Nature Nanotechnology

Biomarker analysis requires detecting analyte classes that span nucleic acids, proteins, small molecules, and metabolites, yet testing remains fragmented across target-specific assays and instruments. Here we report a molecular information-transduction strategy that converts target recognition across molecular classes into a common, error-tolerant DNA code readable by nanopore sequencing. Target recognition triggers a hybridization chain reaction that generates concatemers containing periodically repeated 10-nucleotide target-specific barcodes. A matched-filter decoder exploits this periodicity and the linear scaling of read length with match count to reject spurious matches by two to three orders of magnitude. Multi-class detection is demonstrated for a small molecule (ATP), two cardiovascular-associated microRNAs and thrombin in singleplex and multiplexed assays. By separating molecular recognition from sequence readout, this architecture provides a modular framework for converting heterogeneous analytes into a shared, redundancy-encoded signal for high-fidelity molecular sensing.

The blood-brain barrier (BBB) constitutes a major bottleneck for the systemic delivery of most therapeutic agents to the central nervous system. Here, we report near-infrared reversible optoacoustic modulation of the BBB permeability (NIR-ROAMBBB), leveraging endothelial tight junction targeting hyperbranched gold nanoconstructs (HBGNCs) to amplify localized optoacoustic transduction under femtosecond laser excitation. We first synthesized HBGNCs with tunable particle sizes (62-150 nm) and consistent branch morphologies via a seed-mediated growth approach, and uncovered a non-monotonic relationship between particle dimension and optoacoustic output, where the 62 nm HBGNCs generated nearly twofold stronger optoacoustic signal than gold nanorods and gold nanostars under matched excitations. Conjugation with BV11 antibodies against junctional adhesion molecule A increased HBGNC endothelial association and cerebral accumulation, enabling focal and fluence-dependent transient BBB opening (3-6 h) under 800 nm femtosecond pulsed laser excitation, as validated by in vitro trans-endothelial electrical resistance measurements, ex vivo Evans blue extravasation staining, and in vivo NIR imaging. Featuring deep tissue penetration of NIR light, robust optoacoustic conversion of HBGNCs, and negligible femtosecond laser-induced photothermal damage, this non-invasive strategy enables precise focal modulation of BBB permeability and potential drug delivery.

The molecular programmability of nucleic acids has facilitated the development of architected DNA/RNA nanostructures and their applications in novel materials and technologies. We report how different types of DNA and RNA nanoaggregates, bundling digital information encoded into oligo libraries, can be formed by manipulating the ionic strength of the solution. As DNA or RNA suspensions are immersed in solutions of increasing salt concentrations, we observe the onset of aggregation. Further increase in ionic strength leads to the formation of stable, reproducible, and well-defined aggregates. We show that these nanoaggregates are kinetically trapped at room temperature, stably partition DNA libraries that encode image files, and support file-specific random access by bundling DNA libraries with unique address oligos. The nanoaggregate files can be disrupted and reformed into scrambled bundles using simple external fluid shear or temperature annealing, rapidly obfuscating the data. We term these nanoaggregates nucleic acid PACKeTs: Partitioned Aggregates of Colloidal DNA/RNA through Kinetic Trapping. Overall, the results demonstrate how gaining fundamental insights into ionic colloidal aggregation enables new forms of manipulation of DNA and RNA libraries. This understanding could lead to novel functionalities including kinetically trapped data partitioning, random access, and data encryption or obfuscation.

Existing pooled lipid nanoparticle (LNP) screens lack spatial information on formulation localization, cellular uptake, and associated multicellular tissue responses. Here we introduce NanoSTAMP, a spatially resolved, pooled in vivo screening platform for barcoded LNP libraries that uses fluorescence in situ hybridization (FISH)-based barcode readout and is compatible with spatial omics. NanoSTAMP links LNP formulation to cell-type specific uptake, cargo expression, and nearby multicellular neighborhoods within intact tissue, which enables spatially-informed design of RNA delivery, establishing tissue architecture as a dimension of LNP performance.

