First-generation LUNAR constructs can detect both oligonucleotides and plasmid double-stranded DNA with nanomolar sensitivity in mammalian cells and future work will focus on improving sensitivity, fold-change, and multiplexing capabilities for sequence-specific DNA detection.
Achieving precise and robust cell-surface recognition in complex biological environments is challenging due to inherent trade-offs in affinity, specificity, and off-target binding. Herein, we present a programmable molecular device that integrates Boolean logic computation with spatial confinement to overcome these limitations. Our system employs valence-controllable, split DNAzyme modules assembled on a tetrahedral DNA nanostructure (TDN). The peroxidase-mimicking activity is stringently gated by a cell-surface AND logic, requiring the co-localization of two adjacent modules on target protein clusters for activation. This spatial constraint effectively eliminates stochastic or unintended signal leakage originating from solution-phase reactions or nontarget cells. Upon activation, the DNAzyme catalyzes the biotinylation of neighboring membrane protein clusters, generating stable multivalent adhesion sites. Quantitative dissociation kinetics reveal that the trivalent design of the DNAzyme modules promotes highly cooperative binding, resulting in uniform, long-lived complexes on target cells. We demonstrate that this approach enables specific recognition and highly efficient isolation of target cells from mixed cell populations and clinical samples, showcasing a strategy for programming high-fidelity molecular interactions on interested cell surfaces.
Programmable materials integrated with intelligent signal processing are essential for developing adaptive and autonomous environmental sensing systems. Here, we present a biohybrid material platform in which environmental DNA is captured by streptavidin (SA)-functionalized microparticles and delivered to a cell-free transcription-translation system for intelligent information processing. The microparticles selectively capture biotinylated DNA from their surroundings, which serve as molecular algorithm inputs for downstream biological computation. DNA immobilized on the particle surface remains transcriptionally active, enabling cell-free systems to produce tunable outputs, including (1) linear responses proportional to DNA input concentration and (2) threshold-dependent switching behaviors achieved through competitive binding. By offloading computation to a cell-free biochemical processor, this approach enables scalable, biocompatible sensing without the need for onboard electronics. This biohybrid design provides a versatile framework for engineering intelligent materials with applications in developing smart tools for healthcare and environmental monitoring.
Hailan He, Ting-Yen Wei, W. Ruder· ACS Omega· 0 citations
Cellular signaling networks are orchestrated by complex interactions between gene expression and ion flux, yet tools for simultaneously visualizing these events in living cells remain limited. Herein, we report two orthogonal gold-nanoparticle-based DNA nanosensors that enable simultaneous imaging of sodium/hydrogen exchanger 1 (NHE1) mRNA and Na+ dynamics in hepatocellular carcinoma cells. The sensing mechanism relies on proximity-dependent fluorescence quenching. For mRNA detection, Cy3-labeled reporter strands hybridize to DNA-functionalized gold nanoparticles (AuNPs), holding the fluorophore close to the quenching surface. Target binding triggers strand displacement, releasing Cy3, and restoring emission. For Na+ detection, a Cy5-labeled substrate strand hybridizes with a Na+-specific DNAzyme anchored on AuNPs. Na+ activates the DNAzyme, cleaving the substrate at a defined site and liberating the Cy5 fluorophore. This dual-sensor system enables the quantitative monitoring of both analytes in living cells. Using this platform, we directly visualize that NHE1 mRNA downregulation suppresses intracellular Na+ accumulation, establishing a regulatory link between gene expression and ion homeostasis. Notably, mRNA-targeted hybridization inhibits cancer-cell migration in a dose-dependent manner, revealing a potential therapeutic mechanism. This approach provides a molecular tool for decoding ion-based signaling networks in cancer biology.
We report a fluorescence chip based on a membrane-anchored, bipedal DNAzyme walker assembled on small extracellular vesicles (sEVs) surfaces via catalytic hairpin assembly (CHA). Unlike previously reported single-arm or proximity-ligation-dependent walkers on nanoparticle supports, this CHA-triggered DNAzyme walker is designed with a bipedal architecture and operates directly on the sEVs membrane. In our design, CHA simultaneously generates two DNAzyme arms on the same sEVs, enabling faster substrate cleavage kinetics and superior signal amplification. The assay achieves a theoretical detection limit of 2.8 particles/μL, approximately 1.5-fold lower than a comparable single-arm architecture. Dual recognition of the sEVs lipid bilayer and surface EpCAM protein (using a cholesterol-modified substrate and an anti-EpCAM antibody) effectively eliminates false-positive signals from free EpCAM or soluble interferents. The entire reaction cascade is integrated onto a chip platform, improving reproducibility and point-of-care potential. The chip performs robustly in fetal bovine serum and clinical serum samples, with recovery rates of 99.1-103.8% and strong correlation with nanoparticle tracking analysis. By establishing a CHA-assisted, bipedal walking mechanism on biological membranes, this work opens a new paradigm for designing efficient DNA nanomachines on membrane-enveloped targets.
DNA-based molecular computation enables targeting of cells via multiple surface receptors. However, existing platforms are often limited to single-receptor detection per operation or rely on freely diffusing components, a common source of off-target interference. Here we show an intelligent DNA nanodevice (DND) that integrates multivalent recognition, logic‑gated computation, and spatially precise drug delivery in a single nanostructure. The DND comprises a doxorubicin-loaded tetrahedral DNA framework (tFNA@Dox) connected via three allosteric aptamer arms to a cholesterol-modified membrane anchor. Simultaneous binding of all three aptamers triggers an AND‑logic gate, releasing tFNA@Dox specifically at the target cell membrane. This localized sense‑and‑act mechanism maximizes therapeutic specificity and minimizes systemic exposure. In tumor-bearing mice, DND@Dox effectively accumulated in tumors, significantly inhibited tumor growth under local and systemic administration, and reduced systemic toxicity. This work establishes a versatile platform for logic‑controlled, multimarker‑guided cancer theranostics. DNA device-based targeting has huge potential but can be limited by single target recognition resulting in off target effects. Here, the authors develop a DNA nanodevice that anchors to cell membranes and releases chemotherapy only when three specific cancer markers are detected simultaneously.
Meiqin Zhang, Ying-Sheng Cheng, Nan Chen et al.· Nature Communications· 0 citations