RNA-responsive fluorescent carbon dots for fast and wash-free nucleolus imaging

Comprehensive review on fluorescent carbon dots and their applications in nucleic acid detection, nucleolus targeted imaging and gene delivery

Carbon dots (CDs), including carbon quantum dots, graphene quantum dots, carbon nanodots, and polymer dots, have gained significant attention due to their unique structural and fluorescence characteristics. This review provides a comprehensive overview of the classification, structural characteristics, and fluorescence properties of CDs, followed by an exploration of various fluorescence sensing mechanisms and their applications in gene detection, nucleolus imaging, and gene delivery. Furthermore, the functionalization of CDs with diverse surface ligand molecules, including dye molecules, nucleic acid probes, and metal derivatives, for sensitive nucleic acid detection is systematically examined. Fluorescence imaging of the cell nucleolus plays a vital role in examining intracellular processes and the dynamics of subcellular structures. By analyzing the mechanism of fluorescence and structure-function relationships inherent in CDs, the nucleolus targeting abilities of CDs in various cell lines have been discussed. Additionally, challenges such as the insufficient organelle specificity of CDs and the inconsistent mechanisms underlying nucleolus targeting have also been highlighted. The unique physical and chemical properties of CDs, particularly their strong affinity toward deoxyribonucleic acid (DNA), have spurred interest in gene delivery applications. The use of nuclear-targeting peptides, polymers, and ligands in conjunction with CDs for improved gene delivery applications have been systematically reviewed. Through a comprehensive analysis, the review aims to contribute to a deeper understanding of the potential and challenges associated with CDs in biomedical applications.

Effective Combination of Targeted Therapies with Sonodynamic Treatment for Use in Exploring Differences in Therapeutic Efficacy across Organelle Targets

Acoustic kinetic therapy systems that target specific organelles can improve the precision of a sonosensitizer, which is a perfect combination of targeted therapy and sonodynamic therapy (SDT) and plays an important role in current acoustic kinetic therapy. In this study, we loaded PpIX, a sonosensitizer, on targeted-functional carbon dots (CDs) via an amide reaction and then generated the mitochondria-targeted system (Mit-CDs-PpIX) and nucleus-targeted system (Nuc-CDs-PpIX), respectively, to deliver the sonosensitizer. Both systems exhibited minimal cytotoxicity in the absence of ultrasound stimulation. The efficacy of the targeted SDT systems was investigated using methylthiazol tetrazolium (MTT) assays, live/dead staining, flow cytometry, etc. Compared with the free PpIX and mitochondria-targeted system, the nucleus-targeted system is more potent in killing effect under ultrasound stimulation and induces apoptosis with higher intensity. To achieve the equal killing effect, the effective concentration of Nuc-CDs-PpIX is just one third of that of Mit-CDs-PpIX.

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.

Carbon-dot-triggered aggregation/dispersion of gold nanoparticles for colorimetric detection of nucleic acids and its application in visualization of loop-mediated isothermal amplification

In this study, cationic carbon dots (CDs) were prepared from p-phenylenediamine (pPDA) via a one-step hydrothermal method and used to trigger the aggregation and dispersion of gold nanoparticles (AuNPs) for the colorimetric detection of nucleic acids. Physicochemical characterization results revealed that the CDs are enriched with positively charged surface functional groups with an average size of ∼11 nm. The interaction between the CDs and AuNPs was confirmed via fluorescence and absorption studies. Absorption spectroscopic results revealed that the primary surface plasmon resonance (SPR) band of the AuNPs decreased upon introduction of CDs, and a new band emerged at ∼600 nm, indicating the aggregated assembly of AuNPs. Upon the introduction of double-stranded deoxyribonucleic acid (DNA), the band corresponding to the aggregated AuNPs showed a continuous decrease, accompanied by a simultaneous increase in the primary SPR band, leading to a noticeable purple-to-red color transformation. Based on this phenomenon, a colorimetric assay for DNA was developed, which relies on the interaction between negatively charged DNA and cationic CDs, leaving the AuNPs dispersed. The assay exhibited a linear response within a DNA concentration range of 0.7-14 nM with a detection limit of 1.70 nM. Selectivity results showed that colorimetric assays are specific for both DNA and single-stranded DNA (ssDNA). Smartphone-assisted detection was developed by monitoring the colorimetric response of a AuNPs/CDs probe. As a proof-of-concept experiment, the AuNPs/CDs probe was used to visualize the loop-mediated isothermal amplification (LAMP) of Escherichia coli (E. coli), a robust indicator of sewage contamination in water.

