Designing in vivo active DNAzymes

Target-initiated autocatalytic and concatenated DNAzyme/CHA amplification cascades for highly sensitive fluorescent detection of TET1 dioxygenase

The sensitive detection of the dysregulated expression of ten-eleven translocation 1 (TET1) dioxygenase, a key DNA 5-methylcytosine (5 mC) oxidation regulator in the expression of developmental genes, is of significant importance for the diagnosis of various genetic diseases and cancers. This study describes the establishment of a highly sensitive fluorescent TET1 bioassay based on the 5 mC-modified/Zn2+-dependent DNAzyme-containing hairpin probe and the autocatalytic and concatenated DNAzyme/catalytic hairpin assembly (CHA) signal amplification cascades. TET1 target molecules specifically recognize and cut the 5 mC sites in the hairpin probes to release active DNAzyme sequences, which bind and cleave the double-stem-loop substrate strands to trigger multiple concatenated signal amplification recycling cycles with the presence of the fuel strands and two fluorescently quenched signal hairpins. These DNA reaction cascades thus result in the unfolding of lots of signal hairpins to substantially recover fluorescence for highly sensitive TET1 assay with a calculated detection limit of 6.9 fM. Additionally, such bioassay shows high selectivity toward TET1 and its real applicability has been successfully demonstrated for cancer cell lysate and human serum samples.

Nucleic Acid Drugs in Radiotherapy

Radiotherapy remains a cornerstone of cancer treatment, using high-energy radiation to induce DNA damage in tumor cells, leading to cell death. However, its efficacy is often hindered by challenges such as radiation resistance and side effects. As a powerful class of functional molecules, nucleic acid drugs (NADs) present a promising solution to these limitations. Engineered to target key pathways like DNA repair and tumor hypoxia, NADs can enhance radiotherapy sensitivity. NADs can also serve as delivery vehicles for radiotherapy agents such as radionuclides, improving targeting accuracy and minimizing side effects. This review explores the role of NADs in optimizing radiotherapy, highlighting their mechanisms, clinical applications, and synergies with radiotherapy, ultimately offering a promising strategy for improving patient outcomes in cancer therapy.

Chemical Engineering of DNAzyme for Effective Biosensing and Gene Therapy

RNA-cleaving DNAzymes are in vitro selected functional nucleic acids with inherent catalytic activities. Due to their unique properties, such as high specificity, substrate cleavage capability, and programmability, DNAzymes have emerged as powerful tools in the fields of analytical chemistry, chemical biology, and biomedicine. Nevertheless, the biological applications of DNAzymes are still impeded by several challenges, such as structural instability, compromised catalytic activity in biological environments and the lack of spatiotemporal control designs, which may result in false-positive signals, limited efficacy or non-specific activation associated with side effects. To address these challenges, various strategies have been explored to regulate DNAzyme activity through chemical modifications, enhancing their stability, selectivity, and functionality, thereby positioning them as ideal candidates for biological applications. In this review, a comprehensive overview of chemically modified DNAzymes is provided, discussing modification strategies and the effects of these modifications on DNAzymes. Specific examples of the use of chemically modified DNAzymes in biosensing and gene therapy are also presented and discussed. Finally, the current challenges in the field are addressed and offer perspectives on the potential direction for chemically modified DNAzymes.

Gene therapy for CNS disorders: modalities, delivery and translational challenges

Gene therapy is emerging as a powerful tool to modulate abnormal gene expression, a hallmark of most CNS disorders. The transformative potentials of recently approved gene therapies for the treatment of spinal muscular atrophy (SMA), amyotrophic lateral sclerosis (ALS) and active cerebral adrenoleukodystrophy are encouraging further development of this approach. However, most attempts to translate gene therapy to the clinic have failed to make it to market. There is an urgent need not only to tailor the genes that are targeted to the pathology of interest but to also address delivery challenges and thereby maximize the utility of genetic tools. In this Review, we provide an overview of gene therapy modalities for CNS diseases, emphasizing the interconnectedness of different delivery strategies and routes of administration. Important gaps in understanding that could accelerate the clinical translatability of CNS genetic interventions are addressed, and we present lessons learned from failed clinical trials that may guide the future development of gene therapies for the treatment and management of CNS disorders.

Tunable metal-organic frameworks assist in catalyzing DNAzymes with amplification platforms for biomedical applications

Various binding modes of tunable metal organic frameworks (MOFs) and functional DNAzymes (Dzs) synergistically catalyze the emergence of abundant functional nanoplatforms. Given their serial variability in formation, structural designability, and functional controllability, Dzs@MOFs tend to be excellent building blocks for the precise "intelligent" manufacture of functional materials. To present a clear outline of this new field, this review systematically summarizes the progress of Dz integration into MOFs (MOFs@Dzs) through different methods, including various surface infiltration, pore encapsulation, covalent binding, and biomimetic mineralization methods. Atomic-level and time-resolved catalytic mechanisms for biosensing and imaging are made possible by the complex interplay of the distinct molecular structure of Dzs@MOF, conformational flexibility, and dynamic regulation of metal ions. Exploiting the precision of DNAzymes, MOFs@Dzs constructed a combined nanotherapy platform to guide intracellular drug synthesis, photodynamic therapy, catalytic therapy, and immunotherapy to enhance gene therapy in different ways, solving the problems of intracellular delivery inefficiency and insufficient supply of cofactors. MOFs@Dzs nanostructures have become excellent candidates for biosensing, bioimaging, amplification delivery, and targeted cancer gene therapy while emphasizing major advancements and seminal endeavors in the fields of biosensing (nucleic acid, protein, enzyme activity, small molecules, and cancer cells), biological imaging, and targeted cancer gene delivery and gene therapy. Overall, based on the results demonstrated to date, we discuss the challenges that the emerging MOFs@Dzs might encounter in practical future applications and briefly look forward to their bright prospects in other fields.

