Aptamer-Loop DNA Nanoflower Recognition and Multicolor Fluorescent Carbon Quantum Dots Labeling System for Multitarget Living Cell Imaging.

Visualization of multiple targets in living cells is important for understanding complex biological processes, but it still faces difficulties, such as complex operation, difficulty in multiplexing, and expensive equipment. Here, we developed a nanoplatform integrating a nucleic acid aptamer and DNA nanotechnology for living cell imaging. Aptamer-based recognition probes (RPs) were synthesized through rolling circle amplification, which were further self-assembled into DNA nanoflowers encapsulated by an aptamer loop. The signal probes (SPs) were obtained by conjugation of multicolor emission carbon quantum dots with oligonucleotides complementary to RPs. Through base pairing, RPs and SPs were hybridized to generate aptamer sgc8-, AS1411-, and Apt-based imaging systems. They were used for individual/simultaneous imaging of cellular membrane protein PTK7, nucleolin, and adenosine triphosphate (ATP) molecules. Fluorescence imaging and intensity analysis showed that the living cell imaging system can not only specifically recognize and efficiently bind their respective targets but also provide a 5-10-fold signal amplification. Cell-cycle-dependent distribution of nucleolin and concentration-dependent fluorescence intensity of ATP demonstrated the utility of the system for tracking changes in cellular status. Overall, this system shows the potential to be a simple, low-cost, highly selective, and sensitive living cell imaging platform.

Bodipy-Based highly sensitive hydrogen sulfide fluorescent probe and its fluorescence imaging in cells and zebrafish.

Hydrogen sulfide (H2S) is a crucial endogenous gasotransmitter that plays a role in various physiological and pathological processes. Therefore, accurate and rapid monitoring of H2S in organisms is highly significant for understanding the underlying pathological mechanisms and facilitating early diagnosis of related diseases. In this study, we developed a novel fluorescent probe, B-CHO-NO2, based on a bodipy fluorophore, which exhibits excellent sensitivity and selectivity towards H2S. The design of the probe exploits the nucleophilicity of H2S by introducing a formyl group as the ortho-participating moiety, significantly enhancing the reaction rate with H2S. In cellular and zebrafish models, the probe B-CHO-NO2 successfully achieved fluorescence imaging of endogenous and exogenous H2S. The development of probe B-CHO-NO2 provides a powerful tool for biological studies of H2S and diagnosis of related diseases.

Construction of a Spatial-Confined Self-Stacking Catalytic Circuit for Rapid and Sensitive Imaging of Piwi-Interacting RNA in Living Cells.

Piwi-interacting RNAs (piRNAs) are small noncoding RNAs that repress transposable elements to maintain genome integrity. The canonical catalytic hairpin assembly (CHA) circuit relies on random collisions of free-diffused reactant probes, which substantially slow down reaction efficiency and kinetics. Herein, we demonstrate the construction of a spatial-confined self-stacking catalytic circuit for rapid and sensitive imaging of piRNA in living cells based on intramolecular and intermolecular hybridization-accelerated CHA. We rationally design a 3WJ probe that not only accelerates the reaction kinetics by increasing the local concentration of reactant probes but also eliminates background signal leakage caused by cross-entanglement of preassembled probes. This strategy achieves high sensitivity and good specificity with shortened assay time. It can quantify intracellular piRNA expression at a single-cell level, discriminate piRNA expression in tissues of breast cancer patients and healthy persons, and in situ image piRNA in living cells, offering a new approach for early diagnosis and postoperative monitoring.

Fluorescent DNA tetrahedral probe with catalytic hairpin self-assembly reaction for imaging of miR-21 and miR-155 in living cells.

A CHA-based fluorescent DNA tetrahedral probe (FDTp) has been designed to detect the microRNAs miR-21 and miR-155 sensitively and specifically in living cells. The design consisted of functional elements (H1, H2, and Protector) connected to a DNA tetrahedron modified with two pairs of fluorophores and quenching groups. In the presence of miR-21, the chain displacement effect was triggered and Cy3 fluorescence was emitted. In the presence of miR-155, the signal of the catalytic hairpin assembly (CHA) between H1 and H2 on FDTp was amplified, making the fluorescence of FAM sensitive to miR-155. Using this method, the detection limit for miR-155 was 5 pM. The FDTp successfully imaged miR-21 and miR-155 in living cells and distinguished a variety of cell lines based on their expression levels of miR-21 and miR-155. The detection and imaging of dual targets in this design ensured the accuracy of tumor diagnosis and provided a new method for early tumor diagnosis.