Erythrocytes, commonly known as red blood cells (RBCs), constitute the most abundant cell type in vertebrate mammals. Due to their unique biological and physical attributes, RBCs have been the focus of extensive research in biomedical engineering. Methods have been developed to transform RBCs into adaptable carriers for molecular payloads, thereby extending their functional capabilities beyond what they naturally transport and accomplish. Concurrently with RBCs applied science, cell-free gene expression (CFE) has advanced into a tractable technology that can be integrated with a broad range of materials. In this work, we harness the advantages of CFE to engineer RBCs into hybrid synthetic cells. We encapsulate CFE reactions within RBC ghosts to execute elementary gene circuits, including biosensors, and to synthesize phages from their genomes. Furthermore, we engineer and functionalize the outer membrane of mature RBCs to attach diverse payloads, such as a SARS-CoV-2 antigen recognized by a specific antibody. CFE interfaces remarkably well with RBCs, enabling their rapid, low-cost transformation into red blood synthetic cells (RBSCs) with potential biomedical and biotechnological applications.

Despite advances in immunotherapy, most solid tumors remain resistant to treatment. Immune cell engagers redirect cytotoxic lymphocytes against cancer, but limited tumor access, immunosuppressive microenvironments and systemic immune activation limit efficacy. Here we develop live immune modulating engagers (LIME), a modular platform where non-pathogenic, tumor-tropic Escherichia coli display tandem single-chain variable fragments targeting a tumor-associated antigen and an activating receptor on T or natural killer cells. LIME bridged effector and tumor cells, induced transcriptional programs of T cell activation, metabolism and proliferation, and enhanced cytotoxicity across cancer cell lines and patient-derived organoids. In mouse models, LIME safely accumulated in tumors, outperformed tarlatamab in small cell lung cancer, and induced durable immunity in lymphoma. RAS inhibition and PD-L1 blockade enhanced LIME activity in pancreatic cancer and induced humoral responses. Multi-lineage immune modulation remained tumor-confined, without organ toxicity. These findings establish LIME as a versatile living therapeutic platform for programmable, tumor-restricted immune orchestration.

Extracellular vesicle (EV)-derived microRNAs serve as important biomarkers for cancer diagnosis, yet their accurate detection remains limited by insufficient control of nucleic acid recognition and signal activation. Here, we identified a previously unrecognized feature of CRISPR/Cas12a, in which incorporation of ribonucleotides into single stranded DNA targets modulates Cas12a activation efficiency, revealing a hybrid DNA/RNA-dependent regulation of Cas12a activity. Leveraging this mechanism, we established a programmable detection strategy that enables sequence dependent tuning of Cas12a activation without the need for target amplification. By coupling DNAzyme mediated cleavage with Cas12a trans-cleavage, a cascade signal amplification system was established, enabling highly sensitive and selective detection of miRNAs. To facilitate clinical applications, an EV-based sample processing strategy was integrated to simplify isolation of EV associated miRNAs and allow direct miRNA detection without conventional RNA extraction. The resulting platform demonstrated robust discrimination of multiple miRNA targets in clinical cohorts and supported accurate classification of cancer subtypes according to expression signatures. By integrating machine learning analysis, the system accurate distinguished breast cancer (BC) patients from healthy donors (HD), as well as triple-negative breast cancer (TNBC) from BC. This study provides a mechanism-guided strategy for programmable CRISPR-based nucleic acid detection in complex biological samples.

Mechanical amplification of minute length changes enables precise measurements across many orders of magnitude, from macroscopic metrology to optical instrumentation. Extending this principle to molecular systems could provide a route to monitoring nanoscale structural changes without relying on analyte labeling or fluorescence-based distance measurements. Here we present a DNA origami nanomechanical amplifier that converts subnanometre-scale molecular conformational changes into amplified mechanical displacements that can be tracked in real time at the single-molecule level. The platform resolves geometric changes associated with DNA hybridization, secondary-structure formation, DNA strand-exchange dynamics, and ligand-induced aptamer folding, enabling quantitative analysis of molecular kinetics and direct observation of transient intermediates and heterogeneous conformational ensembles. By translating molecular recognition events into mechanically amplified signals, our approach establishes a general framework for monitoring binding-coupled conformational dynamics and extends the scope of single-molecule measurements beyond conventional optical readouts.

DNA-based technologies rely on short, transient hybridization events, but selecting sequences with desired kinetic properties remains largely empirical because hybridization kinetics are difficult to predict from sequence and slow to measure one sequence at a time. Here, we introduce SPARXS-Hyb, an implementation of SPARXS (Single-molecule Parallel Analysis for Rapid eXploration of Sequence space) for multiplexed sequence-resolved screening of DNA hybridization. Using a surface-immobilized docking-strand library and a quencher-labelled imager-strand library, we screened 128 different DNA sequences in a single kinetic measurement, exposing all sequences to identical experimental conditions. This multiplexed approach removes a major confounding factor of serial measurements, allowing sequence-dependent differences to be compared directly. The resulting dataset reveals sequence-dependent transient binding behaviours and enabled us to identify a sequence with which an order-of-magnitude higher sampling rate can be achieved in DNA-PAINT (DNA points accumulation for imaging in nanoscale topography), a super-resolution microscopy technique based on DNA hybridization. By enabling multiplexed screening across a sequence library, SPARXS-Hyb provides a route to kinetics-guided sequence selection for programmable transient interactions in DNA nanotechnology.

