Nature Nanotechnology

DNA origami is becoming an attractive platform for data storage, yet current approaches rely on the limited stability of DNA hybridization, preventing them from fully utilizing the stability and cost-effective copying inherent to classical sequence-based storage. Here we introduce DNA Origami for Combinatorial data Storage (DOCS), where we encode information into the scaffold molecule using a combinatorial enzymatic approach. This enables text encoding that is biologically cloneable, stable at high temperatures, and randomly accessible. We further demonstrate the DOCS platforms combinatorial power by creating a stochastic molecular authentication system. Finally, we show using simulations that expanding the information capacity of data carriers allows for the storage and recovery of large files up to several hundred kilobytes in size. DOCS provides a robust, scalable strategy for molecular data storage and security that bridges the gap between classical DNA data storage strategies and DNA nanostructure-based methods.

Spatial and temporal organisation of membrane-associated components is fundamental to cellular signalling, yet remains difficult to engineer in minimal synthetic systems. In synthetic cells, DNA and RNA nanotechnology offer programmable molecular organisation at membranes, while in vitro transcription (IVT) enables gene expression-driven regulation. However, integrating these systems within cell-like compartments, such as giant unilamellar vesicles (GUVs), remains challenging due to undesirable interactions between transcription machinery and nucleic acid assemblies. Here, we present a modular strategy that couples in situ RNA production to dynamic DNA localisation at GUV synthetic cell membranes. RNA strands, transcribed within GUVs, function as linkers that recruit DNA-conjugated cargo to lipid membranes, enabling programmable spatial organisation. Using this framework, we achieved reversible membrane localisation through toehold-mediated strand displacement and RNase H-mediated degradation. This work establishes a gene expression-driven platform for programmable and dynamic control of membrane-associated components in synthetic cells, providing a foundation for constructing dynamic signalling assemblies and higher-order cellular behaviours. O_FIG O_LINKSMALLFIG WIDTH=191 HEIGHT=200 SRC="FIGDIR/small/738173v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@9d8b5org.highwire.dtl.DTLVardef@726fd1org.highwire.dtl.DTLVardef@10b09bforg.highwire.dtl.DTLVardef@1ad19b5_HPS_FORMAT_FIGEXP M_FIG C_FIG

Bispecific T-cell engagers (TCEs) are a promising class of cancer immunotherapies, but their clinical use is limited by toxicity and insufficient specificity. Tuning the T cell- tumor interface through engager architecture may address these drawbacks. To this end, we engineered hybrid constructs composed of two nanobodies targeting CD3 and the model tumor antigen HER2, respectively, connected by rigid DNA linkers of variable length. Using cytotoxicity assays and hybrid biophysical platforms, we demonstrate a linker-length dependence of cell spreading on antigen, target killing and cytokine release, revealing a functional decoupling between killing and cytokine secretion, and implicating the glycocalyx as a key player. Through the addition of EGFR targeting, we also generate trispecific constructs implementing an "OR-gate" logic to address tumor heterogeneity and reduce resistance due to antigen loss. Overall, these versatile constructs show great therapeutic promise, and at the same time serve as platforms to test hypotheses on biophysical mechanisms.

Living cells rely on filaments and condensates as key organizers of their interior. Developing these structural primitives together inside synthetic compartments using programmable components is a step toward building functional synthetic cells, composite biomaterials, and synthetic tissues. Here, we demonstrate that DNA nanotubes and DNA condensates can be co-assembled within cell-sized compartments, including water-in-oil droplets and giant unilamellar vesicles (GUVs). The two nanostructures form as expected, producing a single condensate surrounded by nanotubes in diverse morphologies that depend on DNA and salt concentration, as well as compartment size. By incorporating photoactivatable DNA linkers, we can control the order of assembly and trigger reconfiguration of nanotube networks into ring-shaped bundles enclosing a condensate, architectures reminiscent of a cellular nucleus within a cytoskeletal ring. An isothermal assembly protocol based on monovalent salts further extends this approach to GUVs. Together, these results establish DNA filaments and condensates as programmable, composable organizers of synthetic cell interiors.

