Nanoscopic Imaging of Nucleolar Stress Enabled by Protein-Mimicking Carbon Dots

Carbon dots as versatile nanomaterials in sensing and imaging: Efficiency and beyond

Carbon dots (CDs) have emerged as a versatile and promising carbon-based nanomaterial with exceptional optical properties, including tunable emission wavelengths, high quantum yield, and photostability. CDs are appropriate for various applications with many benefits, such as biocompatibility, low toxicity, and simplicity of surface modification. Thanks to their tunable optical properties and great sensitivity, CDs have been used in sensing as fluorescent probes for detecting pH, heavy metal ions, and other analytes. In addition, CDs have demonstrated potential as luminescence converters for white organic light-emitting diodes and light emitters in optoelectronic devices due to their superior optical qualities and exciton-independent emission. CDs have been used for drug administration and bioimaging in the biomedical field due to their biocompatibility, low cytotoxicity, and ease of functionalization. Additionally, due to their stability, efficient charge separation, and low recombination rate, CDs have shown interesting uses in energy systems, such as photocatalysis and energy conversion. This article highlights the growing possibilities and potential of CDs as adaptable nanomaterials in a variety of interdisciplinary areas related to sensing and imaging, at the same time addressing the major challenges involved in the current research and proposing scientific solutions to apply CDs in the development of a super smart society.

Self-Assembled DNA Nanospheres Driven by Carbon Dots for MicroRNAs Imaging in Tumor via Logic Circuit

DNA nanostructures with diverse biological functions have made significant advancements in biomedical applications. However, a universal strategy for the efficient production of DNA nanostructures is still lacking. In this work, a facile and mild method is presented for self-assembling polyethylenimine-modified carbon dots (PEI-CDs) and DNA into nanospheres called CANs at room temperature. This makes CANs universally applicable to multiple biological applications involving various types of DNA. Due to the ultra-small size and strong cationic charge of PEI-CDs, CANs exhibit a dense structure with high loading capacity for encapsulated DNA while providing excellent stability by protecting DNA from enzymatic hydrolysis. Additionally, Mg2+ is incorporated into CANs to form Mg@CANs which enriches the performance of CANs and enables subsequent biological imaging applications by providing exogenous Mg2+. Especially, a DNAzyme logic gate system that contains AND and OR Mg@CANs is constructed and successfully delivered to tumor cells in vitro and in vivo. They can be specifically activated by endogenic human apurinic/apyrimidinic endonuclease 1 and recognize the expression levels of miRNA-21 and miRNA-155 at tumor sites by logic biocomputing. A versatile pattern for delivery of diverse DNA and flexible logic circuits for multiple miRNAs imaging are developed.

Carbon Dots: Synthesis, Characterizations, and Recent Advancements in Biomedical, Optoelectronics, Sensing, and Catalysis Applications

Carbon nanodots (CNDs), a fascinating carbon-based nanomaterial (typical size 2-10 nm) owing to their superior optical properties, high biocompatibility, and cell penetrability, have tremendous applications in different interdisciplinary fields. Here, in this Review, we first explore the superiority of CNDs over other nanomaterials in the biomedical, optoelectronics, analytical sensing, and photocatalysis domains. Beginning with synthesis, characterization, and purification techniques, we even address fundamental questions surrounding CNDs such as emission origin and excitation-dependent behavior. Then we explore recent advancements in their applications, focusing on biological/biomedical uses like specific organelle bioimaging, drug/gene delivery, biosensing, and photothermal therapy. In optoelectronics, we cover CND-based solar cells, perovskite solar cells, and their role in LEDs and WLEDs. Analytical sensing applications include the detection of metals, hazardous chemicals, and proteins. In catalysis, we examine roles in photocatalysis, CO2 reduction, water splitting, stereospecific synthesis, and pollutant degradation. With this Review, we intend to further spark interest in CNDs and CND-based composites by highlighting their many benefits across a wide range of applications.