Meticulously Designed Carbon Dots as Photo-Triggered RNA-Destroyer for Evoking Pyroptosis

An ideal photosensitizer for photodynamic therapy should not only possess high reactive oxygen species (ROS) generation efficiency but also maximize utilization of the in situ produced ROS species, where the latter is closely related to its intracellular location. However, rational design of such photosensitizer without tedious conjugation procedures remains a grand challenge. Here, we report the one-pot preparation of carbon dots (CDs)-based photosensitizer from levofloxacin and neutral red featuring both high 1O2 quantum yield (φΔ = 38.85%) and superior RNA selectivity. Moreover, the φΔ value shows a further 40% improvement and reaches 54.33% in response to RNA binding. Owing to these combined attributes, the CDs could exert great damage to the cellular RNA system (termed the RNA-destroyer) under extremely low dosage of light irradiation (15 mW cm-2, 1 min). It induces pyroptotic cell death and causes rapid release of different cytokines that served as molecular markers in photodynamic immunotherapy. This work represents the meticulously designed CDs with high ROS generation and utilization efficiency via good organization of the photosensitive and targeting modularity. Moreover, it is the first CDs-based pyroptosis inducer to the best of our knowledge.

Large Stokes shift benzothiazolium cyanine dyes with improved intramolecular charge transfer (ICT) for cell imaging applications

Intramolecular Charge Transfer (ICT) is a crucial photophysical phenomenon that can be used to improve the Stokes' shift in fluorescent dyes. The introduction of molecular asymmetry is a promising approach to mitigate significant drawbacks of the symmetric cyanine dyes due to their narrow Stokes' shifts (Δλ < 20 nm). In this feature article, we discuss recent progress towards improving the Stokes' shift (Δλ > 100 nm) in benzothiazolium-based fluorophore systems via efficient ICT and recent discoveries related to potentially useful live cell imaging applications of these asymmetric cyanine dyes. This article explores three interesting asymmetric benzothiazolium dye designs (D-π-A, π-A and D-π-2A) in detail while discussing their optical properties. The key advantage of these probes is the synthetic tunability of the probe's photophysical properties and cellular selectivity by simply modifying the donor (D) or the acceptor (A) group in the structure. These new asymmetric ICT fluorophore systems exhibit large Stokes' shifts, high biocompatibility, wash-free staining, red to NIR emission and facile excitation with commercially available laser wavelengths.

Visual Monitoring of Nucleic Acid Dynamic Structures during Cellular Ferroptosis Using Rationally Designed Carbon Dots with Robust Anti-Interference Ability to Reactive Oxygen Species

Ferroptosis triggered by an iron-dependent accumulation of lipid reactive oxygen species (ROS) has drawn widespread attention. Directly visualizing the dynamic structures of nucleic acids during the ferroptosis of cells is of great importance considering their vital roles in numerous biological functions. However, direct imaging remains challenging, largely due to the extremely high concentrations of ROS generated during ferroptosis, which can affect the imaging of nucleic acid targeted fluorescent probes. To overcome this challenge, nucleic acid-responsive carbon dots (CDs) providing favorable optical properties together with high chemical stability were synthesized. Furthermore, the CDs penetrated the cell membrane quickly and accumulated in the nuclei of cells. The robust anti-interference ability to ROS allows the CDs to visualize the dynamic structures of nucleic acids during ferroptosis. Moreover, the CDs were successfully employed in the imaging of nucleic acids during cell division. The nuclei-targeting CDs show great potential as a powerful tool for imaging nuclei in ferroptosis-related biological and clinical research.

Evaluation of chemotherapeutic response in living cells using subcellular Organelle‒Selective amphipathic carbon dots

Monitoring of structural changes in subcellular organelles is critical to evaluate the chemotherapeutic response of cells. However, commercial organelle selective fluorophores are easily photobleached, and thus are unsuitable for real-time and long-term observation. We have developed photostable carbon-dot liposomes (CDsomes)-based fluorophores for organellar and suborganellar imaging to circumvent these issues. The CDs synthesized through a mild pyrolysis/hydrolysis process exhibit amphipathic nature and underwent self-assembly to form liposome-like structures (CDsomes). The controlled hydrophilicity or hydrophobicity-guided preparation of CDsomes are used to selectively and rapidly (<1 min) stain nucleolus, cytoplasm, and membrane. In addition, the CDsomes offer universal high-contrast staining not only in fixed cells but also in living cells, allowing real-time observation and morphological identification in the specimen. The as-prepared CDsomes exhibit excitation-dependent fluorescence, and are much more stable under photoirradiation (e.g., ultraviolet light) than traditional subcellular dyes. Interestingly, the CDsomes can be transferred to daughter cells by diluting the particles, enabling multigenerational tracking of suborganelle for up to six generations, without interrupting the staining pattern. Therefore, we believe that the ultra-photostable CDsomes with high biocompatibility, and long-term suborganellar imaging capabilities, hold a great potential for screening and evaluating therapeutic performance of various chemotherapeutic drugs.