Modular synthesis of pentacyclic-fused pyranoquinoliziniums as organelle-selective fluorescent probes.

On basis of their unique chemical and photophysical properties, and excellent biological activities, quinoliziniums have been widely used in various research fields. Herein, modular synthetic strategies for efficient synthesis of novel fluorescent quinoliziniums by using one-pot and stepwise rhodium(III)-catalyzed C-H annulations were developed. In the one-pot synthesis, the reaction between 2-aryl-4-quinolones (1) and 1,2-diarylalkynes (2) proceeded in a chemo- and regioselective manner to give quinolinone-fused isoquinolines (3) and pentacyclic-fused pyranoquinoliziniums (4). The structural diversity of pentacyclic-fused pyranoquinoliziniums (4) was expanded by the stepwise synthesis from 3 and 2, allowing the strategic incorporation of electron-donating (OMe and OH) and electron-withdrawing (Cl) substituents on the top and bottom parts of the pyranoquinoliziniums (4). These newly synthesized pyranoquinoliziniums (4) exhibited tunable absorptions (455-532 nm), emissions (520-610 nm), fluorescence lifetime (0.3-5.6 ns), large Stokes shifts (up to 120 nm), and excellent fluorescence quantum yields (up to 0.73) upon adjusting the different substituents. The the unique arrangement of N and O atoms and extended π-conjugation of 4 could cause the relocation of HOMO comparing with our previous quinoliziniums. Importantly, pyranoquinoliziniums (4a-4g and 4i) targeted the mitochondria, while 4h was localized in lysosome. Due to the remarkable photophysical properties and the potential for organelle targeting of the novel class of quinoliziniums, they could be further applied for biological, chemical and material applications.

Triphenylphosphine-bonded coumaranone dyes realize dual color imaging of mitochondria and nucleoli.

Probing intracellular organelles with fluorescent dyes offers opportunities to understand the structures and functions of these cellular compartments, which is attracting increasing interests. Normally, the design principle varies for different organelle targets as they possess distinct structural and functional profiles against each other. Therefore, developing a probe with dual intracellular targets is of great challenge. In this work, a new sort of donor-π-bridge-acceptor (D-π-A) type coumaranone dyes (CMO-1/2/3/4) have been prepared. Four fluorescent probes (TPP@CMO-1/2/3/4) were then synthesized by linking these coumaranone dyes with an amphiphilic cation triphenylphosphonium (TPP). Interestingly, both TPP@CMO-1 and TPP@CMO-2 exhibited dual color emission upon targeting to two different organelles, respectively. The green emission is well localized in mitochondria, while, the red emission realizes nucleoli imaging. RNA is the target of TPP@CMOs, which was confirmed by spectroscopic analysis and computational calculation. More importantly, the number and morphology changes of nucleoli under drug stress have been successfully evaluated using TPP@CMO-1.

A lysosome-targeted fluorescent probe for fluorescence imaging of hypochlorous acid in living cells and in vivo.

Lysosomes, as crucial acidic organelles in cells, play a significant role in cellular functions. The levels and distribution of hypochlorous acid (HOCl) within lysosomes can profoundly impact their biological functionality. Hence, real-time monitoring of the concentration of HOCl in lysosomes holds paramount importance for further understanding various physiological and pathological processes associated with lysosomes. In this study, we developed a bodipy-based fluorescent probe derived from pyridine and phenyl selenide for the specific detection of HOCl in aqueous solutions. Leveraging the probe's sensitive photoinduced electron transfer effect from phenyl selenide to the fluorophore, the probe exhibited satisfactory high sensitivity (with a limit of detection of 5.2 nM and a response time of 15 s) to hypochlorous acid. Further biological experiments confirmed that the introduction of the pyridine moiety enabled the probe molecule to selectively target lysosomes. Moreover, the probe successfully facilitated real-time monitoring of HOCl in cell models stimulated by N-acetylcysteine (NAC) and lipopolysaccharide (LPS), as well as in a normal zebrafish model. This provides a universal method for dynamically sensing HOCl in lysosomes.

A Highly Selective Fluorescent Probe for Hydrogen Sulfide and its Application in Living Cell.

A new Near-infrared fluorescent probe for hydrogen sulfide detection was synthesized by employing dicyanoisophorone based fluorescence dye as a fluorophore and methyl 3-(2-(carbonyl)phenyl)-2-cyanoacrylate group as the response unit. The Probe DCI-H2S showed a long emission wavelength (λem = 674 nm). Based on the H2S-induced addition-cyclization of deprotecting methyl 3-(2-(carbonyl)phenyl)-2-cyanoacrylate group, the probe DCI-H2S showed high selectivity, sensitivity and response speed toward hydrogen sulfide under room temperature. These numerous advantages of the probe DCI-H2S make it to potentially detect endogenous hydrogen sulfide in living organisms.

