Oncolytic Hairpin DNA Pair: Selective Cytotoxic Inducer through MicroRNA-Triggered DNA Self-Assembly

A DNA tetrahedron-based light-controlled intramolecular CHA for spatiotemporal imaging of miRNA in living cells with high sensitivity and imaging contrast

miRNA is an effective disease diagnostic biomarker. Developing efficient miRNA in living cells analysis methods, holds significant importance for disease diagnosis and understanding disease progression. Strategies combining DNA nanostructures and enzyme-free amplification have been developed for highly sensitive and rapid imaging of miRNA. However, due to nonspecific amplification of enzyme-free amplification inherent in the probe assembly process and during transfection, these strategies suffer from significant background signals and reduced sensitivity, limiting their further application. To overcome these limitations, we have developed a DNA tetrahedral-based and photocontrolled intramolecular CHA strategy (TCHA-P) to achieve spatiotemporal, highly sensitive, and accurate imaging of miRNA in living cells. In this strategy, the DNA tetrahedron not only serves as a transfection vector but also enhances the local concentration of reactant probes, boosting the reaction kinetics and sensitivity of CHA. Additionally, the light-controlled group (PC-linker) can trigger CHA at selected times and locations, enhancing the spatiotemporal precision of miRNA imaging and ensuring high sensitivity and accuracy by eliminating nonspecific amplification during the assembly and transfection processes. Using miR-10b as a proof-of-concept model, the proposed strategy demonstrated higher signal-to-noise ratio compared to traditional CHA, with a detection limit of 28 pM. Living cell imaging experiments showed that the strategy could effectively differentiate the expression of miR-10b between normal breast cells and breast cancer cells, providing high imaging contrast. The strategy holds promise for broadening the path of nucleic acid amplification-based imaging and is expected to become an effective tool in nucleic acid-based disease diagnosis, treatment, and drug development.

Dna-based nanostructures for tumor microenvironment-responsive drug delivery

DNA nanostructures, with sequence programmability, biocompatibility, and structural versatility, have emerged as promising tools for biomedical applications, particularly in targeted drug delivery and therapeutic interventions. The tumor microenvironment (TME) characterized by dysregulated pH gradients, elevated glutathione (GSH), hypoxia, adenosine triphosphate (ATP) abundance, and aberrant enzymatic activity, presenting significant challenges for conventional therapies. DNA-based nanostructure enables precise control over drug-loading efficiency, tumor-targeting specificity, and spatiotemporal release mechanisms makes them ideal for tumor-target drug delivery. In this review, we highlight recent advances in versatile TME-responsive DNA-based nanostructures for precise therapeutic drug delivery. First, we discuss the fundamental design principles governing the structural configuration and functional integration of DNA nanostructures in TME-responsive drug delivery. Next, we summarize the mechanisms by which TME characteristics, including pH gradients, glutathione (GSH), adenosine triphosphate (ATP), enzymatic activity, and multiple stimuli, regulate the targeting and controlled release of therapeutic payloads in DNA-based nanostructures. Finally, this review provides an outlook on future research directions aim at further optimizing the designability of DNA nanostructure-based drug delivery systems, underscoring the necessity of interdisciplinary collaboration. It is expected that these principles facilitate the future development of next-generation DNA nanostructure-based drugs with smart, precise, safe, and potent therapeutic capabilities.

Harnessing Nanomaterials for Enhanced DNA-Based Biosensing and Therapeutic Performance

The integration of nanomaterials with DNA-based systems has emerged as a transformative approach in biosensing and therapeutic applications. Unique features of DNA, like its programmability and specificity, complement the diverse functions of nanomaterials, leading to the creation of advanced systems for detecting biomarkers and delivering treatments. Here, we review the developments in DNA-nanomaterial conjugates, emphasizing their enhanced functionalities and potential across various biomedical applications. We first discuss the methodologies for synthesizing these conjugates, distinguishing between covalent and non-covalent interactions. We then categorize DNA-nanomaterials conjugates based on the properties of the DNA and nanomaterials involved, respectively. DNA probes are classified by their application into biosensing or therapeutic uses, and, several nanomaterials are highlighted by their recent progress in living biological. Finally, we discuss the current challenges and future prospects in this field, anticipating that significant progress in DNA-nanomaterial conjugates will greatly enhance precision medicine.

Amplified Production of a DNA Decoy Catalyzed by Intracellular MicroRNA

DNA decoys inhibit cellular transcription factors and are expected to be among the nucleic acid drugs used to downregulate the transcription process. However, spatially controlling the on/off efficacy of DNA decoys to avoid side effects on normal cells is challenging. To reduce undesired decoy function in normal cells, we adopted catalytic hairpin assembly (CHA) to produce a DNA duplex from a hairpin DNA pair in response to a specific microRNA (miRNA). We designed the DNA hairpin pairs to form a DNA decoy that binds to nuclear factor kappa B (NF-κB), whose overexpression is related to many diseases, including cancer. The transformation of the DNA hairpin pair to the NF-κB DNA decoy was catalyzed by miR-21, which is expressed in various types of cancers. Intracellular CHA progression and the inhibitory effect against NF-κB were observed only in miR-21 overexpressing cancer cells. The intracellular miR-21-catalyzed production of the NF-κB DNA decoy has the potential to reduce side effects on normal cells, thereby strengthening the therapeutic profile of the CHA-decoy system. The ability to customize the combination of catalytic miRNA and target transcription factors would allow our technology to serve as a "personalized drug discovery system" for a variety of challenging diseases, including cancer.

