A Bright Red Molecular Marker for Super-Resolution Imaging of DNA Nanoscale Organization in Cells

SEZ-NDEA, a long-range emissive molecular marker, can be used in fluorescence microscopy for super-resolution imaging (SRRF) of DNA nanoscale organization in cells. The developed probe stains the cell nucleus with minimum cytoplasmic leakage with good contrast. It showed good photostability in cellular medium.

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.

Imaging G-Quadruplex Nucleic Acids in Live Cells Using Thioflavin T and Fluorescence Lifetime Imaging Microscopy

Visualization of guanine-rich oligonucleotides that fold into G-quadruplex (G4) helical structures is of great interest in cell biology. There is a large body of evidence that suggests that these noncanonical structures form in vivo and play important biological roles. A promising recent development highlighted fluorescence lifetime imaging microscopy (FLIM) as a robust technique for the direct and quantitative imaging of G4s in live cells. However, this method requires specialized, bespoke synthetic dyes that are not widely available. Herein, we demonstrate that the fluorescence lifetime of commercially available environmentally sensitive dyes Thioflavin T (ThT) and Thiazole Orange (TO) is strongly dependent on the type of DNA topology they bind to, with G4s showing long and distinctive decay times that should allow G4 detection in the biological environment. We applied this observation to visualize G4s in live U2OS cells using FLIM of ThT, upon alteration in G4 levels due to competitive binding or nuclease treatment of cells.

Molecular probes for super-resolution imaging of drug dynamics

Super-resolution molecular probes (SRMPs) are essential tools for visualizing drug dynamics within cells, transcending the resolution limits of conventional microscopy. In this review, we provide an overview of the principles and design strategies of SRMPs, emphasizing their role in accurately tracking drug molecules. By illuminating the intricate processes of drug distribution, diffusion, uptake, and metabolism at a subcellular and molecular level, SRMPs offer crucial insights into therapeutic interventions. Additionally, we explore the practical applications of super-resolution imaging in disease treatment, highlighting the significance of SRMPs in advancing our understanding of drug action. Finally, we discuss future perspectives, envisioning potential advancements and innovations in this field. Overall, this review serves to inform and practitioners about the utility of SRMPs in driving innovation and progress in pharmacology, providing valuable insights for drug development and optimization.

Nucleic Acid-Templated Synthesis of Cationic Styryl Dyes in Vitro and in Living Cells

A novel method for synthesizing cationic styryl dyes through a nucleic acid-templated reaction has been developed. This approach overcomes issues associated with traditional synthesis methods, such as harsh conditions, low throughput, and wasteful chemicals. The presence of a nucleic acid template accelerated the styryl dye formation from quaternized heteroaromatic and cationic aldehyde substrates. These styryl dyes show remarkable optical properties change when bound to nucleic acids, hence the success of the synthesis could be readily monitored in situ by UV-Vis and fluorescence spectroscopy and the optical properties data were also observable at the same time. This method provides the desired products from a broad range of coupling partners. By employing different substrates and templates, it is possible to identify new dyes that can bind to a specific type of nucleic acid such as a G-quadruplex. The templated dye synthesis is also successfully demonstrated in live HeLa cells. This approach is a powerful tool for the rapid synthesis and screening of dyes specific for diverse types of nucleic acids or cellular organelles, facilitating new biological discoveries.

Precisely modulating the chromatin tracker via substituent engineering: reporting pathological oxidative stress during mitosis

An in-depth understanding of cancer-cell mitosis presents unprecedented advantages for solving metastasis and proliferation of tumors, which has aroused great interest in visualizing the behavior via a luminescence tool. We developed a fluorescent molecule CBTZ-yne based on substituent engineering to acquire befitting lipophilicity and electrophilicity for anchoring lipid droplets and the nucleus, in which the low polarity environment and nucleic acids triggered a "weak-strong" fluorescence and "short-long" fluorescence-lifetime response. Meaningfully, CBTZ-yne visualized chromatin condensation, alignment, pull-push, and separation as well as lipid droplet dynamics, for the first time, precisely unveiling the asynchronous cellular mitosis processes affected by photo-generation reactive oxygen species according to the subtle change of fluorescence-lifetime. Our work suggested a new guideline for tracking the issue of the proliferation of malignant tumors in photodynamic therapy.

