pH-Responsive Graphene Oxide-DNA Nanosystem for Live Cell Imaging and Detection

Advances on carbon nanomaterials and their applications in medical diagnosis and drug delivery

Carbon nanomaterials are indispensable due to their unique properties of high electrical conductivity, mechanical strength and thermal stability, which makes them important nanomaterials in biomedical applications and waste management. Limitations of conventional nanomaterials, such as limited surface area, difficulty in fine tuning electrical or thermal properties and poor dispersibility, calls for the development of advanced nanomaterials to overcome such limitations. Commonly, carbon nanomaterials were synthesized by chemical vapor deposition (CVD), laser ablation or arc discharge methods. The advancement in these techniques yielded monodispersed carbon nanotubes (CNTs) and allows p-type and n-type doping to enhance its electrical and catalytic activities. The functionalized CNTs showed exceptional mechanical, electrical and thermal conductivity (3500-5000 W/mK) properties. On the other hand, carbon quantum dots (CQDs) exhibit strong photoluminescence properties with high quantum yield. Carbon nanohorns are another fascinating type of nanomaterial that exhibit a unique structure with high surface area and excellent adsorption properties. These carbon nanomaterials could improve waste management by adsorbing pollutants from water and soil, enabling precise environmental monitoring, while enhancing wastewater treatment and drug delivery systems. Herein, we have discussed the potentials of all these carbon nanomaterials in the context of innovative waste management solutions, fostering cleaner environments and healthier ecosystems for diverse biomedical applications such as biosensing, drug delivery, and environmental monitoring.

Colorimetric and handheld pH meter dual-signal readout platform for E. coli detection based on a cascade reaction

A dual-signal readout has been designed detecting platform based on a cascade reaction for Escherichia coli (E. coli) detection by using colorimetric approach and a handheld pH meter. The immunoreaction was conducted using polydopamine@copper ferrite-Ag nanoparticles (PDA@CuFe₂O₄-Ag NP) and a glucose oxidase (GOD)-conjugated graphene oxide-gold nanosheet composite (GOD-GO/Au NS) to synthesize a sandwich complex mode between targets. Together with the formation of immune complexes, the GOD-GO/Au NS can catalyze glucose to produce gluconic acid and hydrogen peroxide (H₂O₂). The gluconic acid produced altered the pH of the detection solution. Since the PDA@CuFe₂O₄-Ag NP have good peroxidase-like activity, they can catalyze the oxidation of TMB to the blue product oxTMB once H₂O₂ is produced in the reaction system, and the absorbance change of oxTMB at 652 nm can be recorded using ultraviolet-visible (UV-Vis) spectroscopy. Interestingly, the PDA@CuFe₂O₄-Ag NP composites can consume the generated H₂O₂, and can create a reaction cycle that promotes glucose oxidation. Under optimal conditions, the proposed dual-channel signal platform is proportional to the logarithm of the E. coli concentration within a range of 10²-10⁷ cfu mL^-1. Additionally, the devised approach was successfully used to detect E. coli at the required levels in real samples. This dual-mode detection method notably enhances the accuracy and diversity of detection, and curbs the false negative and positive rates.

A label- and enzyme-free fluorescence assay based on thioflavin T–induced G-quadruplexes for the detection of telomerase activity

A label- and enzyme-free fluorescence assay based on thioflavin T–induced G-quadruplexes is developed to sensitively and specifically detect telomerase activity. Thioflavin T has a dual role as an efficient inducer and fluorescent probe, and the incorporation of thioflavin T into the thioflavin T–induced G-quadruplexes results in an intense fluorescence enhancement. In the presence of thioflavin T and K+, G-quadruplexes are formed by elongation of the telomerase substrate primer that is catalyzed by telomerase extracted from cancer cells. Thus, the telomerase activity in cancer cell extracts can be evaluated by measuring the thioflavin T fluorescence. More importantly, thioflavin T can specifically recognize and bind to G-quadruplexes, whereas it cannot recognize single- and double-stranded DNAs, which leads to the thioflavin T–based fluorescence assay exhibiting a reduced background and improved signal-to-noise ratio. As a result, the proposed assay has the linear range from 5 to 200 HeLa cells and the detection limit is 34 HeLa cells, which holds great potential for use in the detection of telomerase activity and the diagnosis of cancer.

