Rational Design of a Dual-Layered Metal–Organic Framework Nanostructure for Enhancing the Cell Imaging of Molecular Beacons

Electrochemiluminescence resonance energy transfer detection of HBsAg based on Co doped 3D porous luminol-based conjugates and quencher UiO-66-NH2@Au

An electrochemiluminescence (ECL) biosensor based on ECL resonance energy transfer (ECL-RET) was designed to sensitively detect hepatitis B virus surface antigen (HBsAg). In this ECL-RET system, luminol was employed as ECL donor, and gold nanoparticles functionalized zirconium organoskeleton (UiO-66-NH2@Au) was prepared and served as ECL acceptor. The UiO-66-NH2@Au possessed an ultraviolet-visible (UV-vis) absorption between 400 nm and 500 nm, and the absorption spectra overlapped with the ECL spectrum of luminol. Furthermore, Graphene oxide-poly(aniline-luminol)-cobalt nanoparticles conjugates (GO-PALu-Co) was prepared to optimize the ECL behavior through the catalysis of Cobalt nanoparticles and served as a stable 3D porous film to load capture probe primary antibody (Ab1). Based on the ECL-RET biosensing method, the UiO-66-NH2@Au-labeled Ab2 and target HBsAg could pair with primary antibody Ab1 to form sandwich-type structure, and the ECL signal of GO-PALu-Co was quenched. Under optimized experimental conditions, the ECL-RET analytical method represented eminent analytical performance for HBsAg detection with a wide linear relationship from 2.2 × 10-13 to 2.2 × 10-5 mg/mL, and a detection limit of 9 × 10-14 mg/mL (S/N = 3), with spiked sample recoveries ranging from 97.27 % to 102.73 %. The constructed sensor has good stability, reproducibility, and specificity. It can be used to detect HBsAg in human serum and has the potential to be used for the sensitive detection of other disease biomarkers.

Graphene oxide-functionalized molecular beacon for real-time interference-free detection of Ki-67 mRNA in living cells

Molecular beacons (MBs) based on hairpin-shaped oligonucleotides are captivating owing to their capability to enable effective real-time detection of cytosolic mRNA in living cells. However, DNase in the nucleus and lysosome could induce the degradation of oligonucleotides in MBs, leading to the generation of false-positive signals. Herein, a graphene oxide (GO) nanosheet was applied as a nanocarrier for MBs to greatly enhance the anti-interference of the easily designed nanoprobe. Advantageously, the absorption capacity of GO for MBs increased with the decrease in pH values, providing the MB-GO nanoprobe with the ability to detect the expression of cytosolic Ki-67 mRNA without interference from DNase Ⅱ in lysosomes. Moreover, the size of GO nanosheets was considerably higher than that of the nuclear pore complex (NPC), which prevented nanoprobes from transition through the NPCs, thereby avoiding the generation of false-positive signals in the nucleus. Altogether, the present work affords a convenient approach for the successful detection of Ki-67 mRNA expression in the cytosol without interference from DNase Ⅰ/Ⅱ in the nucleus/lysosome, which may be potentially further applied for the detection of other cytosolic RNAs.

Isolation and characterizations of multidrug-resistant human cancer cells by a biodegradable nano-sensor

Multidrug resistance (MDR) remains a significant challenge in cancer therapy, with inherent and acquired resistance distinct. While conventional drug selection processes enable the isolation of cancer cells with acquired multidrug resistance, identifying cancer cells with inherent drug resistance remains challenging. Herein, we proposed a molecular beacon (MB)-based strategy to identify and isolate the inherent MDR cancer cells. A lipid/PLGA core-shell nanoparticulate system (DNCP) was designed to deliver MB for intracellular MDR1 mRNA imaging. DNCP-MB - possess a surface potential of -8 mV and a size of 150 nm - demonstrated effective delivery of MB, remarkable selectivity towards the selected intracellular mRNA targets, and low cytotoxicity. Following DNCP transfection, fluorescence-activated cell sorting (FACS) was employed to differentiate MCF-7 cells into two distinct sub-populations: the Top 10 cells with a high level of MDR gene expression and the Bottom 10 cells with a low level of MDR gene expression, which represent inherent drug-resistant and non-drug-resistant cells, respectively. Intriguingly, we observed a positive correlation between elevated MDR1 mRNA expression and increased migration, enhanced proliferation rate, and tighter spheroid formation. Moreover, we conducted RNA sequencing analysis on the Top 10, Bottom 10, and MCF-7/ADR cells. The findings revealed a notable disparity in the gene ontology enrichment analysis of differentially expressed genes between the Top 10 and Bottom 10 cells when compared to the Bottom 10 and MCF-7/ADR cells. This novel approach provides a promising avenue for isolating inherent drug-resistant cells and holds significant potential in unraveling the mechanisms underlying inherent drug resistance.