Precise drug delivery within anatomically complex tissues demands systems capable of both active navigation and deep tissue access, properties that have remained difficult to reconcile in existing nanocarriers and microrobots. Here we introduce Dynabots, a dynamic microrobotic assembly constructed from multifunctional nanoparticles covalently linked by thermally cleavable molecular connectors. This nanoparticle-rich architecture enables the integration of magnetic, imaging, and therapeutic components while preserving a high content of functional material. Collective assembly imparts enhanced magnetic responsiveness and maneuverability, enabling controlled navigation through tortuous biological environments. Upon exposure to mild thermal stimuli, the assemblies undergo programmed disassembly, releasing individual nanoparticles that can diffuse through tissue for localized therapeutic action. We establish the programmable transitions, biocompatibility, and therapeutic efficacy of this process across in vitro and in vivo models, including real-time fluoroscopic guidance within anatomically realistic phantoms and live rodent and porcine systems. By integrating magnetic control, reconfigurable architecture, and stimulus-triggered disassembly, Dynabots unite navigational precision with tissue permeability, providing a versatile platform for adaptive and deep-tissue drug delivery.

DNA is highly programmable and efficient for encoding information. In this work, we use the paranemic crossover (PX) DNA structures for a binary-encoded system. As substrates for data storage, we designed a combination of PX and anti-PX structures where the four strands of the PX motif are complementary to those in the anti-PX motif. To write data, we programmed encoding elements in each of the four strands of the PX and anti-PX motifs. The encoded data remains encrypted until the samples are processed at a specific temperature, when the PX and anti-PX motifs reassociate to four distinct duplexes, defined by the encoding elements and retrieved using an electrophoretic readout. We show that the encoded information is stable for several days when stored at 20 {degrees}C, 37 {degrees}C or outdoors, with the encrypted structures showing higher nuclease resistance compared to the decrypted structures. Using this strategy, we demonstrate hexadecimal encoding using a combination of 4 bits, encrypting specific words and color codes. We envision such systems could find use barcoding, secure messaging and authentication.

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.

Fluorescence microscopy is increasingly used to measure molecular organization at length scales where labeling, photophysics and sample preparation can dominate quantitative accuracy. Reference standards are therefore needed that combine defined nanoscale geometry with a protein-like environment and compatibility with biological imaging. Here we introduce circular tandem repeat protein as programmable protein standards for benchmarking sub-10-nm fluorescence microscopy. Using genetic code expansion and bioorthogonal labeling, we generated compact protein rings carrying up to six labeling sites. Photoswitching fingerprint analysis revealed geometry-dependent localization accumulation and blinking kinetics, demonstrating that short-range fluorophore interactions can be assessed as measurable benchmark parameters. DNA-PAINT confirmed accessible docking sites and programmed valency at the single-particle level. We further established recombinant tethering and genetically encoded membrane display, extending the standards to cellular environments. cTRP PicoRulers were also compatible with expansion microscopy. Together, cTRPs provide a modular protein-based platform for evaluating molecular-scale imaging performance in purified and cellular environments.

Deformable condensates offer dynamic interfaces for biomolecule delivery, yet membrane adhesion does not necessarily lead to cellular internalization. The physical transition that determines whether a membrane-bound soft material remains surface-anchored or proceeds through wetting towards productive uptake remains poorly understood, particularly at active living-cell membranes. Here, we engineer sequence-defined DNA condensates through liquid-liquid phase separation (LLPS) and program their interfacial behavior by tuning sticky-end valency and cholesterol organization. These molecular designs precisely regulate condensate fluidity, fusion dynamics and internal organization, generating distinct states of weak contact, persistent anchoring and rapid wetting. Increasing cholesterol-mediated affinity does not enhance uptake. Instead, productive internalization emerges from a balance between membrane adhesion and condensate fluidity and deformability. Native membrane composition further modulates condensate interfacial fate across mammalian cells and plant protoplasts. DNA condensates enrich and deliver CpG ODNs, mRNA ([~]2000 nt) and proteins, while cargo loading experiments reveal that preserving condensate architecture is essential for functional delivery. Our findings identify wetting competence as a design parameter for controlling soft material engagement and cellular entry.