Adsorption of DNA Oligonucleotides by Self-Assembled Metalloporphyrin Nanomaterials

Porphyrin assemblies have controllable morphology, high biocompatibility, and good optical properties and were widely used in biomedical diagnosis and treatment. With the development of DNA biotechnology, combining DNA with porphyrin assemblies can broaden the biological applications of porphyrins. Porphyrin assemblies can serve as nanocarriers for DNA, although the fundamental interactions between them are not well understood. In this work, zinc meso-tetra(4-pyridyl)porphyrin (ZnTPyP) assemblies were prepared in the presence of various surfactants and at different pH values, yielding a variety of aggregation forms. Among them, the hexagonal stacking form exposes more pyridine substituents, and the hydrogen bonding force between the substituents and the DNA bases allows the DNA to be quickly adsorbed on the surface of the assemblies. The effects of DNA sequence and length were systematically tested. In particular, the adsorption of duplex DNA was less efficient compared to the adsorption of single-stranded DNA. This fundamental study is useful for the further combination of DNA and porphyrin assemblies to prepare new functional hybrid nanomaterials.

Graphene Oxide-Based Stimuli-Responsive Platforms for Biomedical Applications

Graphene is a two-dimensional sp2 hybridized carbon material that has attracted tremendous attention for its stimuli-responsive applications, owing to its high surface area and excellent electrical, optical, thermal, and mechanical properties. The physicochemical properties of graphene can be tuned by surface functionalization. The biomedical field pays special attention to stimuli-responsive materials due to their responsive abilities under different conditions. Stimuli-responsive materials exhibit great potential in changing their behavior upon exposure to external or internal factors, such as pH, light, electric field, magnetic field, and temperature. Graphene-based materials, particularly graphene oxide (GO), have been widely used in stimuli-responsive applications due to their superior biocompatibility compared to other forms of graphene. GO has been commonly utilized in tissue engineering, bioimaging, biosensing, cancer therapy, and drug delivery. GO-based stimuli-responsive platforms for wound healing applications have not yet been fully explored. This review describes the effects of different stimuli-responsive factors, such as pH, light, temperature, and magnetic and electric fields on GO-based materials and their applications. The wound healing applications of GO-based materials is extensively discussed with cancer therapy and drug delivery.

Environmental and intercellular Pb2+ ions determination based on encapsulated DNAzyme in nanoscale metal-organic frameworks

With the merits of low cost, simple synthesis procedure, and high affinity for metal ions, deoxyribozyme (DNAzyme) have played important roles in metal ions detection. However, the intracellular applications of DNAzyme are limited because of enzymatic degradation and inefficient cellular uptake. To address these problems, GR-5 as model DNAzyme was encapsulated into zeolitic imidazolate frameworks-8 (ZIF-8) nanoparticles by biomimetic mineralization. The positively charged ZIF-8 with high DNAzyme loading capacity retained their ability to enter cells. Compared with free DNAzyme, the biomimetic mineralization synthesis method has greatly improved the stability of pristine DNAzyme. The as-synthesized DNAzyme@ZIF-8 composite exhibited good stability resisting DNase I, and was used as a sensitive fluorescent nanoprobe for Pb²⁺ determination and successfully achieved selective and sensitive determination for Pb²⁺ at λ_ex/λ_em = 494/522 nm in real samples. The linear range for the determination of Pb²⁺ is 50 to 500 nM. Moreover, the highly active DNAzyme delivered by ZIF-8 allows noninvasive imaging of Pb²⁺ measurement in living cells. This strategy will extend the suitability of functional nucleic acids for in vitro and in vivo bioanalysis and bioimaging. Graphical abstract.

Promoting DNA Adsorption by Acids and Polyvalent Cations: Beyond Charge Screening

Adsorbing DNA oligonucleotides onto nanoparticles is the first step in developing DNA-based biosensors, drug delivery systems, and smart materials. Since DNA is a polyanion, it is repelled by negatively charged nanoparticles, which constitute the majority of commonly used nanomaterials. Adding salt such as NaCl to screen charge repulsion is a standard method of promoting DNA adsorption. However, Na⁺ does not supply additional attractive forces. In addition, adding a high concentration of NaCl can cause the aggregation of nanomaterials. In this feature article, we mainly summarize the methods developed in our laboratory to promote DNA adsorption by lowering the pH and by adding polyvalent metal ions, especially transition-metal ions. Various materials including noble metals (gold, silver, and platinum), 2D materials (graphene oxide, MoS₂, WS₂, and MXene), polydopamine, and several metal oxides are discussed. In general, low pH can protonate DNA bases and nanoparticle surfaces, reducing charge repulsion and even leading to attraction, although DNA folding at low pH can sometimes be detrimental to adsorption. Polyvalent metal ions can bridge additional interactions to achieve otherwise impossible adsorption. On the basis of the current understanding, a few future research directions are proposed to further improve DNA adsorption.

