Cationic red emitting fluorophore: A light up NIR fluorescent probe for G4-DNA

A two-in-one probe: imaging lipid droplets and endoplasmic reticulum in tandem

The endoplasmic reticulum (ER) and lipid droplets (LDs) intricately interact in cellular processes, with the ER serving as a hub for lipid synthesis and LDs acting as storage organelles for lipids. Developing fluorescent probes that can simultaneously visualise the ER and LDs provides a means for real-time and specific visualisation of these subcellular organelles and elucidating their interaction. Herein, we present synthetically simple and novel donor-π-acceptor styryl fluorophores (PFC, PFN and PFB) incorporating pentafluorophenyl (PFP) to demonstrate exquisite discriminative imaging of ER and LD with a single excitation wavelength. The PFP moiety aids the ER selectivity, while the overall hydrophobicity of the molecule aids in the LD targeting. Furthermore, the fluorophores are utilised in studying the changes in size, distribution, and biogenesis of LDs within ER regions after treatment with oleic acid. Strong emission, lower concentrations ∼100 nM requirement, minimal cytotoxicity, and photostability make these fluorophores excellent tools for probing sub-cellular dynamics.

A ratiometric nanoprobe for the in vivo bioimaging of hypochlorous acid to detect drug-damaged liver and kidneys

As the organs responsible for toxin transformation and excretion in the body, damage to the liver and kidneys induced by inevitable drug toxicity is the main cause of acute liver and kidney injury. P-Acetamidophenol overdose leads hypochlorous acid (HClO) to accumulate in the mitochondria of tissues, ultimately resulting in acute liver and kidney injury in humans, despite its clinical use as an antipyretic medicine. Herein, we report an HClO-activatable self-assembling ratiometric nanoprobe NRH-800-PEG for screening the upregulation of HClO by colocalization in mitochondria while monitoring the changes in the endogenous HClO levels in cells with ratiometric signals. Furthermore, NRH-800-PEG was constructed to evaluate injury by fluorescence ratio imaging in the tissues of inflammatory mice. Our strategy offers a novel tool for assessing disease progression during drug-induced liver and kidney injury.

Fluorescence turn-on probes for intracellular DNA/RNA distribution based on asymmetric bis(styryl) dyes

Two bis(styryl) dyes, varying in type of spacer between two mono(styryl) units, were tested for interactions with ct-DNA or cl-RNA. Both compounds showed strong affinity toward ds-DNA/ss-RNA, the binding mode of the interaction is shifting between DNA groove binding to RNA intercalation. Consequently, interaction with DNA shows a stronger flare-up of fluorescence (151 times for dye 1 and 118 times for dye 2) than when binding with RNA (23 times and 36 times correspondingly). The presence of energy transfer in the bis(styryl) system increases the Stokes shift of the dye, so when irradiating the system in the region of 370-380 nm, fluorescence is detected at 610-620 nm. The biological experiments showed that the efficient intracellular fluorescence quench was observed in the DNase digest test suggested that dyes can be applied by recognition of DNA in the presence of RNA molecules.

Amphiphilicity-Controlled Localization of Red Emitting Bicationic Fluorophores in Tumor Cells Acting as Bio-Probes and Anticancer Drugs

Small organic molecules arouse lively interest for their plethora of possible biological applications, such as anticancer therapy, for their ability to interact with nucleic acids, or bioimaging, thanks to their fluorescence emission. Here, a panchromatic series of styryl-azinium bicationic dyes, which have already proved to exhibit high water-solubility and significant red fluorescence in water, were investigated through spectrofluorimetric titrations to assess the extent of their association constants with DNA and RNA. Femtosecond-resolved transient absorption spectroscopy was also employed to characterize the changes in the photophysical properties of these fluorophores upon interaction with their biological targets. Finally, in vitro experiments conducted on tumor cell lines revealed that some of the bicationic fluorophores had a peculiar localization within cell nuclei exerting important antiproliferative effects, others were instead found to localize in the cytoplasm without leading to cell death, being useful to mark specific organelles in light of live cell bioimaging. Interestingly, this molecule-dependent behavior matched the different amphiphilicity featured by these bioactive compounds, which are thus expected to be caught in a tug-of-war between lipophilicity, ensured by the presence of aromatic rings and needed to pass cell membranes, and hydrophilicity, granted by charged groups and necessary for stability in aqueous media.