Many bacterial species naturally secrete membrane vesicles (MVs) that mediate the intercellular transport of biomolecules, including nucleic acids, proteins, and metabolites. Beyond their native physiological roles, MVs hold considerable potential for biomedical applications. Here, we demonstrate that MVs from several Bacillus species exhibit potent intrinsic adjuvant activity, efficaciously eliciting immune responses and facilitating antigen-specific antibody production in mice. Exploiting this adjuvanticity, we engineered a highly adaptable universal vaccine platform that uses B. subtilis MVs as self-adjuvanting carriers. This system employs a modular "plug-and-display" architecture that covalently anchors recombinant antigens to the MV surface through a multi-step bioconjugation cascade. After validation of this methodology using a model antigen, we adapted the platform to target Yersinia pestis, the causative agent of plague. We formulated a Y. pestis vaccine by labeling the MV surface with a modified capsule antigen fraction 1 (mCaf1). Intranasal administration of the mCaf1-MV vaccine effectively elicited both systemic and mucosal immunity. Crucially, this vaccine conferred highly efficacious protection against a lethal Y. pestis infection in a murine model. These findings demonstrate the exceptional protective efficacy of the B. subtilis MV platform and highlight its broad potential for the rapid development of mucosal vaccines against diverse emerging pathogens.

Glycine is a vital extracellular signal in bacteria, plants, and the brain. Although RNA-based sensors detect glycine in cells, their extracellular application in native biological environments is limited by enzymatic degradation from nucleases. Mirror-image RNA is nuclease-resistant and preserves the tertiary structure required for RNA function, but synthesizing long L-RNAs such as the 170-nt glycine sensor (glyS) remains challenging. Here, we applied cross-chiral ligation with natural D-RNA ribozymes to assemble a mirror-image L-RNA glycine sensor (L-glyS). Optimization of the ligation conditions enabled up to 68% conversion to the full-length sensor. L-glyS displayed nuclease resistance and maintained glycine-dependent fluorescence in serum, where the original D-glyS lost function. These results establish cross-chiral ligation as a strategy for constructing long, functional L-RNAs and broaden the possible applications of RNA-based sensors to extracellular detection of small molecules.

Three-dimensional protein crystals are ordered, porous macroscopic materials with potential applications in catalysis, biosensing, and biomedicine. However, most protein crystals are obtained by empirical screening, providing limited control over the lattice architecture, pore geometry or component composition that determine material function. Here, we present a modular strategy for the programmable design of highly porous, framework-like protein crystals using predefined protein-protein interactions. This strategy yielded over 30 distinct protein crystals, including single-component and multicomponent P213 and I213 lattices that grow to over 100 micrometers in size. Small-angle X-ray scattering and electron microscopy showed close agreement between experimental lattices and computational models. RFdiffusion-guided design generated isomorphous variants with matched lattice parameters, enabling coherent protein crystal alloys, epitaxial core-shell growth and reversible shell assembly. The designed crystals exhibit tunable mesoporous architectures, with limiting apertures of 2-18 nm, and support genetically encoded incorporation of fluorescent protein guests. These results establish a general route to programmable lattice engineering of protein crystals and position them as genetically encoded, compositionally tunable mesoporous materials.

The rise of antifungal resistance and limited antifungal drug classes creates an urgent need for biomaterials with localized, programmable activity. Here, we engineered curli nanofibers displaying the antifungal peptide heliomicin and unexpectedly discovered that wild-type CsgA itself exhibits intrinsic antifungal activity against Candida albicans, reducing fungal viability by approximately 2 log units. Heliomicin fusion enhanced this activity to a 3.5-log fungicidal reduction while preserving nanofiber self-assembly, hydrogel formation, mechanical properties, and 3D printability. Mechanistic analyses linked enhanced activity to membrane disruption and expansion of the cationic surface of CsgA. Heliomicin-CsgA hydrogels further reduced fungal burden and suppressed hyphal development in an ex vivo porcine skin infection model. These findings reveal that extracellular protein nanofibers can harbor intrinsic biological activities that can be uncovered and enhanced through protein engineering, establishing a strategy for developing intrinsically bioactive, programmable biomaterials for localized therapeutic applications against fungal pathogens and potentially other microbial infections.