A covalent organic framework-derived M1 macrophage mimic nanozyme for precise tumor-targeted imaging and NIR-II photothermal catalytic chemotherapy

Nanoprobes for efficient tumor-targeted imaging and therapy are urgently needed for clinical tumor theranostics. Herein, inspired by the heterogeneity of the tumor microenvironment, we report a covalent organic framework (COF)-derived biomimetic nanozyme for precise tumor-targeted imaging and NIR-II photothermal-catalysis-enhanced chemotherapy (PTCEC). Using a crystalline nanoscale COF as the precursor, a peroxidase-like porous N-doped carbonous nanozyme (PNC) was obtained, which was cloaked with an M1 macrophage cell membrane (M1m) to create a multifunctional biomimetic nanoprobe for tumor-targeted imaging and therapy. The M1m coating enabled the nanoprobe to target cancer cells and tumor tissues for highly efficient tumor imaging and drug delivery. The peroxidase-like activity of the PNC allowed for the conversion of intratumoral H2O2 into toxic ˙OH that synergized with its NIR-II photothermal effect to strengthen the chemotherapy. Therefore, highly efficient tumor-targeted imaging and NIR-II PTCEC were realized with an M1 macrophage mimic nanoprobe. This work provides a feasible tactic for a biomimetic theranostic nanoprobe and will inspire the development of new bioactive nanomaterials for clinical tumor theranostic applications.

Stimuli-responsive probes for amplification-based imaging of miRNAs in living cells

MicroRNAs (miRNAs) have emerged as important biomarkers in biomedicine and bioimaging due to their roles in various physiological and pathological processes. Real-time and in situ monitoring of dynamic fluctuation of miRNAs in living cells is crucial for understanding these processes. However, current miRNA imaging probes still have some limitations, including the lack of effective amplification methods for low abundance miRNAs bioanalysis and uncontrollable activation, leading to background signals and potential false-positive results. Therefore, researchers have been integrating activatable devices with miRNA amplification techniques to design stimuli-responsive nanoprobes for "on-demand" and precise imaging of miRNAs in living cells. In this review, we summarize recent advances of stimuli-responsive probes for the amplification-based imaging of miRNAs in living cells and discuss the future challenges and opportunities in this field, aiming to provide valuable insights for accurate disease diagnosis and monitoring.

Nanoporous Crystalline Materials for the Recognition and Applications of Nucleic Acids

Nucleic acid plays a crucial role in countless biological processes. Hence, there is great interest in its detection and analysis in various fields from chemistry, biology, to medicine. Nanoporous crystalline materials exhibit enormous potential as an effective platform for nucleic acid recognition and application. These materials have highly ordered and uniform pore structures, as well as adjustable surface chemistry and pore size, making them good carriers for nucleic acid extraction, detection, and delivery. In this review, the latest developments in nanoporous crystalline materials, including metal organic frameworks (MOFs), covalent organic frameworks (COFs), and supramolecular organic frameworks (SOFs) for nucleic acid recognition and applications are discussed. Different strategies for functionalizing these materials are explored to specifically identify nucleic acid targets. Their applications in selective separation and detection of nucleic acids are highlighted. They can also be used as DNA/RNA sensors, gene delivery agents, host DNAzymes, and in DNA-based computing. Other applications include catalysis, data storage, and biomimetics. The development of novel nanoporous crystalline materials with enhanced biocompatibility has opened up new avenues in the fields of nucleic acid analysis and therapy, paving the way for the development of sensitive, selective, and cost-effective diagnostic and therapeutic tools with widespread applications.

