Ratiometric Fluorescence Imaging for the Distribution of Nucleic Acid Content in Living Cells and Human Tissue Sections

Novel förster resonance energy transfer (FRET)-based ratiometric fluorescent probe for detection of cyanides by nucleophilic substitution of aromatic hydrogen (SNArH)

The development of novel fluorescent probes for real-time detection of cyanides (CN-) in environmental and biological systems has become a significant focus in chemical sensing. Particularly, ratiometric fluorescence sensing offers a unique method for precise and quantitative detection of cyanides, even under complex conditions. We report herein the design of a new ratiometric fluorescent probe for cyanides based on modulation of Förster resonance energy transfer (FRET) coupled with novel cyanide-induced nucleophilic substitution of aromatic hydrogen (SNArH). The target probe (R1) is developed by introducing coumarin fluorophores as FRET donors into a 3-nitro-naphthalimide acceptor, which is easily synthesized and exhibits a colorimetric change from colorless to faint yellow and a significant ratiometric fluorescence shift (Δλ = 114 nm) upon cyanide binding. A clear ratiometric signal at I582/I468 was obtained, with a limit of detection of 5.69 μM. The sensing mechanism was confirmed through 1H NMR titration and LC-MS analysis. Additionally, R1-loaded strips were easily prepared, serving as a portable device for detecting CN- with visible color changes. The probe R1 has been successfully utilized for real-time monitoring of cyanide in food materials and water samples. Importantly, fluorescence bioimaging studies in HeLa cells were conducted, demonstrating the probe's capability for ratiometric detection of exogenous CN- in living systems.

Targeted Conversion from Mitochondria to the Nucleus of Hydroxystyrylpyridinium by Introducing Only an Additional o-Hydroxyl Group

Aromatic cationic groups serve as crucial building blocks for the design of fluorescent probes targeting both the nucleus and mitochondria. Therefore, it is a significant challenge to develop aromatic cation-based probes that accurately image the nucleus without interference from mitochondria. However, this also presents an opportunity for rational design by modifying probes originally targeting mitochondria to redirect their targeting toward the nucleus. This study showcases the rapid development of a novel nucleus-targeting probe (DHSP) through a targeted conversion strategy based on structure modification of hydroxystyrylpyridinium (HSP), a well-established two-photon fluorescent probe that targets mitochondria. Importantly, DHSP, which is derived exclusively from introducing only an additional o-hydroxyl group into HSP, exhibits robust DNA-binding capability comparable to a commercially available nuclear dye 4',6-diamidino-2-phenylindole (DAPI). As a result, it rapidly enters the nucleus within 5 min and finds successful application in two-photon cellular and intravital imaging of the nucleus.

Cellular and Intravital Nucleus Imaging by a D-π-A Type of Red-Emitting Two-Photon Fluorescent Probe

The advancement in fluorescent probe technology for visualizing nuclear morphology and nucleic acid distribution in live cells and in vivo has attracted considerable interest within the biomedical research community, as it offers invaluable insights into cellular dynamics across various physiological and pathological contexts. In this study, we present a novel two-photon nucleus-imaging fluorescent probe called Nu-red, which is a typical donor(D)-π-acceptor(A) rotor composed of the donor (dihydroquinoline) and acceptor (pyridiniumylpentadienitrile) parts linked by a single bond. This probe offers several advantages, including long-wavelength excitation and emission (λex/λem = 610/664 nm), favorable quantum yields (1.35-22.15%), excellent two-photon absorption cross-section (425.92 GM), high selectivity and sensitivity, high DNA-binding affinity (Ka = 3.7 × 107 M-1, comparable to that of the commercial nucleus stain Hoechst 33342), rapid entry into the nucleus (1 min), low cytotoxicity, membrane-permeability, good water solubility, applicability to various cell lines, and compatibility with other commercial probes. Leveraging these aforementioned advantages, Nu-red was successfully employed to visualize cell division in living cells, distinguish abnormal division cells from normal ones, and track morphological changes in the nucleus during cell apoptosis. More notably, Nu-red was utilized to visualize nuclear shrinkage and pyknosis in the brain of a living mouse model of ischemic stroke.

Functionalized DNA Origami-Enabled Detection of Biomarkers

Biomarkers are crucial physiological and pathological indicators in the host. Over the years, numerous detection methods have been developed for biomarkers, given their significant potential in various biological and biomedical applications. Among these, the detection system based on functionalized DNA origami has emerged as a promising approach due to its precise control over sensing modules, enabling sensitive, specific, and programmable biomarker detection. We summarize the advancements in biomarker detection using functionalized DNA origami, focusing on strategies for DNA origami functionalization, mechanisms of biomarker recognition, and applications in disease diagnosis and monitoring. These applications are organized into sections based on the type of biomarkers - nucleic acids, proteins, small molecules, and ions - and concludes with a discussion on the advantages and challenges associated with using functionalized DNA origami systems for biomarker detection.