Blinking Carbon Dots as a Super-resolution Imaging Probe

Single-molecule localization microscopy (SMLM) emerges as a powerful approach for super-resolution imaging that provides unprecedented resolution at the nanometer length scale. However, the development of appropriate probes with specific photophysical traits and characteristics is crucial for this approach. This study demonstrates two different fluorescent carbon dots (CDs) derived from the same molecular precursor─one emitting in red and the other in green─as a SMLM-based super-resolution imaging probe for different applications with an average localization precision of 20 nm and a resolution of 60 nm. Both the CDs exhibit spontaneous blinking with high photon count and low duty cycle but with different blinking cycles. The red emissive CDs with a lower blinking cycle are ideal for quantitative analysis, whereas green emissive CDs with a higher blinking cycle are ideal for high-resolution imaging. We show that the difference in blinking features is linked to their chemical compositions, and the presence of much denser trap states in red emitting CDs is responsible for the reduction of its blinking cycle. This study shows that CDs can be designed as a potential probe for SMLM-based super-resolution imaging for diverse bioimaging applications.

Intrinsic Burst-Blinking Nanographenes for Super-Resolution Bioimaging

Single-molecule localization microscopy (SMLM) is a powerful technique to achieve super-resolution imaging beyond the diffraction limit. Although various types of blinking fluorophores are currently considered for SMLM, intrinsic blinking fluorophores remain rare at the single-molecule level. Here, we report the synthesis of nanographene-based intrinsic burst-blinking fluorophores for highly versatile SMLM. We image amyloid fibrils in air and in various pH solutions without any additive and lysosome dynamics in live mammalian cells under physiological conditions. In addition, the single-molecule labeling of nascent proteins in primary sensory neurons was achieved with azide-functionalized nanographenes via click chemistry. SMLM imaging reveals higher local translation at axonal branching with unprecedented detail, while the size of translation foci remained similar throughout the entire network. These various results demonstrate the potential of nanographene-based fluorophores to drastically expand the applicability of super-resolution imaging.

Carbon Dots-Types, Obtaining and Application in Biotechnology and Food Technology

Materials with a "nano" structure are increasingly used in medicine and biotechnology as drug delivery systems, bioimaging agents or biosensors in the monitoring of toxic substances, heavy metals and environmental variations. Furthermore, in the food industry, they have found applications as detectors of food adulteration, microbial contamination and even in packaging for monitoring product freshness. Carbon dots (CDs) as materials with broad as well as unprecedented possibilities could revolutionize the economy, if only their synthesis was based on low-cost natural sources. So far, a number of studies point to the positive possibilities of obtaining CDs from natural sources. This review describes the types of carbon dots and the most important methods of obtaining them. It also focuses on presenting the potential application of carbon dots in biotechnology and food technology.

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.

Progress in drug delivery and diagnostic applications of carbon dots: a systematic review

Carbon dots (CDs), which have particle size of less than 10 nm, are carbon-based nanomaterials that are used in a wide range of applications in the area of novel drug delivery in cancer, ocular diseases, infectious diseases, and brain disorders. CDs are biocompatible, eco-friendly, easy to synthesize, and less toxic with excellent chemical inertness, which makes them very good nanocarrier system to deliver multi-functional drugs effectively. A huge number of researchers worldwide are working on CDs-based drug delivery systems to evaluate their versatility and efficacy in the field of pharmaceuticals. As a result, there is a tremendous increase in our understanding of the physicochemical properties, diagnostic and drug delivery aspects of CDs, which consequently has led us to design and develop CDs-based theranostic system for the treatment of multiple disorders. In this review, we aim to summarize the advances in application of CDs as nanocarrier including gene delivery, vaccine delivery and antiviral delivery, that has been carried out in the last 5 years.

RNA-Targeting Carbon Dots for Live-Cell Imaging of Granule Dynamics

It is significant to monitor the different RNA granules dynamics and phase separation process inside cells under various stresses, for example, oxidative stress. The current small-molecule RNA probes work well only in fixed cells and usually encounter problems such as insufficient stability and biocompatibility, and thus a specific RNA-targeting fluorescent nanoprobe that can be used in the living cells is urgently desired. Here, the de novo design and microwave-assisted synthesis of a novel RNA-targeting, red-emissive carbon dots (named as M-CDs) are reported by choosing neutral red and levofloxacin as precursors. The as-synthesized M-CDs is water-soluble with a high fluorescence quantum yield of 22.83% and can selectively bind to RNA resulting in an enhanced red fluorescence. More interestingly, such an RNA-targeting, red-emissive M-CDs can be fast internalized into cells within 5 s and thus used for real-time imaging the dynamic process of intracellular stress granules under oxidative stress, revealing some characteristics of granules that have not been identified by previously reported RNA and protein biomarkers. This research paves a new pathway for visualizing bulk RNA dynamics and studying phase-separation behaviors in living cells by rational design of the fluorescent carbon dots in terms of structure and functionality.