Stabilization and fluorescence light-up of G-quadruplex nucleic acids using indolyl-quinolinium based probes

G-Quadruplexes (G4s) are four-stranded motifs formed by G-rich nucleic acid sequences. These structures harbor significant biological importance as they are involved in telomere maintenance, transcription, and translation. Owing to their dynamic and polymorphic nature, G4 structures relevant for therapeutic applications need to be stabilized by small-molecule ligands. Some of these ligands turn on fluorescence upon binding to G4 structures, which provides a powerful detection platform for G4 structures. Herein, we report the synthesis of fluorescent ligands based on the indolyl-quinolinium moiety to specifically stabilize G4 structures and sense DNA. CD titration and melting experiments have shown that the lead ligand induces the formation of parallel G4 with preferential stabilization of the c-MYC and c-KIT1 promoter G4s over the telomeric, h-RAS1 G4, and duplex DNA. Fluorimetric titration data revealed fluorescence enhancement when these ligands interact with G4 DNA structures. The fluorescence lifetime experiment of the ligand with different DNAs revealed three excited state lifetimes (ns), which indicates more than one binding site. MD studies showed that the ligand exhibits 3 : 1 stoichiometry of binding with c-MYC G4 DNA and revealed the unique structural features, which impart selectivity toward parallel topology. The ligand was found to have low cytotoxicity and exhibited preferential staining of DNA over RNA. Collectively, the results presented here offer avenues to harness indolyl-quinolinium scaffolds for sensing and selective stabilization of G4 structures.

Selective, pH-Dependent Colorimetric and Fluorimetric Detection of Quadruplex DNA with 4-Dimethylamino(phenyl)-Substituted Berberine Derivatives

The 9- and 12-dimethylaminophenyl-substituted berberine derivatives 3 a and 3 b were readily synthesized by Suzuki-Miyaura reactions and shown to be useful fluorescent probes for the optical detection of quadruplex DNA (G4-DNA). Their association with the nucleic acids was investigated by spectrometric titrations, CD and LD spectroscopy, and with DNA-melting analysis. Both ligands bind to duplex DNA by intercalation and to G4-DNA by terminal π stacking. At neutral conditions, they bind with higher affinity (Kb =105 -106  M-1 ) to representative quadruplex forming oligonucleotides 22AG, c-myc, c-kit, and a2, than to duplex calf thymus (ct) DNA (Kb =5-7×104  M-1 ). At pH 5, however, the affinity of 3 a towards G4-DNA 22AG is higher (Kb =1.2×106  M-1 ), whereas the binding constant towards ct DNA is lower (Kb =3.9×103  M-1 ) than under neutral conditions. Notably, the association of the ligand with DNA results in characteristic changes of the absorption and emission properties under specific conditions, which may be used for optical DNA detection. Other than the parent berberine, the ligands do not show a noticeable increase of their very low intrinsic emission intensity upon association with DNA at neutral conditions. In contrast, a fluorescence light-up effect was observed upon association to duplex (Φfl =0.01) and quadruplex DNA (Φfl =0.04) at pH 5. This fluorimetric response to G4-DNA association in combination with the distinct, red-shifted absorption under these conditions provides a simple and conclusive optical detection of G4-DNA at lower pH.