Cytotoxicity and Immune Dysfunction of Dendritic Cells Caused by Graphene Oxide

Graphene, known as “black gold”, has important applications in various fields. In previous studies, it has been proved that graphene oxide (GO) which is a derivative of graphene has low toxicity. However, the immunotoxicity of GO has not been fully elucidated. In this work, we used DC2.4 cell line to investigate the in vitro immunotoxicity of two types of GO, mono-layer GO (mono-GO) and multi-layer GO (multi- GO). We found that mono-GO had less effect on cell viability than multi-GO, but both mono-GO and multi-GO significantly induced the generation of ROS in DC2.4 cells. Interestingly, mono-GO caused DC2.4 cells to aggregate, thus changed the cell morphology significantly. However, no similar influence occurred for multi-GO. In addition, the results showed that these two GOs obviously enhance the release of TNF-α by DC2.4 cells with and without LPS stimulation. GO did not affect the level of IL-6 released from DC2.4 cells, but multi-GO promoted the release of IL-6 while mono-GO inhibited the production of IL-6 when cells were in response to LPS stimulation. Whole-transcriptome sequencing analysis found some immune-related differentially expressed genes including H2-DMb1, Ncbp3, Oas2, Men1, Fas, Cd320, Cd244, and Tinagl1 which are engaged in the immune system process. These results suggested that both mono-GO and multi-GO are immunotoxic to DC2.4 cells, which provides important basis for subsequent biological and clinical medical applications.

Hydrophobic Interaction: A Promising Driving Force for the Biomedical Applications of Nucleic Acids

The comprehensive understanding and proper use of supramolecular interactions have become critical for the development of functional materials, and so is the biomedical application of nucleic acids (NAs). Relatively rare attention has been paid to hydrophobic interaction compared with hydrogen bonding and electrostatic interaction of NAs. However, hydrophobic interaction shows some unique properties, such as high tunability for application interest, minimal effect on NA functionality, and sensitivity to external stimuli. Therefore, the widespread use of hydrophobic interaction has promoted the evolution of NA-based biomaterials in higher-order self-assembly, drug/gene-delivery systems, and stimuli-responsive systems. Herein, the recent progress of NA-based biomaterials whose fabrications or properties are highly determined by hydrophobic interactions is summarized. 1) The hydrophobic interaction of NA itself comes from the accumulation of base-stacking forces, by which the NAs with certain base compositions and chain lengths show properties similar to thermal-responsive polymers. 2) In conjugation with hydrophobic molecules, NA amphiphiles show interesting self-assembly structures with unique properties in many new biosensing and therapeutic strategies. 3) The working-mechanisms of some NA-based complex materials are also dependent on hydrophobic interactions. Moreover, in recent attempts, NA amphiphiles have been applied in organizing macroscopic self-assembly of DNA origami and controlling the cell-cell interactions.

Nucleic-Acid Structures as Intracellular Probes for Live Cells

The chemical composition of cells at the molecular level determines their growth, differentiation, structure, and function. Probing this composition is powerful because it provides invaluable insight into chemical processes inside cells and in certain cases allows disease diagnosis based on molecular profiles. However, many techniques analyze fixed cells or lysates of bulk populations, in which information about dynamics and cellular heterogeneity is lost. Recently, nucleic-acid-based probes have emerged as a promising platform for the detection of a wide variety of intracellular analytes in live cells with single-cell resolution. Recent advances in this field are described and common strategies for probe design, types of targets that can be identified, current limitations, and future directions are discussed.

Well-Optimized Conjugated GO-DNA Nanosystem for Sensitive Ratiometric pH Detection in Live Cells

Intracellular pH is a vital parameter which can reflect the physiological process, and the detection of intracellular pH with a high signal-to-noise ratio (SNR) remains a challenge. Compared to pH biosensors based on a single-wavelength signal, it is much easier to obtain better sensitivity and higher SNR from the biosensors by two-wavelength ratiometric signals. In this study, we used DNA-grafted graphene oxide (GO) to ratiometrically detect intracellular pH ranging from basic to acidic. A high SNR with a 35-fold difference in the ratiometric output has been achieved through careful optimization: (1) A high DNA conjugation yield of 45% has been gained through utilizing the partial double-stranded assembly strategy. (2) Herring sperm DNA (HSD) plays an important role in improving the sensitivity of the nanosystem by purifying and passivating the surface of GO; therefore, the concentration of HSD has been optimized to pursue the most sensitive ratiometric response. Apart from the ultrahigh SNR, fabricated GO-AR-Cy5/IFO-Cy3 exhibited excellent stability and biocompatibility in biological environments. Further experiments demonstrated that the nanosystem worked well in live cells in response to pH changes. It is possible to distinguish small pH differences and realize quantitative detection based on ratiometric fluorescence imaging by laser scanning confocal microscope analysis, which makes the nanosystem a promising candidate for further biological study and clinical applications.