Conjugated Oligoelectrolyte with DNA Affinity for Enhanced Nuclear Imaging and Precise DNA Quantification

Precise DNA quantification and nuclear imaging are pivotal for clinical testing, pathological diagnosis, and drug development. The detection and localization of mitochondrial DNA serve as crucial indicators of cellular health. We introduce a novel conjugated oligoelectrolyte (COE) molecule, COE-S3, featuring a planar backbone composed of three benzene rings and terminal side chains. This unique amphiphilic structure endows COE-S3 with exceptional water solubility, a high quantum yield of 0.79, and a significant fluorescence Stokes shift (λex = 366 nm, λem = 476 nm), alongside a specific fluorescence response to DNA. The fluorescence intensity correlates proportionally with DNA concentration. COE-S3 interacts with double-stranded DNA (dsDNA) through an intercalation binding mode, exhibiting a binding constant (K) of 1.32 × 106 M-1. Its amphiphilic nature and strong DNA affinity facilitate its localization within mitochondria in living cells and nuclei in apoptotic cells. Remarkably, within 30 min of COE-S3 staining, cell vitality can be discerned through real-time nuclear fluorescence imaging of apoptotic cells. COE-S3's high DNA selectivity enables quantitative intracellular DNA analysis, providing insights into cell proliferation, differentiation, and growth. Our findings underscore COE-S3, with its strategically designed, shortened planar backbone, as a promising intercalative probe for DNA quantification and nuclear imaging.

Fluorimetric Cell Analysis with 9-Aryl-Substituted Berberine Derivatives as DNA-Targeting Fluorescent Probes

DNA-sensitive fluorescent light-up probes based on berberine are presented. This biogenic fluorophore was chosen as central unit to use its potential biocompatibility and its DNA-binding properties. To provide predictable fluorescence quenching in aqueous solution and a fluorescence light-up effect upon DNA binding, aryl substituents were attached at the 9-position by Suzuki-Miyaura coupling reactions. The 9-arylberberine derivatives have a very low fluorescence quantum yield (Φfl =<0.02), which is caused by the radiationless deactivation of the excited state by torsional relaxation about the biaryl axis. In addition, these berberine derivatives intercalate into DNA with high affinity (Kb =2.0-22×104  M-1 ). Except for the nitrophenyl- and hydroxyphenyl-substituted derivatives, all tested compounds exhibited a pronounced fluorescence light-up effect upon association with DNA, because the deactivation of the excited-state by torsional relaxation is suppressed in the DNA binding site. Most notably, it was shown exemplarily with the 9-(4-methoxyphenyl)- and the 9-(6-methoxynaphthyl)-substituted derivatives that these properties are suited for fluorimetric cell analysis. In particular, these probes generated distinct staining patterns in eukaryotic cells (NIH 3T3 mouse fibroblasts), which enabled the identification of nuclear substructures, most likely heterochromatin or nucleoli, respectively.

Nucleolus imaging based on naphthalimide derivatives

Nucleolus was an important cellular organelle. The abnormal morphology and number of the nucleolus have been considered as diagnostic biomarkers for some human diseases. However, the imaging agent based on nucleolus was limited. In this manuscript, a series of nucleolar fluorescent probes based on naphthalimide derivatives (NI-1 ∼ NI-5) had been designed and synthesized. NI-1 ∼ NI-5 could penetrate cell membranes and nuclear membranes, achieve clear nucleolar staining in living cells. These results suggested that the presence of amino groups on the side chains of naphthalimide backbone could enhance the targeting to the cell nucleolus. In addition, the molecular docking results showed that NI-1 ∼ NI-5 formed hydrogen bonds and hydrophobic interactions with RNA, and exhibited enhanced fluorescence upon binding with RNA. These results will provide favorable support for the diagnosis and treatment of nucleolus-related diseases in the future.

