Novel DNA nanoflower biosensing technologies towards next-generation molecular diagnostics

Commercial Strip-Inspired One-Pot CRISPR-Based Chip for Multiplexed Detection of Respiratory Viruses

The absence of sensitive, multiplexed, and point-of-care assays poses a critical obstacle in promptly responding to emerging human respiratory virus (HRV) pandemics. Herein, RECOGNIZER (re-building commercial pregnancy strips via large-size nanoflowers), an innovative one-pot CRISPR assay, is presented that employs commercially available strips to identify several types of HRVs. The superiority of the RECOGNIZER assay mainly relies on two aspects: (i) DNA nanoflowers possessing a high surface-to-volume ratio and well-defined surface allow for a considerable probe loading density and minimized non-specific interaction, achieving an impressive signal-to-noise proportion exceeding tenfold at 1 nM target. (ii) The design of the one-pot reaction, multi-channel chip, and custom-made app enables the rapid, sample-to-answer, and multiplexed analysis of four HRVs in 25 min. This assay demonstrates a sensitivity of 5.42 pM for synthetic SARS-CoV-2 RNA and 10 copies µL-1 for SARS-CoV-2 plasmids after pre-amplification. Finally, the proposed approach indicated 100% accuracy in 50 clinical swab samples, demonstrating the robust performance in distinguishing SARS-CoV-2 from other HRVs. The versatility and scalability of RECOGNIZER renders it a user-friendly platform for virus infection monitoring, offering significant potential for improving pandemic response efforts.

Copper ions coordination-promoted self-assembly of DNA nanoflowers as cascade catalytic nanoreactor for colorimetric biosensor

The controllable geometry and multifunctionality of DNA nano-bioreactors hold immense promise for disease diagnosis. Herein, a facile rolling circle amplification (RCA)-based crystallization method has been developed for highly efficient self-assembly of three-dimensional (3D) DNA nano-bioreactors, which show excellent cascade catalytic performance by confining bio-enzyme (glucose oxidase (GOx) used in this case) and copper ions (Cu2+) in DNA nanoflowers (DNFs) structure. The participation of Cu2+ during the self-assembly process not only endows the nano-bioreactors (designated as GOx/Cu@DNFs) with inspiring peroxidase-like activity but also greatly improves the assembly efficiency and yield via the effective coordination between Cu2+ and RCA-generated long concatemeric DNAs. The integration of GOx and Cu2+ in the constrained flower-like DNA nanomatrices makes for the efficient inter-catalyst communication, resulting in the striking enhancement of biocatalytic cascade activity. Based on the prepared nano-bioreactors, a colorimetric biosensor has been constructed for glucose detection, achieving a wide linear range (2-400 μM) and a low detection limit (0.45 μM). Furthermore, the proposed sensing strategy enables the accurate determination and discrimination of glucose levels in healthy and diabetic sera, delivering gratifying outcomes. Overall, the meticulously crafted cascade nano-bioreactors not only illuminate the design of multifunctional nanomaterials based on RCA, but also expand the conceptual framework of the universal analytical method for determining small molecules with catalytic reactions to generate H2O2.

Therapeutic targeting of the protein tyrosine kinase-7 in cancer: an overview

The protein tyrosine kinase-7 (PTK7) is an evolutionarily conserved transmembrane receptor that has emerged as a potential therapeutic target for human tumors. PTK7 is a pseudokinase that is involved in the modulation of the Wnt signaling pathway through interactions with other receptors. These interactions result in targeted gene activation that regulates cell polarity, migration, and proliferation during embryogenesis. Aside of this role during development, PTK7 has been shown as overexpressed in numerous cancers including colon carcinoma, leukemia, neuroblastoma, hepatoma, and ovarian cancer. The activity of PTK7 and the direct correlation with poor prognosis have fostered preclinical investigations and phase I clinical trials, aiming at inhibiting PTK7 and inducing antitumoral effects. In this review, we provide an exhaustive overview of the diverse approaches that use PTK7 as a new molecular target for cancer therapy in different tumor types. We discuss current therapies and future strategies including chimeric antigen receptor-T cells, antibody-drug conjugates, aptamers, based on up-to-date literature and ongoing research progress.

