Nature Nanotechnology

Biological cells use cations as signalling messengers to regulate a variety of responses. Linking cations to the functionality of synthetic membranes is thus crucial to engineering advanced biomimetic agents, such as synthetic cells. Here, we introduce bio-inspired DNA-based receptors that exploit non-canonical G-quadruplexes for cation-actuated structural and functional responses in synthetic lipid membranes. Membrane confinement grants cationdependent control over receptor assembly and, when supplemented with hemin co-factors, their peroxidase DNAzyme activity. Cationmediated control extends to receptor lateral distribution to localise DNA-based catalysis within phase-separated membrane domains of model synthetic cells, imitating the localisation of multimeric membrane complexes to signalling hubs in living cells. Our modular strategy paves the way for engineering from the bottom-up cation-responsive pathways for sensing, signalling, and communication in synthetic cellular systems.

The T cell receptor (TCR) is thought to be a mechanosensor, meaning that it transmits mechanical force to its antigen and leverages the force to amplify the specificity and magnitude of TCR signaling. The past decade has witnessed the development of molecular probes which have revealed many aspects of receptor mechanotransduction. However, most force probes are immobilized on hard substrates, thus failing to reveal mechanics in the physiological context of cell membranes. In this report, we developed DNA origami tension sensors (DOTS) which bear force sensors on a DNA origami breadboard and allow mapping of TCR mechanotransduction at dynamic intermembrane junctions. We demonstrate that TCR-antigen bonds experience 5-10 pN forces, and the mechanical events are dependent on cell state, antigen mobility, antigen potency, antigen height and F-actin activity. We tethered DOTS onto a microparticle to mechanically screen antigen in high throughput using flow cytometry. Finally, DOTS were anchored onto live B cell membranes thus producing the first quantification of TCR mechanics at authentic immune cell-cell junctions.

In the quest to create increasingly complex synthetic cell-mimicking systems, a wide range of DNA nanostructures have been developed to coat, permeabilize, sculpt, or otherwise functionalize lipid vesicles. In a complementary strategy, DNA architectures have been used as scaffolds to direct the growth of lipid membrane vesicles. Here we introduce a simple and broadly applicable method to realize freestanding, membrane-mimicking DNA shells: DNA shells are first assembled on the outer surface of giant unilamellar vesicles and then liberated by surfactant-mediated liposome removal. The resulting structures faithfully retain the geometry of their membrane template. We demonstrate the approach with two distinct classes of DNA tectons: a complex barrel-shaped DNA origami with programmable inter-subunit interactions, and a simple nanostar-inspired motif composed of only eleven oligonucleotides. The site-specific addressability of the former enable the rational design of binding interfaces, as demonstrated by controlled multilayer formation. The success of both strategies underscores the generality of our approach and the feasibility of creating shell-like compartments from different DNA architectures. This method enables the construction of tunable, DNA-only containers spanning the size range of eukaryotic cells, offering a fundamentally new type of compartmentalization for bottom-up synthetic biology.

Large-scale nanoarrays of single biomolecules enable high-throughput assays while unmasking the underlying heterogeneity within ensemble populations. Until recently, creating such grids which combine the unique advantages of microarrays and single-molecule experiments (SMEs) has been particularly challenging due to the mismatch between the size of these molecules and the resolution of top-down fabrication techniques. DNA Origami Placement (DOP) combines two powerful techniques to address this issue: (i) DNA origami, which provides a [~] 100-nm self-assembled template for single-molecule organization with 5 nm resolution, and (ii) top-down lithography, which patterns these DNA nanostructures, transforming them into functional nanodevices via large-scale integration with arbitrary substrates. Presently, this technique relies on state-of-the-art infrastructure and highly-trained personnel, making it prohibitively expensive for researchers. Here, we introduce a bench-top technique to create meso-to-macro-scale DNA origami nanoarrays using self-assembled colloidal nanoparticles, thereby circumventing the need for top-down fabrication. We report a maximum yield of 74%, two-fold higher than the statistical limit of 37% imposed on non-specific molecular loading alternatives. Furthermore, we provide a proof-of-principle for the ability of this nanoarray platform to transform traditionally low-throughput, stochastic, single-molecule assays into high-throughput, deterministic ones, without compromising data quality. Our approach has the potential to democratize single-molecule nanoarrays and demonstrates their utility as a tool for biophysical assays and diagnostics.