Enhanced DNA Entropy-Driven Circuit by Locked Nucleic Acids and Simulation-Guided Localization.

Signal amplification methods based on DNA molecular interactions are promising tools for detecting various biomarkers in low abundance. The entropy-driven circuit (EDC), as an enzyme-free signal amplification method, has been used in detecting and imaging a variety of biomarkers. The localization strategy can effectively increase the local concentration of the DNA reaction modules to improve the signal amplification effect. However, the localization strategy may also amplify the leak reaction of the EDC, and effective signal amplification can be limited by the unclear structure-function relationship. Herein, we utilized locked nucleic acid (LNA) modification to enhance the stability of the localized entropy-driven circuit (LEDC), which suppressed a 94.6% leak signal. The coarse-grained model molecular simulation was used to guide the structure design of the LEDC, and the influence of critical factors such as the localized distance and spacer length was analyzed at the molecular level to obtain the best reaction performance. The sensitivities of miR-21 and miR-141 detected by a simulation-guided optimal LEDC probe were 17.45 and 65 pM, 1345 and 521 times higher than free-EDC, respectively. The LEDC was further employed for the fluorescence imaging of miRNA in cancer cells, showing excellent specificity and sensitivity. This work utilizes LNA and molecular simulations to comprehensively improve the performance of a localized DNA signal amplification circuit, providing an advanced DNA probe design strategy for biosensing and imaging as well as valuable information for the designers of DNA-based probes.

Virus tracking technologies and their applications in viral life cycle: research advances and future perspectives.

Viruses are simple yet highly pathogenic microorganisms that parasitize within cells and pose serious threats to the health, economic development, and social stability of both humans and animals. Therefore, it is crucial to understand the dynamic mechanism of virus infection in hosts. One effective way to achieve this is through virus tracking technology, which utilizes fluorescence imaging to track the life processes of virus particles in living cells in real-time, providing a comprehensively and detailed spatiotemporal dynamic process and mechanism of virus infection. This paper provides a broad overview of virus tracking technology, including the selection of fluorescent labels and virus labeling components, the development of imaging microscopes, and its applications in various virus studies. Additionally, we discuss the possibilities and challenges of its future development, offering theoretical guidance and technical support for effective prevention and control of the viral disease outbreaks and epidemics.

Modulation of aluminum sensing properties of a sulphone group containing chemosensor and its biological applications.

A chemosensor with two binding pockets facilitates binding of one metal ion in either of the pockets providing a better chance for the interaction and hence recognition of the cation. We report here a chemosensor, namely 2,2'-(1E)-(5,5'-sulfonylbis(2-hydroxy-5,1-phenylene))bis(azan-1-yl-1-ylidene)bis(methan-1-yl-1-ylidene)dinaphthalen-1-ol (H4L-naph), for selective sensing of Al3+ in DMF- HEPES buffer (1:4, v/v, pH 7.4). It shows almost 100-fold fluorescence enhancement at 532 nm (λex = 482 nm) in the presence of Al3+. Its quantum yield and excited state lifetime enhances significantly with the cations. H4L-naph forms a 1:2 complex with Al3+ with an association constant value of 2.18 × 104 M-2. Fluorescence enhancement may be attributed to CHEFF mechanism and restriction of >CN isomerization. Effect of the presence of naphthyl rings instead phenyl ring of a previously reported probe has resulted shifting of excitation/emission peak towards longer wavelength. The probe has been applied to image Al3+ in L6 cells with no significant cytotoxicity.

A benzo BODIPY based fluorescent probe for selective visualization of hypochlorous acid in living cells and zebrafish.

Hypochlorous acid (HOCl) is an essential endogenous reactive oxygen species in biological systems, playing a critical role in various physiological processes. Real-time monitoring of HOCl concentration in living organisms is essential for understanding its biological functions and pathological roles. In this study, we developed a novel fluorescent probe based on benzobodipy, BBDP, for rapid and sensitive detection of HOCl in aqueous solutions. The probe exhibited a significant fluorescence turn-on response to HOCl based on its specific oxidation reaction towards diphenylphosphine, with high selectivity, instantaneous response (less than 10 s), and low detection limit (21.6 nM). Furthermore, bioimaging results illustrated that the probe could be applied for real-time fluorescence imaging of HOCl in live cells and zebrafish. The development of BBDP may provide a new tool for exploring the biological functions of HOCl and its pathological roles in diseases.