An Activatable Phototheranostic Probe for Anti-hypoxic Type I Photodynamic- and Immuno-Therapy of Cancer

Photodynamic therapy (PDT), which utilizes type I photoreactions, has great potential as an effective cancer treatment because of its hypoxia-tolerant superiority over the commonly used type II pathway. A few type I photosensitizers are exploited; however, they majorly induce cytotoxicity and possess poor tumor specificity and low-efficient theranostics. To resolve this issue, herein an aminopeptidase N (APN)-activated type I phototheranostic probe (CyA) is reported for anti-hypoxic PDT in conjunction with immunotherapy for effective cancer treatment. CyA can specifically activate near-infrared fluorescence, photoacoustic signals, and phototoxicity following APN-induced substrate cleavage and the subsequent generation of active phototheranostic molecules (such as CyBr). CyA endows specific imaging capabilities and effective phototoxicity toward tumor cells overexpressing APN under both normoxia and hypoxia. In addition, the locally activatable PDT induces systemic antitumor immune responses. More importantly, the integration of localized activated PDT and systemic immunotherapy evokes enhanced therapeutic effects with improved tumor inhibition efficiency in live mice compared with individual treatments. This study aims to present an activatable phototheranostic probe for effective hypoxia-tolerant PDT and combination therapy.

Harnessing a 4-Formyl-Aniline Handle to Tune the Stability of a DNA Aptamer-Protein Complex via Fluorescent Surrogates

Interactions between DNA aptamers and protein targets hold promise for the development of pharmaceuticals and diagnostics. As such, the utilization of fluorescent nucleobase surrogates in studying aptamer-protein interactions is a powerful tool due to their ability to provide site-specific information through turn-on fluorescence. Unfortunately, previously described turn-on probes serving as nucleobase replacements have only been strongly disruptive to the affinity of aptamer-protein interactions. Herein, we present a modified TBA15 aptamer for thrombin containing a fluorescent surrogate that provides site-specific turn-on emission with low nanomolar affinity. The modification, referred to as AnBtz, was substituted at position T3 and provided strong turn-on emission (Irel ≈ 4) and brightness (ε·Φ > 20 000 cm-1 M-1) with an apparent dissociation constant (Kd) of 15 nM to afford a limit of detection (LOD) of 10 nM for thrombin in 20% human serum. The probe was selected through a modular "on-strand" synthesis process that utilized a 4-formyl-aniline (4FA) handle. Using this platform, we were able to enhance the affinity of the final aptamer conjugate by ∼30-fold in comparison with the initial conjugate design. Molecular dynamics simulations provide insight into the structural basis for this phenomenon and highlight the importance of targeting hydrophobic protein binding sites with fluorescent nucleobase surrogates to create new contacts with protein targets.

In Response to Precision Medicine: Current Subcellular Targeting Strategies for Cancer Therapy

Emerging as a potent anticancer treatment, subcellular targeted cancer therapy has drawn increasing attention, bringing great opportunities for clinical application. Here, two targeting strategies for four main subcellular organelles (mitochondria, lysosome, endoplasmic reticulum, and nucleus), including molecule- and nanomaterial (inorganic nanoparticles, micelles, organic polymers, and others)-based targeted delivery or therapeutic strategies, are summarized. Phototherapy, chemotherapy, radiotherapy, immunotherapy, and "all-in-one" combination therapy are among the strategies covered in detail. Such materials are constructed based on the specific properties and relevant mechanisms of organelles, enabling the elimination of tumors by inducing dysfunction in the corresponding organelles or destroying specific structures. The challenges faced by organelle-targeting cancer therapies are also summarized. Looking forward, a paradigm for organelle-targeting therapy with enhanced therapeutic efficacy compared to current clinical approaches is envisioned.

Cationic Oligopeptides with Amino Groups as Synthetic Nucleolar Localization Signals for the Rational Design of Nucleolus-Staining Probes

Cationic oligopeptides with amino groups were found to function as synthetic nucleolar localization signals for directing various fluorophores to the nucleolus with high selectivity in the cells with a view toward the development of nucleolus-staining probes.

Small-Molecule 3D Ligand for RNA Recognition: Tuning Selectivity through Scaffold Hopping

Targeting RNAs with small molecules is considered the next frontier for drug discovery. In this context, the development of compounds capable of binding RNA structural motifs of low complexity with high affinity and selectivity would greatly expand the number of targets of potential therapeutic value. In this study, we demonstrate that tuning the three-dimensional shape of promiscuous nucleic acid binders is a valuable strategy for the design of new selective RNA ligands. Indeed, starting from a known cyanine, the simple replacement of a phenyl ring with a [2.2]paracyclophane moiety led to a new compound able to discriminate between nucleic acids showing different structural characteristics with a marked affinity and selectivity for an octahairpin loop RNA sequence. This shape modification also affected the in cellulo behavior of the cyanine. These results suggest that scaffold hopping is a valuable strategy to improve the selectivity of RNA/small-molecule interactions and highlight the need to explore a new chemical space for the design of selective RNA ligands.