Photoactivated DNA Nanodrugs Damage Mitochondria to Improve Gene Therapy for Reversing Chemoresistance

Multidrug resistance (MDR) is a major cause of chemotherapy failure in oncology, and gene therapy is an excellent measure to reverse MDR. However, conventional gene therapy only modulates the expression of MDR-associated proteins but hardly affects their existing function, thus limiting the efficiency of tumor treatment. Herein, we designed a photoactivated DNA nanodrug (MCD@TMPyP4@DOX) to improve tumor chemosensitivity through the downregulation of MDR-related genes and mitochondria-targeted photodynamic therapy (PDT). The self-assembled DNA nanodrug encodes the mucin 1 (MUC1) aptamer and the cytochrome C (CytC) aptamer to facilitate its selective targeting to the mitochondria in tumor cells; the encoded P-gp DNAzyme can specifically cleave the substrate and silence MDR1 mRNA with the help of Mg2+ cofactors. Under near-infrared (NIR) light irradiation, PDT generates reactive oxygen species (ROS) that precisely damage the mitochondria of tumor cells and break single-stranded DNA (ssDNA) to activate MCD@TMPyP4@DOX self-disassembly for release of DOX and DNAzyme. We have demonstrated that this multifunctional DNA nanodrug has high drug delivery capacity and biosafety. It enables downregulation of P-gp expression while reducing the ATP on which P-gp pumps out drugs, improving the latency of gene therapy and synergistically reducing DOX efflux to sensitize tumor chemotherapy. We envision that this gene-modulating DNA nanodrug based on damaging mitochondria is expected to provide an important perspective for sensitizing tumor chemotherapy.

DNAzyme Nanoconstruct-Integrated Autonomously-Adaptive Coatings Enhance Titanium-Implant Osteointegration by Cooperative Angiogenesis and Vessel Remodeling

Orthopedic implants have a high failure rate due to insufficient interfacial osseointegration, especially under osteoporotic conditions. Type H vessels are CD31+EMCN+ capillaries with crucial roles in mediating new bone formation, but their abundance in osteoporotic fracture site is highly limited. Herein, we report a nanoengineered composite coating to improve the in situ osseointegration of a Ti implant for osteoporotic fracture repair, which is realized through inhibiting the stimulator of interferon genes (STING) in endothelial cells (ECs) to stimulate type H vessel formation. Autonomously catalytic DNAzyme-ZnO nanoflowers (DNFzns) were prepared through rolling circle amplification (RCA) of STING mRNA-degrading DNAzymes, which were then integrated on the Ti surface and further sequentially complexed with thioketal-bridged polydopamine and naringenin (Ti/DNFzn/PDA-Nar). ECs and mesenchymal stem cells (MSCs) can be recruited to the implant surface by galvanotaxis, accounting for the negative charges of DNFzn/PDA-Nar, subsequently released Nar under reactive oxygen species (ROS) stimulation to upregulate endothelial nitric oxide synthase (eNOS) in recruited ECs, leading to enhanced local angiogenesis. Meanwhile, the coordinately released DNFzns would abolish STING expression in ECs to transform the newly formed vessels into Type H vessels, thus substantially promoting the osseointegration of Ti implants. This study provides application prospects for improving implant osteointegration for osteoporotic fracture treatment.

Triple signal amplification strategy for ultrasensitive in situ imaging of intracellular telomerase RNA

Abnormal upregulation of telomerase RNA (TR) is a hallmark event at various stages of tumor progression, providing a universal marker for early diagnosis of cancer. Here, we have developed a triple signal amplification strategy for in situ visualization of TR in living cells, which sequentially incorporated the target-initiated strand displacement circuit, multidirectional rolling circle amplification (RCA), and Mg²⁺ DNAzyme-mediated amplification. All oligonucleotide probes and cofactors were transfected into cells in one go, and then escaped from lysosomes successfully. Owing to the specific base pairing, the amplification cascades could only be triggered by TR and performed as programmed, resulting in a satisfactory signal-to-background ratio. Especially, the netlike DNA structure generated by RCA encapsulated high concentrations of DNAzyme and substrates (FQS) in a local region, thereby improving the reaction efficiency and kinetics of the third amplification cycle. Under optimal conditions, the proposed method exhibited ultrasensitive detection of TR mimic with a detection limit at pM level. Most importantly, after transfection with the proposed sensing platform, tumor cells can be easily distinguished from normal cells based on TR abundance-related fluorescence signal, providing a new insight into initial cancer screening.