Multivalency enables nanostructures to bind molecular targets with high affinity. Although IgG antibodies can be generated against a wide range of antigens, their shape and size cannot be tuned to match a given target. DNA nanotechnology provides an attractive approach for designing customized multivalent scaffolds due to the addressability and programmability of the nanostructure shape and size. Here, we use computational simulation to guide the design and synthesis of a DNA nanostructure-based synthetic antibody ("nano-synbody"). The nano-synbody is comprised of a three-helix bundle DNA nanostructure with three identical arms terminating in a mini-binder protein that targets the SARS-CoV-2 spike protein. The structure was designed to match the valence and distance between the three receptor binding domains (RBDs) in the spike trimer, in order to enhance binding through avidity effects. Moreover, the design allowed for the display of one, two, or three protein-displaying arms, thereby systematically probing the effect of multivalency on binding affinity. The binding strength of the nano-synbody increased with the increasing number of arms, yielding 11.2 pM affinity ([~]100-fold enhancement over monovalent binding) for the wild-type spike protein for the three-arm structure. Moreover, the multivalency was able to yield a 95 pM affinity for the Omicron variant, a mutant against which the monovalent protein was ineffective. The nano-synbody could also block infection of a spike protein-bearing pseudovirus, and similarly demonstrated effective inhibition of the Omicron variant when trimerized. The structure of the three-arm nano-synbody bound to the Omicron variant spike trimer was solved by negative-stain transmission electron microscopy reconstruction, and shows the protein-DNA nanostructure with all three arms bound to the RBD domains, confirming the intended trivalent attachment. Finally, nano-synbody binding could be reversed by removing one, two, or three arms in a programmable fashion, via toehold-mediated strand displacement. The ability to tune the size and shape of the nano-synbody, as well as its potential ability to attach (and then remove) two or more different binding ligands, will enable the high-affinity binding of a range of proteins, and pave the way towards their manipulation using DNA-based nano-robotic devices.

Biological membrane channels mediate information exchange between cells and facilitate molecular recognition1-4. While tuning the shape and function of membrane channels for precision molecular sensing via de-novo routes is complex, an even more significant challenge is interfacing membrane channels with electronic devices for signal readout5-8. This challenge at the biotic-abiotic interface results in low efficiency of information transfer - one of the major barriers to the continued development of high-performance bioelectronic devices9. To this end, we integrate membrane spanning DNA nanopores with bioprotonic contacts to create programmable, modular, and efficient artificial ion-channel interfaces that resolve the iono-electronic disparity between the biotic environment and electronics. Through simulations and experiments, we show that cholesterol modified DNA nanopores spontaneously and with remarkable affinity span the lipid bilayer formed over the planar bio-protonic electrode surface and mediate proton transport across the bilayer. Using the ability to easily modify DNA nanostructures, we illustrate that this bioelectronic device can be programmed for electronic recognition of biomolecular signals such as presence of Streptavidin, without disrupting the native environment of the biomolecule. We anticipate this robust biotic-abiotic interface will allow facile electronic measurement of inter-cellular ionic communication and also open the door for active control of cell behavior through externally controlled selective gating of the channels.

Techniques from structural DNA nanotechnology make it possible to assemble complex 3-dimensional nanostructures with virtually arbitrary control over their sizes, shapes and features at length scales of 3-100 nm, providing a flexible means for constructing nanoscale devices and machines. Here, we assemble micron-length DNA nanotubes and assess their performance as pipes for controlled ion transport. DNA nanotubes grow via assembly of DNA tiles from a seed pore, a 12-helix DNA origami cylinder functionalized with cholesterol, to form a DNA nanotube channel. The central channel of a nanotube can be obstructed via Watson-Crick hybridization of a channel cap, a second DNA origami structure, to the end of a nanotube channel or a nanotube seed pore. Single-channel electrophysiological characterization shows that both nanotube seed pores and nanotube channels display ohmic ion conductance consistent with their central channels diameters. Binding of the channel cap reduces the conductances of both DNA nanotube channels and seed pores, demonstrating control of ion-transport through these micron-length channels. Because these channels could be assembled into branched architectures or routed between specific molecular terminals, these results suggest a route to self-assembling nanofluidic devices and circuits in which transport can be controlled using dynamic biomolecular interactions.

DNA has emerged as a powerful substrate for programming information processing machines at the nanoscale. Among the DNA computing primitives used today, DNA strand displacement (DSD) is arguably the most popular, with DSD-based circuit applications ranging from disease diagnostics to molecular artificial neural networks. The outputs of DSD circuits are generally read using fluorescence spectroscopy. However, due to the spectral overlap of typical small-molecule fluorescent reporters, the number of unique outputs that can be detected in parallel is limited, requiring complex optical setups or spatial isolation of reactions to make output bandwidths scalable. Here, we present a multiplexable sequencing-free readout method that enables real-time, kinetic measurement of DSD circuit activity through highly parallel, direct detection of barcoded output strands using nanopore sensor array technology (Oxford Nanopore Technologies MinION device). We show that engineered reporter probes can be detected and classified with high accuracy at the single-molecule level directly from raw nanopore signals using deep learning. We then demonstrate this methods utility in multiplexed detection of clinically relevant microRNA sequences. These results increase DSD output bandwidth by an order of magnitude over what is possible with fluorescence spectroscopy, laying the foundations for a new paradigm in DNA circuit readout and programmable multiplexed molecular diagnostics using portable nanopore devices.