Light-Driven and Metal-Organic Framework Synergetic Loaded DNA Tetrahedral Amplifier for Exonuclease III-Powered All-in-One Biosensing and Chemotherapy in Live Biosystems

As a result of inaccurate biosensing and difficult synergetic loading, it is challenging to further impel DNA amplifiers to perform therapeutic application. Herein, we introduce some innovative solutions. First, a smart light-driven biosensing concept based on embedding nucleic acid modules with a simple photocleavage-linker is proposed. In this system, the target identification component is exposed on irradiation with ultraviolet light, thus avoiding an always-on biosensing response during biological delivery. Further, in addition to providing controlled spatiotemporal behavior and precise biosensing information, a metal-organic framework is used for the synergetic loading of doxorubicin in the internal pores, whereafter a rigid DNA tetrahedron-sustained exonuclease III-powered biosensing system is attached to prevent drug leakage and enhance resistance to enzymatic degradation. By selecting a next-generation breast cancer correlative noncoding microRNA biomarker (miRNA-21) as a model low-abundance analyte, a highly sensitive in vitro detection ability even allowing to distinguish single-base mismatching is demonstrated. Moreover, the all-in-one DNA amplifier shows excellent bioimaging competence and good chemotherapy efficacy in live biosystems. These findings will drive research into the use of DNA amplifiers in diagnosis and therapy integrated fields.

Monitoring Subtle Changes of Blood-Brain Barrier Permeability via Detection of MiRNA-155 in Brain Microvasculature

The changes of blood-brain barrier (BBB) permeability need to be sensitively reported when purposefully regulating the BBB or during some brain diseases. Currently available techniques for assessment of BBB integrity all suffer from limited sensitivity and only report serious BBB damage. Here, a targeted activatable nanoprobe is created to monitor subtle changes of BBB permeability by detecting the expression levels of BBB permeability-related miRNA (miRNA-155) in brain microvessel endothelial cells (BMECs). The probe is fabricated by coating the BMEC membrane on calcium phosphate (CaP)-mineralized metal-organic framework (MOF) nanoparticles loaded with hybridization chain reaction (HCR) probes. The coating of the BMEC membrane endows the nanoprobe with homologous targeting ability to BBB, and HCR probes released and escaped from lysosomes can be specifically lightened by miRNA-155. The activatable nanoprobe is able to monitor BBB permeability in inflammatory and AD mice. This work provides a new idea for highly sensitive evaluation of the BBB permeability, which has guiding significance in regulating BBB and formulating targeted therapeutic strategies.

Metal-Organic Frameworks Nanocarriers for Functional Nucleic Acid Delivery in Biomedical Applications

Metal-organic frameworks (MOFs), a distinctive funtionalmaterials which is constructed by various metal ions and organic molecules, have gradually attracted researchers' attention from they were founded. In the last decade, MOFs emerge as a biomedical material with potential applications due to their unique properties. However, the MOFs performed as nanocarriers for functional nucleic acid delivery in biomedical applications rarely summarized. In this review, we introduce recent developments of MOFs for nucleic acid delivery in various biologically relevant applications, with special emphasis on cancer therapy (including siRNA, ASO, DNAzyme, miRNA and CpG oligodeoxynucleotides), bioimaging, biosensors and separation of biomolecules. We expect the accomplishment of this review could benefit certain researchers in biomedical field to develop novel sophisticated nanocarriers for functional nucleic acid delivery based on the promising material of MOFs.