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 accurate quantification of biological nanoparticles, such as small extracellular vesicles (sEVs), is fundamentally hindered by a resolution-coincidence trade-off in digital assays. While physical confinement can isolate single particles, conventional optical readouts remain diffraction-limited, causing multi-particle occupancy to be miscounted as single events and thereby restricting the analytical dynamic range. Here, we report a nanoplasmonic platform that overcomes this limit by introducing a geometry-defined interface that uniquely unifies nanoscale compartmentalisation and near-field-assisted super-resolution imaging. Utilising a gold plasmonic nanohole array, the strict geometric periodicity of the lattice simultaneously serves as a template for single-vesicle confinement and a deterministic grid that generates an array of localised surface plasmon resonance near-field hotspots. This position-deterministic illumination pattern imposes known geometric priors on the excitation field, shifting high-spatial-frequency information into the detectable bandwidth to achieve sub-100 nm lateral resolution. This dual-purpose geometric determinism enables high-fidelity digital readout of individual vesicles with significantly fewer sub-images than stochastic, speckle-based metasurface structured illumination microscopy approaches. The assay achieves an analytical limit of detection of 143 sEVs/{micro}L, matching the performance of state-of-the-art single-EV counting technologies. It successfully differentiates distinct sEV subpopulations based on surface biomarker expression, establishing a clear pathway for future clinical liquid biopsy applications. By replacing stochastic loading and illumination with geometric design, this work establishes a robust framework for precise vesicle interrogation with broad implications for emerging translational applications and fundamental biology.

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.

Electrically conductive protein nanowires produced by metal-reducing bacteria have attracted interest as sustainable electronic materials, but their study and engineering have been limited by difficulties in expression, purification, and genetic manipulation. Here we establish Shewanella oneidensis as a heterologous host for production of Geobacter sulfurreducens OmcZ nanowires and progress a complementary in vitro assembly strategy that yields highly pure nanowire preparations. This platform enabled systematic engineering of OmcZ, revealing extensive tolerance to sequence variation and faciliating the design of enhanced-conductivity variants. Guided by comparative analysis of environmental OmcZ homologs, we generated a chimeric nanowire, OmcZ+, that exhibited a [~]3.5-fold increase in bulk conductivity while retaining the overall structure of the parent nanowire. Cryo-electron microscopy revealed unexpected architectural plasticity in OmcZ+ wires, including non-linear dendritic and pentameric assemblies mediated by the solvent-exposed heme VII, suggesting previously unrecognized modes of cytochrome nanowire organization. Incorporation of engineered OmcZ variants into water evaporation-induced electricity generators produced power densities up to [~]25.3 W cm-{superscript 2} and enabled high-performance operation in saline environments, including seawater and human sweat. Together, these results establish a versatile platform for the production, structural analysis, and engineering of cytochrome nanowires, providing a foundation for the development of programmable biological electronic materials.

Cell-free biosensors leverage in vitro gene expression reactions to detect chemicals. While inexpensive, modular, and distributable, these platforms are constrained by slow readouts at ambient temperatures, precluding practical field operation. In cells, phase separation accelerates biochemical reactions; however, recapitulating these gains in vitro has remained challenging for complex biochemistries. Here, we report the first self-assembling coacervate system that accelerates in vitro transcription. Prepared by simple mixing, coacervation with spermine and polyacrylic acid occurs dynamically in response to NTP consumption and co-localizes DNA templates and RNA polymerase to accelerate transcription, mimicking intracellular phenomena. We exploit this discovery to accelerate the cell-free biosensing of six ligands, demonstrating that coacervation can preserve platform modularity, improve sensitivity, retain lyophilization compatibility, function in field matrices, and reduce ambient-temperature time-to-signal by hours. This work contributes to a growing understanding of phase separation in biology and advances the use of membrane-less organization for real-world applications.

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.

Therapeutic genome editing requires delivery of editing molecules to defined cell types, but targeting specificity and efficiency are currently limited. We hypothesized that properties inherent to immune cells, including tissue infiltration and programmed cell recognition, could be harnessed to engineer a cell-based delivery system. We show here that T cells can both produce and transfer editing machinery to target cells. In response to a programmable ligand, engineered T-lymphoid cells can transfer enzymes using complex spatiotemporal logic and deliver cargo in a cell contact-dependent or -independent manner. We demonstrate feasibility of this approach in primary human T cells, establishing a customizable genetic circuit for macromolecular delivery controlled by intercellular interactions.

Localized measurements of electric fields offer a promising route to expand the information content of nanopore-based single-molecule sensing beyond conventional ionic-current blockade. Here, using all-atom molecular dynamics simulations with virtual electric-field probes placed around a graphene nanopore, we show that the local electric-field captures the presence, and distribution of charged amino acids as the peptides translocate through the pore. These field signatures create reproducible peptide-specific fingerprints across independent translocation events and enable substantially improved discrimination between peptides compared with ionic-current traces obtained under the same simulation conditions. Our results suggest that localized nanopore electrometry can provide a complementary, information-rich readout of peptide charge order that is largely inaccessible to conventional current blockade-based measurement. This study establishes a simulation-guided framework for integrating nanoscale electrometry with nanopore platforms for future peptide and protein analysis.