Superior biocompatible carbon dots for dynamic fluorescence imaging of nucleoli in living cells

The nucleolus is a newly developed and promising target for cancer diagnosis and therapy, and its imaging is extremely significant for fundamental research and clinical applications. The unique feature, i.e., high resolution at the subcellular level, makes the fluorescence imaging method a powerful tool for nucleolus imaging. However, the fluorescence imaging of nucleoli in living cells is restricted by the limited availability of fluorescent agents with specific nucleolus-targeting capability and superior biocompatibility. Here, promising carbon dots (CDs) with intrinsic nucleolus-targeting capability were synthesized, characterized and employed for dynamic fluorescence imaging of nucleoli in living cells. The CDs exhibit a high fluorescence quantum yield of 0.2, excellent specificity and photostability, and superior biocompatibility, which were systematically demonstrated at the gene, cellular and animal levels and confirmed by their biological effects on embryonic development. All these features enabled CDs to light up the nucleoli for a long time with a high signal-to-noise ratio in living cells and monitor the nucleolar dynamics of malignant cells in camptothecin (CPT) based chemotherapy. Their excellent optical and biological features as well as general nucleolus-targeting capability endow CDs with great potential for future translational research.

Fluorescent Carbon Dots for Super-Resolution Microscopy

Conventional fluorescence microscopy is limited by the optical diffraction of light, which results in a spatial resolution of about half of the light's wavelength, approximately to 250-300 nm. The spatial resolution restricts the utilization of microscopes for studying subcellular structures. In order to improve the resolution and to shatter the diffraction limit, two general approaches were developed: a spatially patterned excitation method and a single-molecule localization strategy. The success of super-resolution imaging relies on bright and easily accessible fluorescent probes with special properties. Carbon dots, due to their unique properties, have been used for super-resolution imaging. Considering the importance and fast development of this field, this work focuses on the recent progress and applications of fluorescent carbon dots as probes for super-resolution imaging. The properties of carbon dots for super-resolution microscopy (SRM) are analyzed and discussed. The conclusions and outlook on this topic are also presented.

Near-Infrared Blinking Carbon Dots Designed for Quantitative Nanoscopy

Blinking carbon dots (CDs) have attracted attention as a probe for single molecule localization microscopy (SMLM), yet quantitative analysis is limited because of inept blinking and low signal-to-noise ratio (SNR). Here we report the design and synthesis of near-infrared (NIR) blinking CDs with a maximum emission of around 750 nm by weaving a nitrogen-doped aromatic backbone with surplus carboxyl groups on the surface. The NIR-CDs allow conjugation to monovalent antibody fragments for labeling and imaging of cellular receptors as well as afford increases of 52% in SNR and 33% in localization precision over visible CDs. Analysis of fluorescent bursts allows for accurate counting of cellular receptors at the nanoscale resolution. Using NIR-CDs-based SMLM, we demonstrate oligomerization and internalization of programmed cell death-ligand 1 by a small molecule inhibitor for checkpoint blockade. Our NIR-CDs can become a generally applicable probe for quantitative nanoscopy in chemistry and biology.