Fluorescein-Stabilized i-Motif DNA and Its Unfolding Leading to a Stronger Adsorption Affinity

Several previous studies have indicated that polydeoxycytidine (poly-C) DNA has an anomalously high affinity for different types of surfaces. It was hypothesized that the formation of an i-motif structure could be a factor responsible for this enhanced affinity, but this is against the notion that a folded molecule should have fewer interactions with a surface. Herein, the properties of poly-C DNA were examined in detail, focusing on the presence or absence of a FAM (carboxyfluorescein) label and its subsequent adsorption on graphene oxide. Fluorescence and CD spectroscopy studies indicated that FAM can stabilize an i-motif structure in C15 DNA. In particular, the fluorescence of FAM is drastically quenched when the DNA is folded. This structure is irreversibly unfolded upon heating. Furthermore, the unfolded structure has an even higher affinity for graphene oxide than the folded structure. Finally, a large portion of the folded C15 unfolds upon desorption from graphene oxide, and unfolding could happen upon adsorption or desorption of the DNA. This study provides a method to further enhance the adsorption stability of poly-C DNA and calls for care when investigating the potential effects of dye labels on DNA.

Dual Engineering Interface-Driven Complementary Graphene Oxide-Protein Dimer Supramolecular Architecture Enables Nucleus Imaging and Therapy

Seeking a versatile nanoplatform for multimodal nucleus imaging and therapy is a challenging task. General complementary bottom-up bionanotechnology for controlling a 3D supramolecular coassembly is proposed. The dual engineering interface proof-of-concept of the supramolecular architecture can be demonstrated via a genetically engineered protein dimer and plasmonically engineered graphene oxide (GO). Incorporation of anisotropic plasmonic nanoparticles as an intercalation layer among the GO 3D supramolecular architecture can provide covalent conjugation sites and simultaneously endow tunable optical properties of GO, ranging from the ultraviolet-to-near-infrared region. Interestingly, the precise design of a specific two-site mutation of the plasmid is favorable for giving an organized coassembly instead of random networks of GO, which contributes to giving continuous distinguishable enhanced Raman imaging for tracking cancer cells. Unexpectedly, penetration into the cell nucleus via the submicro 3D supramolecular coassembly exhibits an excellent nucleus therapeutic potential of cancer cells.

Graphene-Based Smart Platforms for Combined Cancer Therapy

The extensive research of graphene and its derivatives in biomedical applications during the past few years has witnessed its significance in the field of nanomedicine. Starting from simple drug delivery systems, the application of graphene and its derivatives has been extended to a versatile platform of multiple therapeutic modalities, including photothermal therapy, photodynamic therapy, magnetic hyperthermia therapy, and sonodynamic therapy. In addition to monotherapy, graphene-based materials are widely applied in combined therapies for enhanced anticancer activity and reduced side effects. In particular, graphene-based materials are often designed and fabricated as "smart" platforms for stimuli-responsive nanocarriers, whose therapeutic effects can be activated by the tumor microenvironment, such as acidic pH and elevated glutathione (termed as "endogenous stimuli"), or light, magnetic, or ultrasonic stimuli (termed as "exogenous stimuli"). Herein, the recent advances of smart graphene platforms for combined therapy applications are presented, starting with the principle for the design of graphene-based smart platforms in combined therapy applications. Next, recent advances of combined therapies contributed by graphene-based materials, including chemotherapy-based, photothermal-therapy-based, and ultrasound-therapy-based synergistic therapy, are outlined. In addition, current challenges and future prospects regarding this promising field are discussed.

