perillaldehyde. Significant colorimetric and fluorescent changes were triggered through reacting primary amine/hydrazine with the active aldehyde group in perillaldehyde, thus turning on the chromogenic responses of all the indicators. Optimal colorimetric sensing showed good responses to perillaldehyde ranged up to 100 mM in ethanol. Dramatic fluorescence enhancement was also exhibited, illustrating good selectivity as well as high sensitivity (detection limit ∼20.0 μM). Inspired by rapid chemical reactions and distinct optical changes, distinct sensor array strips loaded with the optimal solid-state reactive indicators were developed for evaluating the perillaldehyde content in the perilla frutescence leaves. Smartphone-enabled readout system and digital data processing were further performed for chemometric analysis. A good correlation was obtained and the semiquantitative evaluation of the perillaldehyde content could be achieved within 15 min, possessing the significant features of naked-eye recognition, easy operation, and disposability. To the best of our knowledge, present work demonstrated the use of chromogenic sensing strips to evaluate the active perillaldehyde content in solution and vapor phases for the first time. Taken together, these characteristics also indicate that the present turn-on sensor array has great potential applications in the precise detection and evaluation of perillaldehyde in the forthcoming smart agriculture.

Super-resolution analyzing spatial organization of lysosomes with an organic fluorescent probe

Lysosomes are multifunctional organelles involved in macromolecule degradation, nutrient sensing and autophagy. Live imaging has revealed lysosome subpopulations with dynamics and characteristic cellular localization. An as-yet unanswered question is whether lysosomes are spatially organized to coordinate and integrate their functions. Combined with super-resolution microscopy, we designed a small organic fluorescent probe, TPAE, that targeted lysosomes with a large Stokes shift. When we analyzed the spatial organization of lysosomes against mitochondria in different cell lines with this probe, we discovered different distance distribution patterns between lysosomes and mitochondria during increased autophagy flux. By using SLC25A46 mutation fibroblasts derived from patients containing highly fused mitochondria with low oxidative phosphorylation, we concluded that unhealthy mitochondria redistributed the subcellular localization of lysosomes, which implies a strong connection between mitochondria and lysosomes.

Lysosome-Targeted Biosensor for the Super-Resolution Imaging of Lysosome-Mitochondrion Interaction

Background: The interaction between lysosomes and mitochondria includes not only mitophagy but also mitochondrion–lysosome contact (MLC) that enables the two organelles to exchange materials and information. In our study, we synthesised a biosensor with fluorescence characteristics that can image lysosomes for structured illumination microscopy and, in turn, examined morphological changes in mitochondria and the phenomenon of MLC under pathological conditions.

Methods: After designing and synthesising the biosensor, dubbed CNN, we performed an assay with a Cell Counting Kit-8 to detect CNN’s toxicity in relation to H9C2 cardiomyocytes. We next analysed the co-localisation of CNN and the commercial lysosomal probe LTG in cells, qualitatively analysed the imaging characteristics of CNN in different cells (i.e. H9C2, HeLa and HepG2 cells) via structured illumination microscopy and observed how CNN entered cells at different temperatures and levels of endocytosis. Last, we treated the H9C2 cells with mannitol or glucose to observe the morphological changes of mitochondria and their positions relative to lysosomes.

Results: After we endocytosed CNN, a lysosome-targeted biosensor with a wide, stable pH response range, into cells in an energy-dependent manner. SIM also revealed that conditions in high glucose induced stress in lysosomes and changed the morphology of mitochondria from elongated strips to round spheres.

Conclusion: CNN is a new tool for tracking lysosomes in living cells, both physiologically and pathologically, and showcases new options for the design of similar biosensors.