Functionalized photosensitive metal-organic framework as a theranostic nanoplatform for turn-on detection of MicroRNA and photodynamic therapy

Developing a theranostic platform integrating precise diagnostic and efficient treatment is significant but challenging. Here, we reported a new theranostic platform - hairpin probe - photosensitizing MOFs (HPMOF) composed of photosensitizing MOFs (PMOFs) and hairpin probes labeled with fluorophore and quencher, in which PMOF played the role of photosensitizer and nanocarrier of the hairpin probe. The HPMOF was covered with a layer of ZIF-8 to achieve the dual-layered nanotheranostics (HPMOF@ZIF-8). The HPMOF@ZIF-8 achieved high DNA loading capacity and intracellular delivery for tumor-related miRNA imaging. Moreover, HPMOF@ZIF-8 could generate reactive oxygen species with high efficiency, which induced cell apoptosis, leading to efficient photodynamic therapy. Due to the different expression of miRNA between normal cells and cancer cells, the HPMOF@ZIF-8 could recognize cancer cells through imaging of miRNA, leading to more accurate treatment of cancer, providing a promising theranostic nanoplatform.

ZIF-8 base-aptamer "gate-lock" probes enable the visualization of a cascade response between deoxynivalenol and cytochrome c inside living cells

Zeolitic imidazolate framework (ZIF-8) base-aptamer "gate-lock" biomaterial probes have been synthesized for monitoring intracellular deoxynivalenol (DON) and cytochrome c (cyt c) levels. The aptamer and organic fluorescent dye were regarded as a recognition element and a sensing element, respectively. In the presence of DON, the aptamers of DON and cyt c were specifically bound with the DON and induced cyt c, leading to the dissociation of aptamers from the porous surface of the probes. The gate was subsequently opened to release methylene blue (MB) and Rhodamine 6G (Rh6G), and their fluorescence (emission of MB at 700 nm and Rh6G at 550 nm) significantly recovered within 6 h. Cell imaging successfully monitored the exposure of DON and the biological process of cyt c discharge triggered by the activation of the DON-induced apoptosis pathway. In addition, the response between DON and cyt c was observed during the apoptosis process, which is of high significance for the comprehensive and systematic development of mycotoxins cytotoxicity.

Tetrazine bioorthogonal chemistry derived in vivo imaging

Bioorthogonal chemistry represents plenty of highly efficient and biocompatible reactions that proceed selectively and rapidly in biological situations without unexpected side reactions towards miscellaneous endogenous functional groups. Arise from the strict demands of physiological reactions, bioorthogonal chemical reactions are natively selective transformations that are rarely found in biological environments. Bioorthogonal chemistry has long been applied to tracking and real-time imaging of biomolecules in their physiological environments. Thereinto, tetrazine bioorthogonal reactions are particularly important and have increasing applications in these fields owing to their unique properties of easily controlled fluorescence or radiation off-on mechanism, which greatly facilitate the tracking of real signals without been disturbed by background. In this mini review, tetrazine bioorthogonal chemistry for in vivo imaging applications will be attentively appraised to raise some guidelines for prior tetrazine bioorthogonal chemical studies.

Metal-Organic Framework-Based Biosensor for Detecting Hydrogen Peroxide in Plants through Color-to-Thermal Signal Conversion

Plant biotic or abiotic stresses, such as pathogens, mechanical damage, or high temperature, can increase intracellular H₂O₂ concentration, damaging proteins, lipids, and DNA. Most current H₂O₂ detection methods require the separation or grinding of plant samples, inducing plant stresses, and the process is complicated and time-consuming. This paper constructed a metal-organic framework (MOF)-based biosensor for real-time, remote, and in situ detection of exogenous/endogenous H₂O₂ in plant organs through color-to-thermal signal conversion. By simply spraying horseradish peroxidase, 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), and the precursor of zeolite imidazolate frameworks-8 (ZIF-8), ZIF-8 biosensors were formed in situ on a plant root, petiole, or leaf. This biosensor could report sub-micromolar H₂O₂ in plants since the oxidation products, ABTS^• +, emitted heat when they absorbed energy from near-infrared (NIR) light. Due to the plant's low absorption in the NIR region, the ZIF-8 biosensor allowed for remote thermal sensing of H₂O₂ transport or biotic/abiotic stresses in plants with a high signal-to-noise ratio combining NIR laser and thermometer. Our biosensor can be used for the future development of plant sensors for monitoring plant signaling pathways and metabolism that are nondestructive, minimally invasive, and capable of real-time, in situ analysis.

pH-activated DNA nanomachine for miRNA-21 imaging to accurately identify cancer cell