The synthesis of gold nanoclusters with high stability and their application in fluorometric detection for Hg2+ and cell imaging.

Sensing Hg2+ is significant to protecting human health and environmental ecosystems, for its toxicity and genotoxicity. Here, highly stable fluorescent folic acid (FA)-protected Au nanoclusters (FA-AuNCs) were synthesized by optimizing the reactive parameters with high quantum yield of 34.7%. Main components of Au4L were confirmed by MALDI-TOF, and the electron-rich residues of FA shell enabled FA-AuNCs excellent photostability. FA-AuNCs exhibited sensitive response behavior to Hg2+ with a minimum detectability of 1.3 nM, and presented extreme effect to the detection of Hg2+ in real water. Notably, the cellular imaging and in-situ detection of Hg2+ in cells can be achieved visually. The high selectivity was attributed to the chemical bond formed between Au+ (4f145d10) and Hg2+ (4f145d10). And the internal filter effect and static quenching effect were proved triggering the quenching of FA-AuNCs. The ultra-stable FA-AuNCs provide a potential promising opportunity for the in-situ tracing Hg2+ from environmental and biological samples.

Near-Infrared Fluorescent Probe for Imaging Upregulated Hydrogen Sulfide Levels in Rice under Salt and Drought Stress.

Hydrogen sulfide (H2S) is a hazardous gas found in living organisms and is directly tied to our daily lives. Recent studies show that it plays a significant role in plant growth, development, and response to environmental stresses. However, few of the reported near-infrared (NIR) fluorescent probes have been applied to rice and deeply investigated the influence of the external environment on the biological molecules in its internal environment. Therefore, our team created BSZ-H2S, which has the advantage of an emission wavelength of up to 720 nm with fast response, successfully applying it to cell and zebrafish imaging. More importantly, the probe detected H2S in rice roots by in situ imaging in a facile manner and verified the existence of an upregulation process of H2S in response to salt and drought stress. This work provides a concept for the intervention of external stresses in rice culture.

A new benzo-bodipy based fluorescent probe for the highly sensitive detection of hypochlorous acid and its application in the living cells and zebrafish imaging.

Due to the highly significant biological activity of hypochlorous acid, the monitoring of its concentration in vivo has received extensive attention. In this work, a photoinduced electron transfer (PeT) based benzo-bodipy fluorescent probe BBy-T has been developed for the rapid, sensitive, and selective detection of HClO in an aqueous solution. Based on the HClO-specific oxidation reaction, BBy-T exhibited a distinct fluorescence turn-on response to HClO with a remarkable Stokes shift (84 nm), immediate response (less than 20 s), and low detection limit (13.7 nM). In addition, the bioimaging results indicated that the probe BBy-T could be applied to real-time fluorescence imaging of living HeLa cells as well as living zebrafish.

Synthesis of fluorescent chalcones, photophysical properties, quantitative structure-activity relationship and their biological application.

The development of fluorescent pigments is an area of interest in several research fields due to their high sensitivity. In the current study-eight known and three new N,N-dimethylamino-chalcones (12a-k) were synthesized with good yields using the Claisen-Schmidt reaction. For each molecular system, the photophysical properties, including the maximum absorption wavelength (λAbsorption), molar absorption coefficient (ε), maximum excitation wavelength (λExcitation), maximum emission wavelength (λEmission), Stokes Shift (Δλ), fluorescence quantum yield (Φfl), fluorescence lifetime (τfl), radiative and non-radiative rate constants (kR and kNR, respectively) were evaluated. Variations in each of these properties were analyzed depending on the substituents present on each compound. To relate the chemical structures of the synthesized compounds to their photophysical properties, Hansch analysis (2D-QSPR) was applied. As a result of Hansch analysis, we found different photophysical properties related to molecular orbitals and the energy of their derivatives (Highest Occupied Molecular Orbital-HOMO, Lowest Unoccupied Molecular Orbital-LUMO, Difference between LUMO-HOMO-ΔLH, Chemical potential-µ, Hardness-η, Softness-S, and electrophilic global index-ω) as well as to the atomic charges on atoms C5, Cα, Cß, and CO. The application of this type of analysis has made it possible to understand and subsequently design new molecules with defined photophysical properties. Finally, the compounds were use as fluorescent pigment to get living cell imaging on breast cancer cells, obtaining the compound 12a as promissory alternative.

A tetraphenylethene-based Schiff base AIEgen with a large Stokes shift as probe for highly sensitive and selective detection of aqueous Cu2+ ions and its application in cell imaging.