Dicationic styryl dyes for colorimetric and fluorescent detection of nucleic acids

Nucleic acid staining dyes are important tools for the analysis and visualizing of DNA/RNA in vitro and in the cells. Nevertheless, the range of commercially accessible dyes is still rather limited, and they are often very costly. As a result, finding nontoxic, easily accessible dyes, with desirable optical characteristics remains important. Styryl dyes have recently gained popularity as potential biological staining agents with many appealing properties, including a straightforward synthesis procedure, excellent photostability, tunable fluorescence, and high fluorescence quantum yield in the presence of nucleic acid targets with low background fluorescence signals. In addition to fluorescence, styryl dyes are strongly colored and exhibit solvatochromic properties which make them useful as colorimetric stains for low-cost and rapid testing of nucleic acids. In this work, novel dicationic styryl dyes bearing quaternary ammonium groups are designed to improve binding strength and optical response with target nucleic acids which contain a negatively charged phosphate backbone. Optical properties of the newly synthesized styryl dyes have been studied in the presence and absence of nucleic acid targets with the aim to find new dyes that can sensitively and specifically change fluorescence and/or color in the presence of nucleic acid targets. The binding interaction and optical response of the dicationic styryl dyes with nucleic acid were superior to the corresponding monocationic styryl dyes. Applications of the developed dyes for colorimetric detection of DNA in vitro and imaging of cellular nucleic acids are also demonstrated.

A benzothiazole-based near-infrared fluorescent probe for sensing SO2 derivatives and viscosity in HeLa cells

The unbalanced metabolism of sulfur dioxide can cause various diseases, such as neurological disorders and lung cancer. Until now, some researches revealed that the normal function of lysosomes would be disrupted by its abnormal viscosity. As a signal molecule, sulfur dioxide (SO2) plays an important role in lysosome metabolism. However, the connection of metabolism between the SO2 and viscosity in lysosomes is still unknown. Herein, we developed a benzothiazole-based near-infrared (NIR) fluorescent probe (Triph-SZ), which can monitor the SO2 derivatives and respond to the change of viscosity in lysosomes through two-photon imaging. Triph-SZ present high sensitivity and selectivity fluorescence response with the addition of SO2 derivatives based on the nucleophilic addition, and it also exhibits a sensitive fluorescence enhancement to environmental viscosity, which allows Triph-SZ to be employed to monitor the level of HSO3- and viscosity changes in lysosomes by the two-photon fluorescence lifetime imaging microscopy.

Light-Driven Cascade Mitochondria-to-Nucleus Photosensitization in Cancer Cell Ablation

Nuclei and mitochondria are the only cellular organelles containing genes, which are specific targets for efficient cancer therapy. So far, several photosensitizers have been reported for mitochondria targeting, and another few have been reported for nuclei targeting. However, none have been reported for photosensitization in both mitochondria and nucleus, especially in cascade mode, which can significantly reduce the photosensitizers needed for maximal treatment effect. Herein, a light-driven, mitochondria-to-nucleus cascade dual organelle cancer cell ablation strategy is reported. A functionalized iridium complex, named BT-Ir, is designed as a photosensitizer, which targets mitochondria first for photosensitization and subsequently is translocated to a cell nucleus for continuous photodynamic cancer cell ablation. This strategy opens new opportunities for efficient photodynamic therapy.

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

The misregulation of nucleic acids behavior leads to cell dysfunction and induces serious diseases. A ratiometric fluorescence probe is a powerful tool to study the dynamic behavior and function relationships of nucleic acids. However, currently, no such effective probe has been reported for in situ, real-time tracking of nucleic acids in living cells and tissue sections. Herein, the unique probe named QPP-AS was rationally designed for ratiometric fluorescence response to nucleic acids through skillful regulation of the intramolecular charge-transfer capabilities of the electron acceptor and donor. Encouraged by the advantages of the selective nucleic acid response, ideal biocompatibility, and high signal-to-noise ratio, QPP-AS has been applied for in situ, real-time ratiometric fluorescence imaging of nucleic acids in living cells for the first time. Furthermore, we have demonstrated that QPP-AS is capable of visualizing the dynamic behavior of nucleic acids during different cellular processes (e.g., cell division and apoptosis) by ratiometric fluorescence imaging. More significantly, QPP-AS has been successfully used for ratiometric fluorescence imaging of nucleic acids in human tissue sections, which provides not only the cell contour, nuclear morphology, and nuclear-plasma ratio but also the nucleic acid content information and may greatly improve accuracy in clinicopathological diagnosis.