Transforming cancer detection and treatment with nanoflowers

Nanoflowers, an innovative class of nanoparticles with a distinctive flower-like structure, have garnered significant interest for their straightforward synthesis, remarkable stability, and heightened efficiency. Nanoflowers demonstrate versatile applications, serving as highly sensitive biosensors for rapidly and accurately detecting conditions such as diabetes, Parkinson's, Alzheimer's, and foodborne infections. Nanoflowers, with their intricate structure, show significant potential for targeted drug delivery and site-specific action, while also exhibiting versatility in applications such as enzyme purification, water purification from dyes and heavy metals, and gas sensing through materials like nickel oxide. This review also addresses the structural characteristics, surface modification, and operational mechanisms of nanoflowers. The nanoflowers play a crucial role in preventing premature drug leakage from nanocarriers. Additionally, the nanoflowers contribute to averting systemic toxicity and suboptimal therapy efficiency caused by hypoxia in the tumor microenvironment during chemotherapy and photodynamic therapy. This review entails the role of nanoflowers in cancer diagnosis and treatment. In the imminent future, the nanoflowers system is poised to revolutionize as a smart material, leveraging its exceptional surface-to-volume ratio to significantly augment adsorption efficiency across its intricate petals. This review delves into the merits and drawbacks of nanoflowers, exploring synthesis techniques, types, and their evolving applications in cancer.

Preparation of DNA nanoflower-modified capillary silica monoliths for chiral separation

Innovative chiral capillary silica monoliths (CSMs) were developed based on DNA nanoflowers (DNFs). Baseline separation of enantiomers such as atenolol, tyrosine, histidine, and nefopam was achieved by using DNF-modified CSMs, and the obtained resolution value was higher than 1.78. To further explore the effect of DNFs on enantioseparation, different types of chiral columns including DNA strand containing the complementary sequence of the template (DCT)-modified CSMs, DNF2-modified CSMs, and DNF3-modified CSMs were prepared as well. It was observed that DNF-modified CSMs displayed better chiral separation ability compared with DCT-based columns. The intra-day and inter-day repeatability of model analytes' retention time and resolution kept desirable relative standard deviation values of less than 8.28%. DNF2/DNF3-modified CSMs were able to achieve baseline separation of atenolol, propranolol, 2'-deoxyadenosine, and nefopam enantiomers. Molecular docking simulations were performed to investigate enantioselectivity mechanisms of DNA sequences for enantiomers. To indicate the successful construction of DNFs and DNF-modified CSMs, various charaterization approaches including scanning electron microscopy, agarose gel electrophoresis, dynamic light scattering analysis, electroosmotic flow, and Fourier-transform infrared spectroscopy were utilized. Moreover, the enantioseparation performance of DNF-modified CSMs was characterized in terms of sample volume, applied voltage, and buffer concentration. This work paves the way to applying DNF-based capillary electrochromatography microsystems for chiral separation.

Aptamer-Loop DNA Nanoflower Recognition and Multicolor Fluorescent Carbon Quantum Dots Labeling System for Multitarget Living Cell Imaging