MicroRNA (miRNA) imaging has been employed to distinguish cancer cells from normal cells by exploiting the overexpression of miRNA in cancer. Inspired by the acidic extracellular tumor microenvironment, we designed a pH-activated DNA nanomachine to enable the specific detection of cancer cells using miRNA imaging. The DNA nanomachine was engineered by assembling two hairpins (Y1 and Y2) onto the surface of a ZIF-8 metal-organic framework (MOF), which decomposed under acidic conditions to release the adsorbed DNA hairpin molecules in situ. The released hairpins were captured by the target miRNA-21 and underwent catalytic hairpin assembly amplification between Y1 and Y2. The detection limit for miRNA assays using the DNA nanomachine was determined to be 27 pM, which is low enough for sensitive detection in living cells. Living cell imaging of miRNA-21 further corroborated the application of the DNA nanomachine in the identification of cancer cell.

Advances in Nanoparticles for Effective Delivery of RNA Therapeutics

RNA therapeutics, including messenger RNA (mRNA) and small interfering RNA (siRNA), are genetic materials that mediate the translation of genetic direction from genes to induce or inhibit specific protein production. Although the interest in RNA therapeutics is rising globally, the absence of an effective delivery system is an obstacle to the clinical application of RNA therapeutics. Additionally, immunogenicity, short duration of protein expression, unwanted enzymatic degradation, and insufficient cellular uptake could limit the therapeutic efficacy of RNA therapeutics. In this regard, novel platforms based on nanoparticles are crucial for delivering RNAs to the targeted site to increase efficiency without toxicity. In this review, the most recent status of nanoparticles as RNA delivery vectors, with a focus on polymeric nanoparticles, peptide-derived nanoparticles, inorganic nanoparticles, and hybrid nanoparticles, is discussed. These nanoparticular platforms can be utilized for safe and effective RNA delivery to augment therapeutic effects. Ultimately, RNA therapeutics encapsulated in nanoparticle-based carriers will be used to treat many diseases and save lives.

DNA-Templated Bioorthogonal Reactions via Catalytic Hairpin Assembly for Precise RNA Imaging in Live Cells

There has been a significant interest in developing proximity-induced bioorthogonal reactions for nucleic acid detection and imaging, owing to their high specificity and tunable reaction kinetics. Herein, we reported the first design of a fluorogenic sensor by coupling a bioorthogonal reaction with a DNA cascade circuit for precise RNA imaging in live cells. Two DNA hairpin probes bearing tetrazines or vinyl ether caged fluorophores were designed and synthesized. Upon target mRNA triggering catalytic hairpin assembly, the chemical reaction partners were brought in a spatial proximity to yield high effective concentrations, which dramatically facilitated the bioorthogonal reaction efficiency to unmask the vinyl ether group to activate fluorescence. The proposed fluorogenic sensor was demonstrated to have a high signal-to-noise ratio up to ∼30 fold and enabled the sensitive detection of target mRNA with a detection limit of 4.6 pM. Importantly, the fluorogenic sensor presented low background signals in biological environments due to the unique "click to release" feature, avoiding false positive results caused by unspecific degradation. We also showed that the fluorogenic sensor could accurately image mRNA in live cells and distinguish the relative mRNA expression levels in both tumor and normal cells. Benefiting from these significant advantages, our method provides a useful tool for basic studies of bioorthogonal chemistry and early clinical diagnosis.

Advances in FePt-involved nano-system design and application for bioeffect and biosafety

The rapid development and wide application of nanomaterial-involved theranostic agents have drawn surging attention for improving the living standard of humankind and healthcare conditions. In this review, recent developments in the design, synthesis, biocompatibility evaluation and potential nanomedicine applications of FePt-involved nano-systems are summarized, especially for cancer theranostic and biological molecule detection. The in vivo multi-model imaging capability is discussed in detail, including magnetic resonance imaging and computed tomography. Furthermore, we highlight the significant achievements of various FePt-involved nanotherapeutics for cancer treatment, such as drug delivery, chemodynamic therapy, photodynamic therapy, radiotherapy and immunotherapy. In addition, a series of FePt-involved nanocomposites are also applied for biological molecule detection, such as H₂O₂, glucose and naked-eye detection of cancer cells. Ultimately, we also summarize the challenges and prospects of FePt-involved nano-systems in nanocatalytic medicine. This review is expected to give a general pattern for the development of FePt-involved nano-systems in the field of nanocatalytic medicine and analytical determination.