Enantiomeric selectivity of ruthenium (II) chiral complexes with antitumor activity, in vitro and in vivo

Different enantiomers of chiral drugs show distinctive activities. Here, a pair of chiral ruthenium Λ-[Ru(phen)₂(TPEPIP)]²⁺ (Λ-Ru), and Δ-[Ru(phen)₂(TPEPIP)]²⁺ (Δ-Ru) (phen = 1,10-phenanthroline; TPEPIP = 2-(4'-(1,2,2-triphenylvinyl)-[1,1'-biphenyl]-4-yl)-1H-imidazo[4,5-f][1,10]phenanthroline) compounds have been prepared and characterized. Both have aggregation-induced emission characteristics, although Λ-Ru exhibits much higher activity, towards duplex DNA extracted from SGC-7901 cancer cells. In vitro experiments demonstrate that both Λ-Ru and Δ-Ru can induce the apoptosis of tumor cells with Λ-Ru showing greater activity than Δ-Ru. Λ-Ru aggregates in the cell nucleus of SGC-7901 within 5 h which shows that nucleic acids may be the effective target of Λ-Ru. In vivo experiments with nude mice showed that Λ-Ru can inhibit the growth and proliferation of a tumor, in tumor-bearing mice as well as targeting the tumor site, as demonstrated by fluorescence. These results demonstrate the dual-function of Λ-Ru, which could be used for real-time visualization of a chemotherapeutic agent.

Development of a two-photon fluorescent probe to monitor the changes of viscosity in living cells, zebra fish and mice

The detection of viscosity is of great significance for medical research. Herein, we have developed a two-photon fluorescent probe CB-V for monitoring micro-viscosity changes. The fluorescence emission intensity of CB-V increased 9.6-fold from methanol to glycerol exhibiting an excellent fluorescence response. With excellent properties of CB-V, monitoring the viscosity variations has been achieved not only in living cells but also in zebra fish and mice.

A straightforward synthesis of phenyl boronic acid (PBA) containing BODIPY dyes: new functional and modular fluorescent tools for the tethering of the glycan domain of antibodies

We report here on the efficient and straightforward synthesis of a series of modular and functional PBA-BODIPY dyes 1–4. They are an outstanding example of the efficient merge of the versatility of the 3,5-dichloro-BODIPY derivatives and the receptor-like ability of the PBA moiety. The potential bioanalytical applicability of these tools was assessed by measuring the binding to glycan chains of antibodies by a Quartz Crystal Microbalance (QCM).

PBA-BODIPY dyes as functional and modular fluorescent probes for the tethering of the glycan domain of mAbs.

A novel algorithm for second-order calibration of three-way data in fluorescence assays of multiple breast cancer-related DNAs

Fluorescent probes have been valuable tools for bioanalytical multiplex assays. However, as a common phenomenon in multiplex fluorescence assays, spectral overlap usually leads to difficulty in spectral analysis for multiple analytes. Although multiway calibrations have provided mathematic approaches for complex spectral analysis, it remains a grand challenge for these methods in practical applications because of the problems such as prior rank estimation. Herein, we report a novel second-order calibration algorithm of alternating residual trilinearization (ART) for the decomposition of complex spectra generated from multiplex fluorescence assays. By alternating iterative convergence to the spectral profiles of each component in convergence process, ART enables automatic rank estimation for second-order calibration, thus able to avoid the risk of chemical meaningless fitting of component spectra. Combined with fluorescence excitation-emission matrix (EEM) spectroscopy, the performance of ART has been demonstrated by a simulated example and an analytical experiment performed using molecular beacons (MBs) for the simultaneous assay of three breast cancer related DNA targets. The results revealed that the proposed algorithm is capable of automatic estimating the number of underlying components during its convergence process to produce acceptable performance in spectral profile resolution and concentration estimation. Compared with other existing iterative trilinear decomposition strategies such as parallel factor analysis (PARAFAC) requiring a prior rank estimation, the proposed ART therefore provides a robust second-order calibration strategy for complex spectral analysis in multiplex fluorescence assays.