Nitrogen-doped carbon dots as a fluorescent probe for folic acid detection and live cell imaging

The folic acid (FA) level in human body can be used as an indicator for body's normal physiological activities and offer insight into the growth and reproduction of the body's cells. But the abnormal level of FA can cause some diseases. Herein, we designed a simple and convenient approach to prepare fluorescent N-doped carbon dots (N-CDs) for the FA detection. These N-CDs have excellent hydrophilicity, high photostability, and outstanding biocompatibility, as well as excitation-independent emission behavior with typical excitation/emission peaks at 295 nm/412 nm. Upon the existence of FA, the fluorescence emission spectrum of N-CDs was significantly quenched through the synergy of static quenching mechanism and internal filtering effect (IFE). Under optimal conditions, the limit of detection was 28.0 nM (S/N = 3) within the FA concentration range of 0-200.0 μM. In addition, N-CDs were successfully employed to detect FA in real samples such as urine and fetal bovine serum (FBS), with a recovery rate of 99.6%-100.7% for quantitative addition. Furthermore, cell experiments confirmed the low toxicity and the cell imaging performance of these N-CDs, indicating that the obtained N-CDs could be served as a credible quantitative probe for FA analysis in the field of biosensing.

Research Progress in the Synthesis of Targeting Organelle Carbon Dots and Their Applications in Cancer Diagnosis and Treatment

With increasing knowledge about diseases at the histological, cytological to sub-organelle level, targeting organelle therapy has gradually been envisioned as an approach to overcome the shortcomings of poor specificity and multiple toxic side effects on tissues and cell-level treatments using the currently available therapy. Organelle carbon dots (CDs) are a class of functionalized CDs that can target organelles. CDs can be prepared by a "synchronous in situ synthesis method" and "asynchronous modification method." The superior optical properties and good biocompatibility of CDs can be preserved, and they can be used as targeting particles to carry drugs into cells while reducing leakage during transport. Given the excellent organelle fluorescence imaging properties, targeting organelle CDs can be used to monitor the physiological metabolism of organelles and progression of human diseases, which will provide advanced understanding and accurate diagnosis and targeted treatment of cancers. This study reviews the methods used for preparation of targeting organelle CDs, mechanisms of accurate diagnosis and targeted treatment of cancer, as well as their application in the area of cancer diagnosis and treatment research. Finally, the current difficulties and prospects for targeting organelle CDs are prospected.

Quantitative Structure-Activity Relationship Enables the Rational Design of Lipid Droplet-Targeting Carbon Dots for Visualizing Bisphenol A-Induced Nonalcoholic Fatty Liver Disease-like Changes

Lipid droplets (LDs) play indispensable roles in numerous physiological processes; hence, the visualization of the dynamic behavior of LDs in living cells is of great importance in physiological and pathological research. In this article, the quantitative structure-activity relationship (QSAR) theory was employed as an effective design strategy for the development of organelle-targeting carbon dots (CDs). The lipid-water partition coefficient (Log P) of the QSAR was adopted as a key parameter to predict the cellular uptake and subcellular localization of CDs in live cells. By carefully adjusting the molecular structure and lipophilicity of the precursors, p-phenylenediamine-derivatized nucleolus-targeting hydrophilic CDs were converted to lipophilic CDs [4-piperidinoaniline (PA) CDs] with inherent LD-targeting performance. The PA CDs were able to indicate the dynamic behavior of LDs and visualize the changes of bisphenol A-induced nonalcoholic fatty liver disease-like changes in a cellular model. The QSAR strategy of CDs demonstrated here is expected to be increasingly exploited as a powerful design tool for developing various organelle-targeting CDs.

Lysosome targeting, Cr(vi) and l-AA sensing, and cell imaging based on N-doped blue-fluorescence carbon dots

N-doped blue-fluorescence carbon dots (N-CDs) were fabricated via a one-pot hydrothermal method using folic acid and p-phenylenediamine. The obtained N-CDs exhibited strong fluorescence (FL) with a considerable quantum yield (QY) of 21.8% and exceptional optical stability under different conditions. Upon introducing Cr(vi), blue FL of N-CDs was distinctly quenched. On subsequent addition of l-AA, the FL of N-CDs could be partially recovered. The fluorescence changes of N-CDs have been utilized to detect Cr(vi) and l-AA in aqueous solutions with linear ranges of 0.10-150 μM and 0.75-2.25 mM, respectively, as well as limit of detection values of 9.4 nM and 25 μM, respectively. Furthermore, as-obtained N-CDs can be extended to monitor the fluctuation of intracellular Cr(vi) and l-AA. More intriguingly, N-CDs can target lysosomes with a satisfactory Pearson correction coefficient of 0.87, which indicates a promising application prospect in the biomedical field.