The advent of single-molecule nanopore sequencing established a powerful platform for modern genomics by using static biological pores to report the translocation of canonical nucleic acids, enabling rapid, accessible nucleic acid analysis. However, extending this strategy to single-molecule proteomics has stalled against a fundamental biophysical bottleneck. Current efforts in nanopore proteomics attempt to retrofit these static, spatial "caliper" biological nanopores (e.g., -hemolysin, MspA, CsgG, aerolysin) for protein sequencing despite the immense steric, charge, and conformational heterogeneity of proteins. Unlike the chemically uniform, polyanionic phosphodiester backbone of DNA, the proteome contains isosteric and isobaric variants that confound purely volumetric measurements made by static pores. To address this bottleneck, we propose the application of dynamical translocases - naturally evolved, protein-handling nanomachines (e.g., the anthrax toxin protective antigen). Unlike static pores that rely on passive diffusion, dynamical translocases employ target-docking clamp architectures that achieve low nanomolar sensitivity. Active-site conformational dynamics generate high-dimensional kinetic fingerprints that enable molecular discrimination during translocation. By coupling dynamical translocases with Physics-Informed Machine Learning (PIML), we demonstrate that amino-acid side-chain-dependent thermodynamic friction can be mathematically decoded, enabling >90% accurate classification of chemically distinct amino acid classes and doing so label-free without the artificial DNA-handles required by legacy platforms.

Biological systems operate through complex molecular networks programmed by genetic information; however, constructing artificial systems with multilayered control remains a significant challenge. Here, we report a simple and integrated master-key system governed by lock DNA and master key DNA, reversibly switching diverse downstream processes ON/OFF and achieving dynamic cross-talks among distinct molecular components. The system utilizes cationic copolymer chaperones as control nodes, based on poly(L-lysine) or poly(allylamine) grafted with hydrophilic side chains, with a peptide nucleic acid (PNA) plug-in that grants sequence-specificity. We demonstrated two proof-of-concept systems: a nucleic acid-based catalytic network responsive to microRNA let-7b and a peptide-mediated transformation of lipid bilayers from two-dimensional sheets to three-dimensional vesicles. Both systems exhibited precise, modular, and programmable control with high robustness, mimicking the governing role of nucleic acids in biological systems. This strategy provides a versatile design framework for constructing biomimetic molecular networks and studying biological systems.

DNA-barcoded antibodies are central to a broad range of spatial and dissociative assays and applications, including multiplexed imaging, single-cell profiling, and proximity detection. Direct modification of primary antibodies with defined DNA barcodes enables flexible panel design for multiplexed labeling of proteins. However, conventional antibody-oligonucleotide conjugation methods are inefficient, low-throughput, and prone to batch variability, limiting the reliable generation of orthogonally barcoded antibody panels. These challenges are particularly acute during initial panel development, where lengthy protocols, conjugation failures, large antibody input requirements, and the need for custom antibody formulations increase experimental cost and effort. Site-specific conjugation strategies based on antibody Fc-domain binders offer a promising alternative. We streamlined this foundational approach to establish its compatibility with multiplexed imaging in cells and tissues; however, generating a full barcoded library is still resource-intensive. This is because every unique DNA barcode must first be chemically linked to a separate binder before it can be attached to an antibody. To overcome the prominent bottleneck of rapidly and reliably generating DNA-barcoded antibody panels, we introduce the universal oligo adapter (UnO) strategy. UnO fundamentally changes the workflow from barcode-specific conjugation to universal barcode conversion. We build on the established photoreactive protein G binder and combine it with a universal oligonucleotide carrying a second ultrafast photocrosslinking group, 3-cyanovinylcarbazole (cnvK). This creates a dual-functional adapter: one photoreactive group enables covalent attachment to the antibody, while the cnvK-containing universal oligo simultaneously captures a user-defined DNA barcode through hybridization and UV crosslinking in a single step. Rather than preparing separate conjugation reactions for dozens of barcodes, UnO acts as a single reagent that covalently couples any desired barcode onto small quantities of off-the-shelf primary antibodies in minutes. We validate the generalizability and modularity of this approach across subcellular Immuno-SABER and tissue-based CODEX workflows for multiplex immunostaining. By converting antibody barcoding into a modular, one-step nucleic-acid adapter workflow, UnO reduces the cost, time, and complexity of generating DNA-barcoded antibody panels and provides an efficient, accessible solution to a central bottleneck in DNA-enabled multiplexed protein detection.