Microscopic Imaging to Visualize the Distribution of Dietary Nucleic Acids in Food Products of Various Origins

Dietary nucleic acids (dietNAs) are being increasingly recognized as important food components with nutritional value. However, the precise dietary recommendations for dietNAs are limited, because established methods for determining the quantity and nutritional role of dietNAs are still lacking. One of the tools to narrow this gap could be microscopic imaging, as a convenient approach to visualize the abundance and distribution of dietNAs in food products. With the aid of appropriate bioinformatic elaboration, such images may in future enable the direct semiquantitative estimation of these macromolecules in food products. In the presented study, two methods of preparing microscopic sections and staining them with DNA-specific fluorochromes were used for microscopic imaging of dietNAs in food products of plant and animal origin. Procedures for preparing formalin-fixed paraffin-embedded sections and cryosections were compared in terms of their usefulness for routine food analysis. Both methods turned out equally suitable for visualizing dietNA distribution in animal and plant products. However, the use of cryosections allowed a significantly shorter analysis time and reduced the consumption of organic solvents. Both of these advantages make the cryosection method preferable while establishing a dedicated methodology for routine assessment of dietNAs in the food industry.

Recent Development of Lysosome-Targeted Organic Fluorescent Probes for Reactive Oxygen Species

Reactive oxygen species (ROS) are extremely important for various biological functions. Lysosome plays key roles in cellular metabolism and has been known as the stomach of cells. The abnormalities and malfunctioning of lysosomal function are associated with many diseases. Accordingly, the quantitative monitoring and real-time imaging of ROS in lysosomes are of great interest. In recent years, with the advancement of fluorescence imaging, fluorescent ROS probes have received considerable interest in the biomedical field. Thus far, considerable efforts have been undertaken to create synthetic fluorescent probes for sensing ROS in lysosomes; however, specific review articles on this topic are still lacking. This review provides a general introduction to fluorescence imaging technology, the sensing mechanisms of fluorescent probes, lysosomes, and design strategies for lysosome-targetable fluorescent ROS probes. In addition, the latest advancements in organic small-molecule fluorescent probes for ROS detection within lysosomes are discussed. Finally, the main challenges and future perspectives for developing effective lysosome-targetable fluorescent ROS probes for biomedical applications are presented.

PET/d-PET (PdP) Pairing for the Design of Dual-Channel Probes

Design principles of two-channel fluorescence probes are limited. Herein, we report a new principle, i.e., PET/d-PET (PdP) pairing, for the rational design of two-channel probes. Two fluorophores are required in such a PdP-type probe. They mutually quench their fluorescence via PET and d-PET. In the presence of an analyte-of-interest, such a PdP pair is converted into a FRET pair for signaling. The embodiment of such a principle is Rh-TROX, by tethering a rhodamine fluorophore with an ROS-sensitive probe (TotalROX). Fluorescence of both fluorophores in Rh-TROX was quenched as expected. The addition of highly reactive oxidative species led to the recovery of the fluorescence properties of both. The simultaneous fluorescence enhancement in two channels is a viable way to avoid false-positive signals. The new PdP principle could potentially be applied to the development of probes for another range of substrates.

Ratiometric Sensing of Intracellular pH Based on Dual Emissive Carbon Dots

Accurate monitoring of intracellular pH in living cells is critical for developing a better understanding of cellular activities. In the current study, label-free carbon dots (p-CDs), which were fabricated using a straightforward one-pot solvothermal treatment of p-phenylenediamine and urea, were employed to create a new ratiometric pH nanosensor. Under single-wavelength excitation (λ_ex = 500 nm), the p-CDs gave dual emission bands at 525 and 623 nm. The fluorescent intensity ratio (I₅₂₅/I₆₂₃) was linearly related to pH over the range 4.0 to 8.8 in buffer solutions, indicating that the ratiometric fluorescence nanoprobe may be useful for pH sensing. In pH measurements, the p-CDs also demonstrated outstanding selectivity, reversibility, and photostability. Owing to the advantages outlined above, the nanoprobe was used to monitor the pH of HeLa cells effectively. The label-free CD-based ratiometric nanoprobe features comparatively easy manufacturing and longer excitation and emission wavelengths than the majority of previously reported CD-based ratiometric pH sensors, which is ultimately beneficial for applications in biological imaging.