In this work, an AIE-active tetraphenylethene-based Schiff base fluorescent probe 3 with a large Stokes shift (247 nm) was designed and synthesized. It was found that the aggregated probe 3 exhibited very high selectivity and anti-interference ability for Cu2+ in PBS buffer (70% fw) through a fluorescence "turn-off" strategy. Job's plot and NMR analysis indicated the two phenolic hydroxyl groups of the benzene ring and the N atom (-CH=N-) on probe 3 interacted with Cu2+ ions in a 1:1 stoichiometric ratio. A comprehensive analysis of the Stern-Volmer and binding constant indicated a rather strong interaction between probe 3 and Cu2+ ions. Probe 3 illustrated excellent sensitivity toward Cu2+ under ppb level (4.5 nM) and achieved more than 95% recovery in river, lake and tap water toward estimation of Cu2+ ions in the analytical applications. Moreover, probe 3 was able to realize bioimaging of HepG2 cells and be quenched by intracellular Cu2+ ions, making it promising as a sensitive Cu2+ sensor for organisms.

Multiplexed Organelles Portrait Barcodes for Subcellular MicroRNA Array Detection in Living Cells.

Multiplexed profiling of microRNAs' subcellular expression and distribution is essential to understand their spatiotemporal function information, but it remains a crucial challenge. Herein, we report an encoding approach that leverages combinational fluorescent dye barcodes, organelle targeting elements, and an independent quantification signal, termed Multiplexed Organelles Portrait Barcodes (MOPB), for high-throughput profiling of miRNAs from organelles. The MOPB barcodes consist of heterochromatic fluorescent dye-loaded shell-core mesoporous silica nanoparticles modified with organelle targeting peptides and molecular beacon detection probes. Using mitochondria and endoplasmic reticulum as models, we encoded four Cy3/AMCA ER-MOPB and four Cy5/AMCA Mito-MOPB by varying the Cy3 and Cy5 intensity for distinguishing eight organelles' miRNAs. Significantly, the MOPB strategy successfully and accurately profiled eight subcellular organelle miRNAs' alterations in the drug-induced Ca2+ homeostasis breakdown. The approach should allow more widespread application of subcellular miRNAs and multiplexed subcellular protein biomarkers' monitoring for drug discovery, cellular metabolism, signaling transduction, and gene expression regulation readout.

Novel red light-emitting two-photon absorption compounds with large Stokes shifts for living cell imaging.

Three novel donor-π-acceptor two-photon absorption compounds (1PZPy, 2PZIm, 3CZPy) bearing the 10-butyl-10H-phenothiazine (9-butyl-9H-carbazole) donor, the pyridinium (benzimidazolium) acceptor, and the 2,5-divinylthiophene π-bridge were synthesized and fully characterized by 1H NMR, 13C NMR, FT-IR, and HRMS. The linear and nonlinear photophysical properties were systematically investigated. Their absorption properties show a strong solvent dependence, while the emission properties are nearly independent of solvent polarity. All of them possess large Stokes shifts (Δλ=149-190 nm in H2O). 1PZPy and 3CZPy exhibit red fluorescence emission centered at about 635 and 660 nm, respectively. The two-photon absorption cross-sections measured by the open aperture Z-scan technique are determined to be 486 (1PZPy), 601 (2PZIm), and 753 GM (3CZPy) in DMF. The density functional theory calculations were further carried out to reveal their electronic structures. All the target compounds are verified to have low cytotoxicity in the working solution and good capability for one- and two-photon excitation fluorescence imaging, suggesting their potential application in bioimaging. Moreover, they show the organelle targeting ability in living cells with the high Pearson's coefficients above 0.94 for the endoplasmic reticulum.

pH-activated DNA nanomachine for miRNA-21 imaging to accurately identify cancer cell.

MicroRNA (miRNA) imaging has been employed to distinguish cancer cells from normal cells by exploiting the overexpression of miRNA in cancer. Inspired by the acidic extracellular tumor microenvironment, we designed a pH-activated DNA nanomachine to enable the specific detection of cancer cells using miRNA imaging. The DNA nanomachine was engineered by assembling two hairpins (Y1 and Y2) onto the surface of a ZIF-8 metal-organic framework (MOF), which decomposed under acidic conditions to release the adsorbed DNA hairpin molecules in situ. The released hairpins were captured by the target miRNA-21 and underwent catalytic hairpin assembly amplification between Y1 and Y2. The detection limit for miRNA assays using the DNA nanomachine was determined to be 27 pM, which is low enough for sensitive detection in living cells. Living cell imaging of miRNA-21 further corroborated the application of the DNA nanomachine in the identification of cancer cell.