Berberrubine Phosphate: A Selective Fluorescent Probe for Quadruplex DNA

A phosphate-substituted, zwitterionic berberine derivative was synthesized and its binding properties with duplex DNA and G4-DNA were studied using photometric, fluorimetric and polarimetric titrations and thermal DNA denaturation experiments. The ligand binds with high affinity toward both DNA forms (Kb = 2-7 × 105 M-1) and induces a slight stabilization of G4-DNA toward thermally induced unfolding, mostly pronounced for the telomeric quadruplex 22AG. The ligand likely binds by aggregation and intercalation with ct DNA and by terminal stacking with G4-DNA. Thus, this compound represents one of the rare examples of phosphate-substituted DNA binders. In an aqueous solution, the title compound has a very weak fluorescence intensity (Φfl < 0.01) that increases significantly upon binding to G4-DNA (Φfl = 0.01). In contrast, the association with duplex DNA was not accompanied by such a strong fluorescence light-up effect (Φfl < 0.01). These different fluorimetric responses upon binding to particular DNA forms are proposed to be caused by the different binding modes and may be used for the selective fluorimetric detection of G4-DNA.

Imaging mitochondria and plasma membrane in live cells using solvatochromic styrylpyridines

Investigating the dynamics of different biomolecules in the cellular milieu through microscopic imaging has gained paramount importance in the last decade. Continuous developments in the field of microscopy are paralleled by the design and synthesis of fluorophores that target specific compartments within a cell. In this study, we have synthesized four fluorescent styrene derivatives, a neutral styrylpridine, three cationic styrylpyridinium probes with and without cholesterol tether, and investigated their absorption, emission, and cellular imaging properties. The fluorophores show solvatochromic emission attributed to intramolecular charge transfer from donor to acceptor with an emission range of 500-600 nm. The fluorescent cholesterol conjugate labels plasma membrane effectively while the fluorophores devoid of the cholesterol tether label mitochondria. Cholesterol conjugate also shows strong interaction with liposome membrane. Furthermore, the fluorophores alsotrack the mitochondria in live cells with high specificity. Cell viability assay showed overall non-toxic nature of the probes even at higher fluorophore concentrations. Through sidearm modifications, keeping the fluorescent core intact, we successfully targeted specific subcellular compartments of neuronal (N2a) and non-neuronal (HeLa) mammalian cell lines. This strategy of using a single molecular scaffold with subtle substitutions could be ideal in generating a variety of fluorophores targeting other subcellular compartments.

Identification of optimal fluorescent probes for G-quadruplex nucleic acids through systematic exploration of mono- and distyryl dye libraries

A library of 52 distyryl and 9 mono-styryl cationic dyes was synthesized and investigated with respect to their optical properties, propensity to aggregation in aqueous medium, and capacity to serve as fluorescence “light-up” probes for G-quadruplex (G4) DNA and RNA structures. Among the 61 compounds, 57 dyes showed preferential enhancement of fluorescence intensity in the presence of one or another G4-DNA or RNA structure, while no dye displayed preferential response to double-stranded DNA or single-stranded RNA analytes employed at equivalent nucleotide concentration. Thus, preferential fluorimetric response towards G4 structures appears to be a common feature of mono- and distyryl dyes, including long-known mono-styryl dyes used as mitochondrial probes or protein stains. However, the magnitude of the G4-induced “light-up” effect varies drastically, as a function of both the molecular structure of the dyes and the nature or topology of G4 analytes. Although our results do not allow to formulate comprehensive structure–properties relationships, we identified several structural motifs, such as indole- or pyrrole-substituted distyryl dyes, as well as simple mono-stryryl dyes such as DASPMI [2-(4-(dimethylamino)styryl)-1-methylpyridinium iodide] or its 4-isomer, as optimal fluorescent light-up probes characterized by high fluorimetric response (I/I₀ of up to 550-fold), excellent selectivity with respect to double-stranded DNA or single-stranded RNA controls, high quantum yield in the presence of G4 analytes (up to 0.32), large Stokes shift (up to 150 nm) and, in certain cases, structural selectivity with respect to one or another G4 folding topology. These dyes can be considered as promising G4-responsive sensors for in vitro or imaging applications. As a possible application, we implemented a simple two-dye fluorimetric assay allowing rapid topological classification of G4-DNA structures.