Ulcerative colitis (UC) is a global health challenge driven by immune dysregulation and gut microbiota imbalance.1 Current treatments, limited by insufficient efficacy and systemic toxicity during prolonged use, fail to resolve the intertwined immune-microbial pathology.2 Here, we report an orally administered self-assembled hydrogel C2-(IIRR)2I-NH2 (CIR), engineered from host defense peptides, which disrupts the immune-microbiota entanglement. The CIR hydrogel exhibits structural transformation at the inflamed sites rich in liposaccharide (LPS), a pro-inflammatory molecule derived from pathogenic bacteria. Stable {beta}-sheet nanofibers can transfer to bioactive -helix conformations, enabling localized therapeutic action with minimal off-target toxicity. In murine colitis models, CIR restores mucosal integrity and suppresses disease severity, outperforming the first-line drug 5-aminosalicylic acid (5-ASA). Microbiome profiling reveals its capacity to rebalance gut microbiota, depleting LPS produced pathogenic bacteria like Prevotellaceae. Transcriptomic analyses further indicate that CIR silences TLR4-mediated signaling pathway. By synergistically targeting immune dysregulation and microbial dysbiosis, this self-assembled peptide hydrogel establishes a paradigm-shifting strategy for UC, offering clinically translatable potential for multifactorial gastrointestinal disorders.

Mechanotransduction plays a fundamental role in regulating immune cell function, yet how engineered virus-like nanospikes engage mechanosensitive signaling pathways to modulate innate immunity remains poorly understood. Here, we report virus-like nanotopography as a previously unrecognized regulator of Piezo1-mediated mechanotransduction in macrophages using virus-like mesoporous silica nanoparticles (VLPSi) with tunable rigid nanospike lengths. We demonstrate a direct structure-activity relationship between nanospike geometry and Piezo1-dependent Ca{superscript 2}+ influx, with longer nanospikes inducing significantly greater intracellular Ca{superscript 2}+ signaling. Building on this mechanistic insight, we developed biomimetic cancer cell membrane (CM)-coated, MSA-2-loaded VLPSi nanoparticle (CM/MSA-2@VLPSi) and investigate the combination of nanospikes-activated Piezo1 with STING signaling and CM antigens presentation in macrophage immune reprogramming. The resulting biomimetic nanoparticles robustly activate the STING-TBK1-IRF3/NF-{kappa}B axis, increase IFN-{beta} and pro-inflammatory cytokine production, and promote macrophage polarization toward M1 phenotype in a spike-length-dependent manner. Collectively, the present study provides a biomimetic strategy for enhancing the M1 polarization of macrophage through the coordinated regulation of mechanical, inflammatory, and antigenic signals.

Investigating the conformational dynamics of intrinsically disordered proteins (IDPs) is essential to understanding how their structural heterogeneity underlies function and how their dysregulation contributes to diseases. Here, we utilized an MspA nanopore-based approach for studying the conformational dynamics and interactions of IDPs at the single-molecule level. The platform was demonstrated using the intrinsically disordered transactivation domain of tumor suppressor p53 (p53-TAD), one of the important proteins in cancer biology. We showed that MspA can stably capture p53-TAD and resolve up to six distinct current states with frequent interconversions, revealing a rich conformational landscape. The nanopore also detected the effect of a cancer-associated double mutational variant, N29K/N30D. Combining experiments with steered molecular dynamics simulations, we showed that the mutant sampled compact conformational states more frequently than wild type, consistent with previous NMR studies. Importantly, the MspA platform enabled direct monitoring of E3 ligase MDM2 binding to p53-TAD and resolved how this interaction is inhibited by anti-cancer compound epigallocatechin gallate (EGCG). Notably, EGCG stabilizes one of the six states sampled by p53-TAD, providing a mechanistic explanation for its inhibitory effect. Together, these findings demonstrate the promise of the nanopore platform for label-free monitoring of IDP conformational dynamics, modulation, binding and inhibition at single-molecule resolution.