Carbon dot-based nanomaterials: a promising future nano-platform for targeting tumor-associated macrophages

The tumor microenvironment (TME) is the internal environment that tumors depend on for survival and development. Tumor-associated macrophages (TAMs), as an important part of the tumor microenvironment, which plays a crucial role in the occurrence, development, invasion and metastasis of various malignant tumors and has immunosuppressant ability. With the development of immunotherapy, eradicating cancer cells by activating the innate immune system has yielded encouraging results, however only a minority of patients show a lasting response. Therefore, in vivo imaging of dynamic TAMs is crucial in patient-tailored immunotherapy to identify patients who will benefit from immunotherapy, monitor efficacy after treatment, and identify alternative strategies for non-responders. Meanwhile, developing nanomedicines based on TAMs-related antitumor mechanisms to effectively inhibit tumor growth is expected to become a promising research field. Carbon dots (CDs), as an emerging member of the carbon material family, exhibit unexpected superiority in fluorescence imaging/sensing, such as near infrared imaging, photostability, biocompatibility and low toxicity. Their characteristics naturally integrate therapy and diagnosis, and when CDs are combined with targeted chemical/genetic/photodynamic/photothermal therapeutic moieties, they are good candidates for targeting TAMs. We concentrate our discussion on the current learn of TAMs and describe recent examples of macrophage modulation based on carbon dot-associated nanoparticles, emphasizing the advantages of their multifunctional platform and their potential for TAMs theranostics.

Nanoparticles for super-resolution microscopy: intracellular delivery and molecular targeting

Following an overview of the approaches and techniques used to acheive super-resolution microscopy, this review presents the advantages supplied by nanoparticle based probes for these applications. The various clases of nanoparticles that have been developed toward these goals are then critically described and these discussions are illustrated with a variety of examples from the recent literature.

Monitoring Stress Response Difference in Nucleolus Morphology and ATP Content Changes during Hyperthermia Cell Apoptosis with Plasmonic Fluorescent Nanoprobes

The nucleolus, as a main "cellular stress receptor", is the hub of the stress response driving cancer development and has great research value in the field of organelle-targeting photothermal therapy. However, there are few studies focused on monitoring nucleolar stress response and revealing how the energy metabolism of cells regulates the nucleolar stress response during photothermal therapy. Herein, by designing a nucleolus-targeting and ATP- and photothermal-responsive plasmonic fluorescent nanoprobe (AuNRs-CDs) based on gold nanorods (AuNRs) and fluorescent carbon quantum dots (CDs), we achieved real-time fluorescence imaging of nucleus morphology while monitoring changes of ATP content at the subcellular level. We found that the green fluorescence diminished at 5 min of photothermal therapy, and the nucleolus morphology began to shrink and became smaller in cancerous HepG2 cells. In contrast, there is no significant change of green fluorescence in the nucleolar region of normal HL-7702 cells. ATP content monitoring also showed similar results. Apparently, in response to photothermal stimuli, cancerous cells produce more ATP (energy) along with obvious change in nucleolus morphology and state compared to normal cells under the hyperthermia-induced cell apoptosis. The developed AuNRs-CDs as a nucleolus imaging nanoprobe and effective photothermal agent present promising applications for nucleolar stress studies and targeted photothermal therapy.

Carbon Dot Blinking Fingerprint Uncovers Native Membrane Receptor Organizations via Deep Learning

Oligomeric organization of G protein-coupled receptors is proposed to regulate receptor signaling and function, yet rapid and precise identification of the oligomeric status especially for native receptors on a cell membrane remains an outstanding challenge. By using blinking carbon dots (CDs), we now develop a deep learning (DL)-based blinking fingerprint recognition method, named deep-blinking fingerprint recognition (BFR), which allows automatic classification of CD-labeled receptor organizations on a cell membrane. This DL model integrates convolutional layers, long-short-term memory, and fully connected layers to extract time-dependent blinking features of CDs and is trained to a high accuracy (∼95%) for identifying receptor organizations. Using deep blinking fingerprint recognition, we found that CXCR4 mainly exists as 87.3% monomers, 12.4% dimers, and <1% higher-order oligomers on a HeLa cell membrane. We further demonstrate that the heterogeneous organizations can be regulated by various stimuli at different degrees. The receptor-binding ligands, agonist SDF-1α and antagonist AMD3100, can induce the dimerization of CXCR4 to 33.1 and 20.3%, respectively. In addition, cytochalasin D, which inhibits actin polymerization, similarly prompts significant dimerization of CXCR4 to 30.9%. The multi-pathway organization regulation will provide an insight for understanding the oligomerization mechanism of CXCR4 as well as for elucidating their physiological functions.