Cellular and Intravital Imaging of NAD(P)H by a Red-Emitting Quinolinium-Based Fluorescent Probe that Features a Shift of Its Product from Mitochondria to the Nucleus

NAD(P)H is a vital hydrogen donor and electron carrier involved in numerous biological processes. The development of small-molecule tools for intravital imaging of NAD(P)H is significant for further exploring their pathophysiological roles. Herein, we rationally designed a fluorescent probe NADH-R by a simple graft of pyridiniumylbutenenitrile on a 1-methylquinolinium moiety in the 3-position. Benefited from the reduction of quinolinium by NAD(P)H, this probe releases the free push-pull fluorophore NADH-RH, allowing a turn-on red-emitting fluorescence response together with an ultralow detection limit of 12 nM. Under the assistance of the probe, we first monitored exogenous and endogenous generation of NAD(P)H in living cells, subsequently observed dynamic changes of NAD(P)H levels in living cells under different metabolic perturbations, and finally visualized the declined NAD(P)H levels in live mouse brain in a stroke model. Unexpectedly, the time-dependent colocalization experiment revealed that the probe reacts with mitochondrial NAD(P)H, followed by a shift of its reduced product NADH-RH from mitochondria to the nucleus, highlighting that NADH-RH is a novel nucleus-directed dye scaffold, which would facilitate the development of nucleus-targeting fluorescent probes and drugs.

Thiophene and diaminobenzo- (1,2,5-thiadiazol)- based DAD-type near-infrared fluorescent probe for nitric oxide: A theoretical research

A near-infrared fluorescent probe (LS-NO) for the real-time detection of nitric oxide (NO) in inflammatory bowel disease (IBD) was developed recently. The probe used oligoglycol morpholine-functionalized thiophene as strong electron donors and diaminobenzene (1,2,5-thiadiazole) as a weak electron acceptor and NO trapping group. It could detect exogenous and endogenous NO in the lysosomes of living cells with high sensitivity and specificity. To further understand the fluorescent mechanism and character of the probes LS-NO and LS-TZ (after the reaction of the probe LS-NO with NO), the electron transfer in the excitation and emitting process within the model molecules DAD-NO and DAD-TZ was analyzed in detail under the density functional theory. The calculation results indicated the transformation from diaminobenzene (1,2,5-thiadiazole) as a weak electron acceptor to triazolo-benzo-(1,2,5-thiadiazole) as a strong electron acceptor made LS-NO an effective "off-on" near-infrared NO fluorescent probe.

Strategy for Detecting Carbon Monoxide: Cu2+-Assisted Fluorescent Probe and Its Applications in Biological Imaging

Herein, a novel strategy was proposed for identifying carbon monoxide (CO), which plays a crucial part in living systems. For the first time, we have managed to design, synthesize, and characterize successfully this new Cu²⁺-assisted fluorescent probe (DPHP) in detecting CO. Compared with the commonly adopted Pd⁰-mediated Tsuji-Trost reaction recognition method, such a new strategy did not engage costly palladium (II) salt and generated no leaving group, indicating a satisfactory anti-interference ability. The recognition mechanism was confirmed by IR, ¹H NMR titration, HR-MS, cyclic voltammetry, X-ray photoelectron spectroscopy, electron paramagnetic resonance, and optical properties. Surprisingly, it was found that the new method achieved high selectivity and rapid identification of CO with a lower limit of detection (1.7 × 10^-8 M). More intriguingly, it could recognize endogenous and exogenous CO in HeLa cells. The cytotoxicity of this new method was so low that it allowed the detection of CO in mice and zebrafish. Basically, our results trigger a novel viewpoint of rationally designing and synthesizing advanced materials for CO detection with unique features, impelling new research in detection chemistry.

Long-wavelength emission carbon dots as self-ratiometric fluorescent nanoprobe for sensitive determination of Zn2

A novel ratiometric fluorescence nanoprobe based on long-wavelength emission carbon dots (CDs) was designed for high sensitive and selective detection of Zn²⁺. The CDs were conveniently prepared by a one-step solvothermal treatment of formamide and glutathione (GSH). Under single excitation wavelength (420 nm), the obtained CDs exhibit three emission peaks at 470, 650, and 685 nm, respectively. For the long-wavelength emission region of the CDs, the fluorescence at 685 nm can be quenched with different levels upon the addition of most metal ions. However, the presence of Zn²⁺ not only results in the fluorescence quenching at 685 nm effectively but also enhances at 650 nm remarkably, which may be due to the formation of CD-Zn²⁺ chelate complex inducing the dispersion of CDs aggregates and changes in the group distribution on the surface of CDs. Taking the advantage of the unique fluorescence response induced by Zn²⁺, the prepared CDs were successfully employed as nanoprobe for self-ratiometric fluorescence determination of Zn²⁺ with F₆₅₀/F₆₈₅ as signal output. A good linear relationship in the concentration range 0.01 to 2 μM, and a detection limit as low as 5.1 nM has been obtained. The ratiometric nanoprobe was successfully applied to  Zn²⁺ determination  in human serum samples.