Metal-Organic Framework Nanoparticles Power DNAzyme Logic Circuits for Aberrant MicroRNA Imaging

At the molecular level, a large number of studies exist on the use of dynamic DNA molecular circuits for disease diagnosis and biomedicine. However, how to design programmable molecular circuit devices to autonomously and accurately diagnose multiple low-abundance biomolecules in complex cellular environments remains a challenge. Here, we constructed DNAzyme logic circuits for the analysis and imaging of multiple microRNAs in living cells using Cu/ZIF-8 NPs as a nanocarrier of the logic gate modules and the Cu²⁺ cofactor of the Cu²⁺-dependent DNAzyme. The logic gate modules of the logic operation system were adsorbed on the surface of Cu/ZIF-8 NPs via electrostatic interaction. After internalization, pH-responsive Cu/ZIF-8 NPs could efficiently release the logic gate modules and Cu²⁺, which allowed us to realize multiple logic computations initiated by endogenous miRNA, including one YES logic gate and two binary logic gates (OR and AND) in different living cells. Cu²⁺-DNAzyme logic circuits could quickly respond to multiple endogenous miRNAs in the complex cell environment, which also provided a new research method for the application of DNA biocomputing circuits in living cells.

Covalent Organic Framework-Derived Carbonous Nanoprobes for Cancer Cell Imaging

Covalent organic frameworks (COFs) have emerged as promising materials for biomedical applications, but their functions remain to be explored and the potential toxicity concerns should be resolved. Herein, it is presented that carbonization significantly enhances the fluorescence quenching efficiency and aqueous stability of nanoscale COFs. The probes prepared by physisorbing dye-labeled nucleic acid recognition sequences onto the carbonized COF nanoparticles (termed C-COF) were employed for cell imaging, which could effectively light up biomarkers (survivin and TK1 mRNA) in living cells. The C-COF has enhanced photothermal conversion capacity, indicating that the probes are also promising candidates for photothermal therapy. The potential toxicity concern from the aromatic rigid building units of COFs was detoured by carbonization. Overall, carbonization is a promising strategy for developing biocompatible and multifunctional COF-derived nanoprobes for biomedical applications. This work may inspire more versatile COF-derived nanoprobes for bioanalysis and nanomedicine.

Covalent Organic Framework-Based Spherical Nucleic Acid Probe with a Bonding Defect-Amplified Modification Strategy

Developing spherical nucleic acids with new structures holds great promise for nanomedicine and bioanalytical fields. Covalent organic frameworks (COFs) are emerging promising materials with unique properties for a wide range of applications. However, devising COF-based spherical nucleic acid is challenging because methods for the preparation of functionalized COFs are still limited. We report here a bonding defect-amplified modification (BDAM) strategy for the facile preparation of functionalized COFs. Poly(acrylic acid) was employed as the defect amplifier to modify the surface of COF nanoparticles by the formation of amide bonds with amino residues, which successfully converted and amplified the residues into abundant reactive carboxyl groups. Then, amino terminal-decorated hairpin DNA was densely grafted onto the surface of COF nanoparticles (NPs) to give rise to a spherical nucleic acid probe (SNAP). A series of experiments and characterizations proved the successful preparation of the COF-based SNAP, and its application in specifically lighting up RNA biomarkers in living cells for cancer diagnostic imaging was demonstrated. Therefore, the COF-based SNAP is a promising candidate for biomedical applications and the proposed BDAM represents a useful strategy for the preparation of functionalized COFs for diverse fields.

Covalent organic framework-engineered polydopamine nanoplatform for multimodal imaging-guided tumor photothermal-chemotherapy

A covalent organic framework-engineered polydopamine nanoplatform with improved drug loading capacity and reduced premature leakage has been developed for multimodal imaging-guided tumor-targeted photothermal-chemotherapy.