Tandem-Controlled Dynamic DNA Assembly Enables Temporally-Selective Orthogonal Regulation of cGAS-STING Stimulation

Despite advances in the controlled reconfiguration of DNA structures for biological applications, the dearth of strategies that allow for orthogonal regulation of immune pathways remains a challenge. Here, we report for the first time an endogenous and exogenous tandem-regulated DNA assembly strategy that enables orthogonally controlled stimulation of the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway. A DNA motif containing two palindromic sequences is engineered with an abasic site (AP)-connected blocking sequence to inhibit its self-assembly function, while apurinic/apyrimidinic endonuclease 1 (APE1)-triggered enzymatic cleavage of the AP site enables the reconfiguration and self-assembly of DNA motif into long double-stranded structures, thus realizing allosteric activation of the catalytic activity of cGAS to produce 2'3'-cyclic-GMP-AMP for STING stimulation. Importantly, we demonstrate that APE1-regulated DNA assembly allows for cell-selective activation of cGAS-STING signaling. Furthermore, by re-engineering the DNA motif with a photocleavable group, enzyme-triggered DNA assembly allows the cGAS-STING stimulation to operate (switched "ON"), whereas light-mediated fragmentation of the double-stranded DNA enables termination of such stimulation (switched "OFF"), thereby achieving orthogonal control over immune regulation. This work highlights an endogenous and exogenous tandem regulated strategy to modulate the cGAS-STING pathway in an orthogonally controlled manner.

MicroRNA-Triggered Programmable DNA-Encoded Pre-PROTACs for Cell-Selective and Controlled Protein Degradation

Proteolysis-targeting chimeras (PROTACs) have accelerated drug development; however, some challenges still exist owing to their lack of tumor selectivity and on-demand protein degradation. Here, we developed a miRNA-initiated assembled pre-PROTAC (miRiaTAC) platform that enables the on-demand activation and termination of target degradation in a cell type-specific manner. Using miRNA-21 as a model, we engineered DNA hairpins labeled with JQ-1 and pomalidomide and facilitated the modular assembly of DNA-encoded pre-PROTACs through a hybridization chain reaction. This configuration promoted the selective polyubiquitination and degradation of BRD4 upon miR-21 initiation, highlighting significant tumor selectivity and minimal systemic toxicity. Furthermore, the platform incorporates photolabile groups, enabling the precise optical control of pre-PROTACs during DNA assembly/disassembly, mitigating the risk of excessive protein degradation. Additionally, by introducing a secondary ligand targeting CDK6, these pre-PROTACs were used as a modular scaffold for the programmable assembly of active miRiaTACs containing two different warheads in exact stoichiometry, enabling orthogonal multitarget degradation. The integration of near-infrared light-mediated photodynamic therapy through an upconversion nanosystem further enhanced the efficacy of the platform with potent in vivo anticancer activity. We anticipate that miRiaTAC represents a significant intersection between dynamic DNA nanotechnology and PROTAC, potentially expanding the versatility of PROTAC toolkit for cancer therapy.

Local treatment of HVJ-E with T cell costimulatory molecule stimulation elicits systemic anti-tumor effects

The tumor-infiltrating lymphocyte (TIL) is a crucial factor in controlling tumor growth. A therapeutic method activating TIL is desired for treating patients with metastatic tumors. Here, we show that treating a local tumor with a combination therapy of UV-irradiated hemagglutinating virus of Japan envelope (HVJ-E) plus agonist antibodies, including OX40, against T cell costimulatory molecules induces systemic anti-tumor effects in a T cell-dependent manner in multiple cancer cell lines. Transcriptome and T cell receptor repertoire analyses revealed that HVJ-E + anti-OX40 antibody treatment activates CD4 and CD8 T cells and promotes T cell trafficking between tumors. These systemic anti-tumor effects required an association between Nkg2d and Nkg2d ligands. Our findings provide insights into how systemic anti-tumor effects are induced and may help the development of therapeutic strategies for eliciting such effects.

Investigation and Regulation of DNA Nanostructures on Activating cGAS-STING Signaling

DNA nanostructures have shown great potential in biomedical fields. However, the immune responses, especially the activation of the cGAS-STING signaling (A-cGSs), induced by DNA nanostructures, remain incompletely understood. Here, the ability of various DNA nanostructures from double-stranded DNA (dsDNA), single-stranded tiles (SSTs) to DNA origami is investigated on A-cGSs. Unlike natural dsDNA which triggers potent A-cGSs, the structural interconnectivity of various DNA configurations can substantially reduce the occurrence of A-cGSs, irrespective of their form, dimensions, and conformation. However, wireframe DNA nanostructures can activate the cGAS-STING signaling, suggesting that decreasing A-cGSs is dsDNA compactness-dependent. Based on this, a reconfigurable DNA Origami Domino Array (DODA) is used to systematically interrogate how dsDNA influences the A-cGSs and demonstrates that the length, number, and space of dsDNA array coordinately influence the activation level of cGAS-STING signaling, realizing a regulation of innate immune response. The above data and findings enhance the understanding of how DNA nanostructures affect cellular innate immune responses and new insights into the modulation of innate immune responses by DNA nanomedicine.