Nitrogen-doped carbon dots for wash-free imaging of nucleolus orientation

Carbon dots (CDs) are a rising star in the field of cellular imaging, especially cytoplasmic imaging, attributing to the super-stable optical performance and ultra-low biological toxicity. Nucleolus can accurately reflect the expression state of a cell and is strongly linked to the occurrence and development of many diseases, so exploring bran-new CDs for nucleolus-orientation imaging with no-wash technology has important theoretical value and practical significance. Herein, nitrogen-doped carbon dots (N-CDs) with green fluorescence (the relative fluorescence quantum yield of 24.4%) was fabricated by the hydrothermal treatment of m-phenylenediamine and p-aminobenzoic acid. The N-CDs possess small size, bright green fluorescence, abundant surface functional groups, excellent fluorescence stability and good biocompatibility, facilitating that the N-CDs are an excellent imaging reagent for cellular imaging. N-CDs can particularly bind to RNA in nucleoli to enhance their fluorescence, which ensures that the N-CDs can be used in nucleolus-orientation imaging with high specificity and wash-free technique. This study demonstrates that the N-CDs have a significant feasibility to be used for nucleolus-orientation imaging in biomedical analysis and clinical diagnostic applications.

Rapid ex vivo assessment of cancer prognosis by fluorescence imaging of nucleolus using nitrogen doped carbon dots

Cancer severely threatens human health currently, promoting the rapid development of cancer treatment strategies. In addition to cancer therapy, assessment of cancer prognosis, which can evaluate the success with treatment and chances of recovery as well as assist to make subsequent therapeutic schedule, is also remarkably indispensable and important. Conventional technologies can't provide rapid and highly-sensitive assessment of cancer prognosis at cytological level. Herein, an effective nitrogen doped carbon dots with intrinsic nucleolus-targeting capability and high fluorescence quantum yield are synthesized, characterized and employed for fluorescence imaging of nucleolus, which is closely related to the biological alteration of cancer cell. The cancer prognosis thus can be accurately (limit of detection: 50 nM) and rapidly (5 min) assessed at subcellular organelle level from nucleolar characteristics, which are visualized and analyzed by the captured fluorescence images. Outstanding assessment performance endows the proposed technology with great potential for future clinical research.

One-step synthesis of red emission multifunctional carbon dots for label-free detection of berberine and curcumin and cell imaging

In this work, the red emission multifunctional carbon dots (R-CDs) were prepared via one-pot hydrothermal strategy of neutral red (NR) and ethylenediamine (EDA) for the label-free detection of berberine and curcumin, cell imaging, and fluorescent flexible film. The as-fabricated R-CDs not only possess good water dispersibility and excellent fluorescence stability, but also were successfully employed as a photoluminescent nanoprobe for label-free monitoring of berberine (BRH) and curcumin (Cur) based on dynamic quenching and internal filter effect (IFE), respectively. More importantly, as-proposed R-CDs displayed outstanding cellular permeability and lower cytotoxicity for cellular applications, which was consistent with the results of confocal fluorescence imaging and cell viability measurement of SMMC7721 cells. Thus, the multifunctional R-CDs may provide a rich tool library for biosensing and cellular imaging reagent applications. Interestingly, R-CDs were also used to manufacture R-CDs/PVA composites as fluorescent flexible films. To the best of our knowledge, this is the first demonstration of a label-free multifunctional fluorescent nanoprobe for berberine and curcumin based on red emission CDs.

Orange emissive carbon nanodots for fluorescent and colorimetric bimodal discrimination of Cu2+ and pH

We have facilely synthesized orange emissive carbon nanodots (O-CDs) via a hydrothermal method using citric acid and 5-aminosalicylic acid.

Facile and label-free fluorescence sensing of β-galactosidase activity by graphene quantum dots

β-Galactosidase (β-Gal), as a glycoside hydrolase, is closely associated with cell senescence and primary ovarian cancer. However, there is still lack of facile and rapid sensing approach to monitor the β-Gal activity. In this work, a label-free and convenient sensing strategy to detect β-Gal activity has been proposed based on fluorescent graphene quantum dots (GQDs). In the presence of β-Gal, 4-nitrophenyl-β-D-galactopyranoside (NPGal) can be hydrolyzed into 4-nitrophenol (4-NP), which serves as a good quencher to quench the fluorescence of GQDs. The quenching mechanism is proven to be inner filter effect (IFE). Due to the specificity of the enzymatic reaction, this sensing method displays excellent selectivity and high sensitivity. A broad dynamic range from 20 to 200 U L^-1 and a detection limit of 4.4 U L^-1 for the β-Gal assay are achieved. Compared with the previously reported methods, this sensing strategy only needs one fluorescent nanomaterial without any modification and avoids time-consuming handling steps. Therefore, the sensing strategy based on fluorescent GQDs offers great potential for the recognition of disease-correlated enzyme activity.