Visualization of multiple targets in living cells is important for understanding complex biological processes, but it still faces difficulties, such as complex operation, difficulty in multiplexing, and expensive equipment. Here, we developed a nanoplatform integrating a nucleic acid aptamer and DNA nanotechnology for living cell imaging. Aptamer-based recognition probes (RPs) were synthesized through rolling circle amplification, which were further self-assembled into DNA nanoflowers encapsulated by an aptamer loop. The signal probes (SPs) were obtained by conjugation of multicolor emission carbon quantum dots with oligonucleotides complementary to RPs. Through base pairing, RPs and SPs were hybridized to generate aptamer sgc8-, AS1411-, and Apt-based imaging systems. They were used for individual/simultaneous imaging of cellular membrane protein PTK7, nucleolin, and adenosine triphosphate (ATP) molecules. Fluorescence imaging and intensity analysis showed that the living cell imaging system can not only specifically recognize and efficiently bind their respective targets but also provide a 5-10-fold signal amplification. Cell-cycle-dependent distribution of nucleolin and concentration-dependent fluorescence intensity of ATP demonstrated the utility of the system for tracking changes in cellular status. Overall, this system shows the potential to be a simple, low-cost, highly selective, and sensitive living cell imaging platform.

Nano revolution of DNA nanostructures redefining cancer therapeutics-A comprehensive review

DNA nanostructures are a promising tool in cancer treatment, offering an innovative way to improve the effectiveness of therapies. These nanostructures can be made solely from DNA or combined with other materials to overcome the limitations of traditional single-drug treatments. There is growing interest in developing nanosystems capable of delivering multiple drugs simultaneously, addressing challenges such as drug resistance. Engineered DNA nanostructures are designed to precisely deliver different drugs to specific locations, enhancing therapeutic effects. By attaching targeting molecules, these nanostructures can recognize and bind to cancer cells, increasing treatment precision. This approach offers tailored solutions for targeted drug delivery, enabling the delivery of multiple drugs in a coordinated manner. This review explores the advancements and applications of DNA nanostructures in cancer treatment, with a focus on targeted drug delivery and multi-drug therapy. It discusses the benefits and current limitations of nanoscale formulations in cancer therapy, categorizing DNA nanostructures into pure forms and hybrid versions optimized for drug delivery. Furthermore, the review examines ongoing research efforts and translational possibilities, along with challenges in clinical integration. By highlighting the advancements in DNA nanostructures, this review aims to underscore their potential in improving cancer treatment outcomes.

Multi-modal nanoprobe-enabled biosensing platforms: a critical review

Nanomaterials show great potential for applications in biosensing due to their unique physical, chemical, and biological properties. However, the single-modal signal sensing mechanism greatly limits the development of single-modal nanoprobes and their related sensors. Multi-modal nanoprobes can realize the output of fluorescence, colorimetric, electrochemical, and magnetic signals through composite nanomaterials, which can effectively compensate for the defects of single-modal nanoprobes. Following the multi-modal nanoprobes, multi-modal biosensors break through the performance limitation of the current single-modal signal and realize multi-modal signal reading. Herein, the current status and classification of multi-modal nanoprobes are provided. Moreover, the multi-modal signal sensing mechanisms and the working principle of multi-modal biosensing platforms are discussed in detail. We also focus on the applications in pharmaceutical detection, food and environmental fields. Finally, we highlight this field's challenges and development prospects to create potential enlightenment.

Investigation of the Impact of Hydrogen Bonding Degree in Long Single-Stranded DNA (ssDNA) Generated with Dual Rolling Circle Amplification (RCA) on the Preparation and Performance of DNA Hydrogels

DNA hydrogels have gained significant attention in recent years as one of the most promising functional polymer materials. To broaden their applications, it is critical to develop efficient methods for the preparation of bulk-scale DNA hydrogels with adjustable mechanical properties. Herein, we introduce a straightforward and efficient molecular design approach to producing physically pure DNA hydrogel and controlling its mechanical properties by adjusting the degree of hydrogen bonding in ultralong single-stranded DNA (ssDNA) precursors, which were generated using a dual rolling circle amplification (RCA)-based strategy. The effect of hydrogen bonding degree on the performance of DNA hydrogels was thoroughly investigated by analyzing the preparation process, morphology, rheology, microstructure, and entrapment efficiency of the hydrogels for Au nanoparticles (AuNPs)-BSA. Our results demonstrate that DNA hydrogels can be formed at 25 °C with simple vortex mixing in less than 10 s. The experimental results also indicate that a higher degree of hydrogen bonding in the precursor DNA resulted in stronger internal interaction forces, a more complex internal network of the hydrogel, a denser hydrogel, improved mechanical properties, and enhanced entrapment efficiency. This study intuitively demonstrates the effect of hydrogen bonding on the preparation and properties of DNA hydrogels. The method and results presented in this study are of great significance for improving the synthesis efficiency and economy of DNA hydrogels, enhancing and adjusting the overall quality and performance of the hydrogel, and expanding the application field of DNA hydrogels.