The development of sorting strategies that directly report on functional activity remains a bottleneck in synthetic cell research. Current methodologies typically rely on sequential label-dependent probing, which limits throughput. Here, we introduce a label-free, buoyancy-driven selection strategy in which the mode of separation and the mode of decision-making are intrinsically linked, coupling pore activity directly to the synthetic vesicles internal density in a one-pot assay. In this system, sorting emerges intrinsically: Giant unilamellar vesicles (GUVs) that contain a dense medium sediment by default, while only those with functional transmembrane pores undergo solute exchange, leading to density equilibration and flotation. We exploit this principle to separate pore-active from non-functional GUVs without external markers or imaging-based readouts. Using protein pores and DNA origami and DNA tile nanopores, we demonstrate that buoyancy-driven separation enables parallel functional assessment of heterogeneous populations and supports flow-based enrichment of highly active synthetic cells. By directly linking molecular transport performance to GUV buoyancy, this approach collapses decision-making into the physical separation process itself, providing a scalable platform for screening, sorting, and evolving membrane pores in synthetic cell systems.

Programmable technologies that sense specific nucleic acid signatures in living cells and trigger cellular functions hold significant potential for biotechnology and medicine. Here, we developed SONAR (Sensing Of Nucleic acids using ASOs and Reverse-transcriptases), a platform that enables the detection of target DNA and RNA sequences and triggers controlled gene expression in human cells. SONAR operates through circularizable single-stranded DNA (ssDNA) sensors that, upon hybridization with complementary DNA or reverse-transcribed RNA, undergoes target-dependent ligation via endogenous ligases, subsequently driving expression of genetic payloads. For RNA sensing, we employed chemically modified antisense oligonucleotides (ASOs) to prime targeted reverse transcription, generating complementary DNA that promotes ssDNA circularization. We demonstrate SONARs ability to detect DNA, exogenous and endogenous RNA transcripts, coupled with a programmable expression of diverse protein payloads, including reporters, recombinases, and genome editors. This platform establishes a versatile framework for targeted nucleic acid detection and inducible gene expression, with broad applications in diagnostics, therapeutics, and synthetic biology.

Quantitative analysis of protein interactions and the formation of higher-order assemblies in living cells remains a major challenge. Here, we introduce a versatile nanopatterning toolbox that employs capillary nanostamping of functionalized polymers to generate high contrast bio-functionalized nanodot arrays (bNDAs) with diameters below 500 nm. By leveraging orthogonal adaptor designs, we achieve robust immobilization of diverse fluorescent protein fusions, enabling simultaneous and selective recruitment of cytosolic and membrane-associated proteins into discrete nanodomains. This approach of forming cytosolic nanodot arrays (cNDAs) provides striking capabilities for dissecting cytosolic multiprotein complexes with molecular precision. Focusing on the assembly of the multimeric myddosome complex, we demonstrate density-dependent recruitment and co-localization of the core components MyD88, IRAK4, IRAK1, and TRAF6 within cNDAs. Super-resolution microscopy reveals distinct nanoscale clustering of MyD88 and IRAK4 and uncovers the ultrastructural architecture of IRAK4 oligomers. These analyses highlight the spatial organization and hierarchical assembly of the myddosome at the nanoscale in the native cellular context. Collectively, our findings establish cNDAs as a powerful platform for reconstituting and analyzing intricate multiprotein assemblies in live cells, offering new opportunities for elucidating the principles of complex protein networks.

Oxytocin plays a critical role in regulating social behaviors, yet our understanding of its role in both neurological health and disease remains incomplete. Real-time oxytocin imaging probes with the spatiotemporal resolution relevant to its endogenous signaling are required to fully elucidate oxytocin function in the brain. Herein we describe a near-infrared oxytocin nanosensor (nIROx), a synthetic probe capable of imaging oxytocin in the brain without interference from its structural analogue, vasopressin. nIROx leverages the inherent tissue-transparent fluorescence of single-walled carbon nanotubes (SWCNT) and the molecular recognition capacity of an oxytocin receptor peptide fragment (OXTp) to selectively and reversibly image oxytocin. We employ these nanosensors to monitor electrically stimulated oxytocin release in brain tissue, revealing oxytocin release sites with a median size of 3 m which putatively represents the spatial diffusion of oxytocin from its point of release. These data demonstrate that covalent SWCNT constructs such as nIROx are powerful optical tools that can be leveraged to measure neuropeptide release in brain tissue.