As central executioners of cell death, caspases that activate exclusively in diseased cells would provide powerful and specific therapeutic agents. Natural caspase regulation exhibits two universal features that facilitate the engineering of such caspases: proximity-induced subunit assembly and modular separation of substrate recruitment from catalysis. Here, we take advantage of these features to engineer "Raspases," split effector caspases that conditionally reconstitute active complexes upon detection of mutant Ras, an oncogene altered in roughly a quarter of all cancers. When delivered as mRNA in lipid nanoparticles, Raspases selectively eliminate Ras-mutant human cancer lines while sparing wild-type cells. The system is built entirely from human protein domains, can be encoded as a single polyprotein, and can be adapted to trigger pyroptosis. Critically, Raspases match or exceed the potency of alternative Ras-targeting interventions in vitro. These results establish retargeted caspases as a generalizable sense-and-kill platform for selective elimination of diseased cells.

Multicellular organization enables biological functions to be distributed among specialized cells and coordinated through intercellular communication. Integrating this organizational principle with genome replication would link functional division of labor to the propagation of genetic information. Here, we show that genomic RNAs with complementary functions can cooperatively replicate across communicating artificial compartments. We constructed multicell-like colonies from all-aqueous droplets formed by phase separation of two incompatible polymers and stabilized at their interfaces by liposomes and amyloid-like proteins. The droplets assembled spontaneously while remaining permeable to protein-sized macromolecules. Two genomic RNAs encoding a replication enzyme and a metabolic enzyme were distributed in distinct colony-forming droplets and cooperatively replicated through cell-free translation and reciprocal molecular communication. These findings establish that genome replication can be collectively supported by communicating artificial compartments and provide a route toward multicell-like systems that coordinate spatially distributed genetic functions.

Reading both physical and chemical properties of a microenvironment from a single fluorophore remains a challenge. Here we demonstrate that two coexisting molecular equilibria within one near-infrared cyanine, CyC4, encode two mechanistically distinct ratiometric reporting channels. A meso-amino group and a pendant carboxylate form a tunable intramolecular hydrogen bond that toggles the dye between closed (700 nm) and open (780 nm) emissive conformers. Time-dependent density functional theory (TD-DFT) calculations show that the hydrogen bond raises the LUMO and blue-shifts the emission, establishing the 700/780 emission ratio as a local reporter of hydrogen bonding and polarity. Independently, the chromophore self-associates under crowding- and cosolvent-rich conditions into an aggregate with a blue-shifted, H-type absorption signature near 530-540 nm and a distinct emission near 610 nm upon 540 nm excitation. The intensity of this aggregate band relative to the monomer emission (Ra) serves as a ratiometric reporter of crowding and self-association. Because the two channels arise from distinct molecular equilibria (intramolecular hydrogen bonding vs. intermolecular self-association) they are largely decoupled: a glycerol titration series confirms that the self-association channel (Ra) can be moved while the hydrogen-bonding channel stays essentially fixed. Applied to protein-PEG biomolecular condensates, the two ratios move oppositely with increasing salt, showing that the interior's chemical (polarity, hydrogen bonding) and physical (packing, self-association) environments co-vary across the salt series; a single CyC4 measurement thereby maps this coupled microenvironment, providing a general strategy for multiparametric, ratiometric sensing of crowded microenvironments.

Methods for installing synthetic functions on living cell surfaces provide powerful approaches for imaging, sensing, and manipulating cell behavior, but many require genetic modification of the target cell or chemical modification of the plasma membrane. Here, we repurpose the glycosylphosphatidylinositol-anchored protein (GPI-AP)-binding toxin aerolysin as a modular chassis for non-genetic cell-surface functionalization. We show that a non-cytotoxic, monomeric aerolysin mutant retains high-affinity and GPI-AP-dependent cell binding when genetically fused to diverse protein cargos. Fluorescent protein-aerolysin fusions robustly label multiple cell types and remain predominantly associated with the cell surface for at least 24 h, in contrast to wheat germ agglutinin, which is extensively internalized. Aerolysin can also be equipped with SpyTag/SpyCatcher to enable modular assembly with independently expressed protein cargos. Importantly, aerolysin supports functional rather than solely optical modification of the cell surface: fusion to the proximity-labeling enzyme APEX2 enables extracellular protein biotinylation, while fusion to HUH endonuclease tags enables covalent attachment of synthetic DNA to living cells. Using this latter architecture, we developed a DNA hairpin sensor that converts cell-surface nuclease activity into a fluorescent signal and distinguishes cells with different levels of extracellular nuclease activity. Together, these results establish non-cytotoxic aerolysin as a genetically encoded, soluble adapter for installing proteins, enzymes, and programmable nucleic acids onto living cells without modification of the target-cell genome.