Nucleic Acid Materials-Mediated Innate Immune Activation for Cancer Immunotherapy

Abnormally localized nucleic acids (NAs) are considered as pathogen associated molecular patterns (PAMPs) in innate immunity. They are recognized by NAs-specific pattern recognition receptors (PRRs), leading to the activation of associated signaling pathways and subsequent production of type I interferons (IFNs) and pro-inflammatory cytokines, which further trigger the adaptive immunity. Notably, NAs-mediated innate immune activation is highly dependent on the conformation changes, especially the aggregation of PRRs. Evidence indicates that the characteristics of NAs including their length, concentration and even spatial structure play essential roles in inducing the aggregation of PRRs. Therefore, nucleic acid materials (NAMs) with high valency of NAs and high-order structures hold great potential for activating innate and adaptive immunity, making them promising candidates for cancer immunotherapy. In recent years, a variety of NAMs have been developed and have demonstrated significant efficacy in achieving satisfactory anti-tumor immunity in multiple mouse models, exhibiting huge potential for clinical application in cancer treatment. This review aims to discuss the mechanisms of NAMs-mediated innate immune response, and summarize their applications in cancer immunotherapy.

RNA Oncological Therapeutics: Intracellular Hairpin RNA Assembly Enables MicroRNA-Triggered Anticancer Functionality

RNA therapeutics are of global interest because of their versatility in targeting a variety of intracellular and extracellular biomolecules. In that context, long double-stranded RNA (dsRNA) has been studied as an antitumor agent that activates the immune response. However, its performance is constrained by poor cancer selectivity and cell-penetration ability. Here, we designed and synthesized an oncolytic RNA hairpin pair (oHP) that was selectively cytotoxic toward cancer cells expressing abundant oncogenic microRNA-21 (miR-21). Although the structure of each hairpin RNA was thermodynamically metastable, catalytic miR-21 input triggered it to open to generate a long nicked dsRNA. We demonstrated that oHP functioned as a cytotoxic amplifier of information in the presence of miR-21 in various cancer cells and tumor-bearing mice. This work represents the first example of the use of short RNA molecules as build-up-type anticancer agents that are triggered by an oncogenic miRNA.

Nucleic Acid-to-Small Molecule Converter through Amplified Hairpin DNA Circuits

Many microRNAs (miRNAs) are characteristically found in cancer cells, making miRNAs promising marker biomolecules for cancer diagnosis and therapeutics. However, it is challenging to use miRNA as a cancer signature because it is difficult to convert the nucleic acid sequence information into molecular functionality. To address this challenge, we realize nucleic acid-to-small molecule converters using hairpin DNA circuits. Harnessing a Staudinger reduction as a trigger for the conversion, we constructed hybridization chain reaction (HCR) and catalytic hairpin assembly (CHA) circuits that respond to oncogenic miR-21. Fluorophore and dye molecules were released in response to miR-21 through the HCR, providing fluorogenic and chromogenic readouts. Selective cytotoxicity in miR-21-abundant cells was realized by the CHA to release the anticancer drug SN-38. This would be the first example of selective activation of a small-molecule prodrug triggered by oncogenic miRNA in human living cells.

Homogeneous Dual Fluorescence Count of CD4 in Clinical HIV-Positive Samples via Parallel Catalytic Hairpin Assembly and Multiple Recognitions

Regularly measuring the level of CD4+ cells is necessary for monitoring progression and predicting prognosis in patients suffering from an infection with the human immunodeficiency virus (HIV). However, the current flow cytometry standard detection method is expensive and complicated. A parallel catalytic hairpin assembly (CHA)-assisted fluorescent aptasensor is reported for homogeneous CD4 count by targeting the CD4 protein expressed on the membrane of CD4+ cells. Detection was achieved using CdTe quantum dots (QDs) and methylene blue (MB) as signal reporters. CdTe QDs distinguished CHA-assisted release of Ag+ and C-Ag+-C and MB that has differentiated cytosine (C)-rich single-stranded DNA (ssDNA) and C-Ag+-C, generating changes in fluorescence intensity. With the assistance of the CHA strategy and luminescent nanomaterials, this method reached limits of detection of 0.03 fg/mL for the CD4 protein and 0.3 cells/mL for CD4+ cells with linear ranges of 0.1 to 100 fg/mL and 1 to 1000 cells/mL, respectively. The method was validated in 50 clinical whole blood samples consisting of 30 HIV-positive patients, 10 healthy volunteers, and 10 patients with cancer or other chronic infections. The findings from this method were in good agreement with the data from clinical flow cytometry. Due to its sensitivity, affordability, and ease of operation, the current method has demonstrated great potential for routine CD4 counts for the management of HIV, especially in communities and remote areas.