A bacterial enzyme may correct 2-HG accumulation in human cancers

A significant proportion of lower-grade glioma as well as many other types of human cancers are associated with neomorphic mutations in IDH1/2 genes (mIDH1/2). These mutations lead to an aberrant accumulation of 2-hydroxyglutarate (2-HG). Interestingly, even cancers without mIDH1/2 can exhibit increased levels of 2-HG due to factors like hypoxia and extracellular acidity. Mounting evidence demonstrates that 2-HG competitively inhibits α-ketoglutarate dependent enzymes, such as JmjC-domain-containing histone demethylases (JHDMs), ten-eleven translocation enzymes (TETs), and various dioxygenases (e.g., RNA m6A demethylases and prolyl hydroxylases). Consequently, the hypermethylation of DNA, RNA, and histones, and the abnormal activities of hypoxia-inducible factors (HIFs) have profound impacts on the establishment of cancer metabolism and microenvironment, which promote tumor progression. This connection between the oncometabolite 2-HG and glioma holds crucial implications for treatments targeting this disease. Here, I hypothesize that an ectopic introduction of a bacterial 2-hydroxyglutarate synthase (2-HG synthase) enzyme into cancer cells with 2-HG accumulation could serve as a promising enzyme therapy for glioma and other types of cancers. While absent in human metabolism, 2-HG synthase in bacterial species catalyzes the conversion of 2-HG into propionyl-CoA and glyoxylate, two metabolites that potentially possess anti-tumor effects. For a broad spectrum of human cancers with 2-HG accumulation, 2-HG synthase-based enzyme therapy holds the potential to not only correct 2-HG induced cancer metabolism but also transform an oncometabolite into metabolic challenges within cancer cells.

A colorimetric and photothermal dual-mode biosensing platform based on nanozyme-functionalized flower-like DNA structures for tumor-derived exosome detection

Tumor-derived exosomes can be served as a kind of promising biomarkers for early diagnosis of cancers. Herein, a colorimetric/photothermal dual-mode exosomes sensing platform is developed for human breast cancer cell (MCF-7)-derived exosomes based on encapsulation of 3,3',5,5'-tetramethylbenzidine-loaded graphene quantum dot nanozymes (TMB-GQDzymes) into DNA flowers (DFs) via rolling circle amplification (RCA). To achieve specific detection, EpCAM aptamer for MCF-7 cell-derived exosomes is immobilized on the well plate, while the complementary sequence of another CD63 aptamer is designed into the circular template to obtain abundant capture probes. Benefitting from the dual-aptamer recognition strategy, a sandwich structure of EpCAM aptamer/exosomes/TMB-GQDzymes@DFs is formed, in which the GQDzymes can catalyze the oxidation of TMB in the presence of H₂O₂. The resulting products of TMB oxidation (oxTMB) can induce not only the absorption changes but also a near-infrared (NIR) laser-driven photothermal effect, achieving dual-mode detection of exosomes with the limit of detection (LOD) of 1027 particles/μL (colorimetry) and 2170 particles/μL (photothermal detection), respectively. In addition, this sensing platform has demonstrated excellent performance to well distinguish breast cancer patients from healthy individuals in serum samples analysis. Overall, the proposed dual-readout biosensor opens promising prospects for exosome detection in biological study and clinical applications.