An aptamer-based four-color fluorometic method for simultaneous determination and imaging of alpha-fetoprotein, vascular endothelial growth factor-165, carcinoembryonic antigen and human epidermal growth factor receptor 2 in living cells

The extraordinary fluorescence quenching capability of graphene oxide (GO) was coupled to the specific recognition capability of aptamers to design a four-color fluorescent nanoprobe for multiplexed detection and imaging of tumor-associated proteins in living cells. Specifically, alpha-fetoprotein (AFP), vascular endothelial growth factor-165 (VEGF₁₆₅), carcinoembryonic antigen (CEA), and human epidermal growth factor receptor 2 (HER2) were detected. Due to strong π interaction, the fluorescence of labeled aptamers is quenched by GO. Four fluorophore-labeled aptamers that bind the tumor-associated proteins were adsorbed on GO to form the four-color nanoprobe with quenched fluorescence. The nanoprobes were internalized into cells via endocytosis, where the aptamer/GO nanoprobes bind the intracellular tumor-associated proteins. The aptamer-protein complexes thus formed detach from GO, and fluorescence recovers. Each analyte has its typical color (AFP: blue; VEGF165: green; CEA: yellow; HER2: red). As a result, simultaneous detection and imaging of multiple tumor-associated proteins in living cells were achieved. This nanoprobe has a fast response and is highly specific and biocompatible. The linear ranges for AFP, VEGF₁₆₅, CEA, and HER2 are 0.8 nM-160 nM, 0.5 nM-100 nM, 1.0 nM-200 nM, and 1.2 nM-240 nM, respectively. Detection limits were 0.45 nM for AFP, 0.30 nM for VEGF₁₆₅, 0.62 nM for CEA, and 0.96 nM for HER2. The probe allows for a fast distinction between tumor cells and normal cells via imaging. Graphical abstract Schematic presentation of the development of a four-color fluorometic method based on aptamer and graphene oxide for simultaneous detection and imaging of alpha-fetoprotein, vascular endothelial growth factor-165, carcinoembryonic antigen and human epidermal growth factor receptor 2 in living cells.

A graphene oxide nanosensor enables the co-delivery of aptamer and peptide probes for fluorescence imaging of a cascade reaction in apoptotic signaling

Cytochrome c (Cyt c) and caspase-3 are the key mediators in apoptotic signaling. As is known to all, the release of Cyt c from mitochondria is a vital caspase activation pathway and defines the point of no-return in cell apoptosis. However, it has not been reported that any fluorescence imaging tools could allow simultaneous visualization of Cyt c translocation and caspase-3 activation in apoptotic cells. Here, we develop a sensitive nanosensor that holds the capability of imaging of the released Cyt c from the mitochondria and a caspase-3 activation cascade reaction in apoptotic signaling. The nanosensor is constructed by the assembly of a fluorophore (Cy5)-tagged DNA aptamer on graphene nanosheets that have been covalently immobilized with a FAM-labeled peptide. After a spatially selective delivery into the cytoplasm, the Cy5-tagged DNA aptamer assembled on the nanosensor can bind with Cyt c released from the mitochondria to the cytoplasm and dissociate from graphene, triggering a red fluorescence signal. In addition, the caspase-3 activated by the Cyt c released to the cytoplasm can cleave the FAM-labeled peptide and result in a green fluorescence output. The nanosensor exhibits rapid response, high sensitivity and selectivity for in vitro assays, and high contrast imaging of Cyt c and caspase-3 in living cells. It also provides the method for the study of the kinetic relationship between the Cyt c translocation and caspase-3 activation through simultaneous imaging of Cyt c and caspase-3. The developed nanosensor described here will be an efficient and potential platform for apoptosis research.

A common anchor facilitated GO-DNA nano-system for multiplex microRNA analysis in live cells

The design of a nano-system for the detection of intracellular microRNAs is challenging as it must fulfill complex requirements, i.e., it must have a high sensitivity to determine the dynamic expression level, a good reliability for multiplex and simultaneous detection, and a satisfactory biostability to work in biological environments. Instead of employing a commonly used physisorption or a full-conjugation strategy, here, a GO-DNA nano-system was developed under graft/base-pairing construction. The common anchor sequence was chemically grafted to GO to base-pair with various microRNA probes; and the hybridization with miRNAs drives the dyes on the probes to leave away from GO, resulting in "turned-on" fluorescence. This strategy not only simplifies the synthesis but also efficiently balances the loading yields of different probes. Moreover, the conjugation yield of GO with a base-paired hybrid has been improved by more than two-fold compared to that of the conjugation with a single strand. We demonstrated that base-paired DNA probes could be efficiently delivered into cells along with GO and are properly stabilized by the conjugated anchor sequence. The resultant GO-DNA nano-system exhibited high stability in a complex biological environment and good resistance to nucleases, and was able to accurately discriminate various miRNAs without cross-reaction. With all of these positive features, the GO-DNA nano-system can simultaneously detect three miRNAs and monitor their dynamic expression levels.