Remote control of cellular functions via magnetic forces offers unique opportunities in fundamental research and biomedical application. Intracellular delivery of functionalized magnetic nanoparticles (MNP) provides versatile opportunities to assemble signalling platforms for spatiotemporal control by magnetic forces. Such magnetogenetic application, however, has remained highly challenging due to a lack of MNP providing suitable biological, physicochemical and magnetic properties. Here, we achieved single-step surface coating of synthetic maghemite core nanoparticles with green fluo-rescent protein fused to the iron binding site of Mms6 from magnetotactic bacteria. We yielded MNP with intracellular stealth properties (syMagIcS), which could be readily biofunctionalized in situ and translocated within cells via magnetic field gradients. We successfully exploited syMagIcS for spati-otemporal control of Rac1 signalling at the plasma membrane via its guanine nucleotide exchange factor protein TIAM1 and for spatial control of liquid-liquid phase separation using the intrinsically disordered domain of the protein DDX4.

Intricate self-organization is essential in many biological processes, underpinning vital functions and interactions. In an effort to mimic such processes, synthetic biology aims to engineer dynamic structures with controllable functions using nanotechnological tools. A key requirement of engineered building blocks is the ability to assemble and disassemble hierarchically with precision. Using the DNA origami technique, we here present the moDON, a modular DNA origami nanostructure, which is capable of assembling into almost 20 000 diverse monomers, forming complex and controlled superstructures in three dimensions. While shape and addressability of DNA origami are nearly arbitrary, its overall size is limited by the scaffold size. Previous methods of extending the size of DNA origami (e.g. hierarchical assembly, modified scaffolds, etc.), either led to loss over control of shape and addressability beyond monomers or to proportionally increased cost and design effort. With the moDON we were able to overcome both issues. The modular design combines xy- and z-plane assembly methods, enabling the construction of finite and periodic structures beyond 1 GDa. We demonstrate xy-z orthogonality, by enabling controlled selective or parallel assembly and disassembly via distinct orthogonal triggers. The kinetic profile of assembly and disassembly aligns with biological time scales, paving the way for applications in dynamic nanomachinery and advanced biomaterials. Finally, we showcase the conjugation of gold nanoparticles to specific positions within superstructures, underscoring the efficacy of this approach for creating intricate and orthogonal nanoscale architectures with preserved site-specific addressability. The moDON thus offers an efficient, cost-effective solution for constructing large, precisely organized, and fully addressable structures with vast potential in synthetic cellular systems design.

Small extracellular vesicles (sEVs), or exosomes, play important roles in physiological and pathological cellular communication. sEVs contain both short and long non-coding RNAs that regulate gene expression and epigenetic processes. Studying the intricacies of sEV function and RNA-based communication requires tools capable of labeling sEV RNA. Here we developed a novel genetically encodable reporter system for tracking sEV RNAs comprising an sEV-loading RNA sequence, termed the EXO-Code, fused to a fluorogenic RNA Mango aptamer for RNA imaging. This fusion construct allowed the visualization and tracking of RNA puncta and colocalization with markers of multivesicular bodies; imaging RNA puncta within sEVs; and quantification of sEVs. This technology represents a useful and versatile tool to interrogate the role of sEVs in cellular communication via RNA trafficking to sEVs, cellular sorting decisions, and sEV RNA cargo transfer to recipient cells.

To meet the constantly improving spatial resolution offered by advanced microscopy techniques to study sub-cellular structures in biology, there is a need for small, monovalent probes that label proteins of interest with high specificity and minimal distance to the target, and are compatible with various imaging modalities. In this direction, we designed a strategy to generate minimal-size probes composed of a controlled 1:1 conjugate between a small domain binder and a 1.4 nm-gold nanoparticle with direct access to fluorescent labelling for dual light-electron microscopy. Our approach was applied to the widely used single-domain antibody against GFP (GBP). The modified GBP-gold conjugate retained normal binding to purified GFP in vitro, specifically labelled COS-7 cells and neurons expressing GFP-tagged synaptic membrane proteins, and penetrated readily into tight cell-cell contacts including neuronal synapses. The optional fluorescence labelling with a second ALFA nanobody allowed dSTORM imaging, while the silver-enhanced nanogold particle detected in TEM was used to characterize the number and nanoscale organization of individual proteins in the synaptic cleft. We counted a small number of endogenous neurexins in the pre-synapse and a larger number of AMPA receptors in the post-synapse, often aligned in nanodomains. This GBP-gold probe thus emerges as a potent tool to label an ever-increasing repertoire of GFP-tagged proteins in numerous biological organisms and models.

Efficient siRNA delivery by lipid nanoparticles (LNPs) is widely attributed to carrier composition, yet how intraparticle packing governs function remains unclear. Here, we developed a single-particle fluorescence microscopy assay that simultaneously quantifies size and siRNA loading of individual, chromophore-labeled LNPs. Imaging [~]0.5M particles per hour uncovered two major packing modes: a high and a low order corroborated by cryo-EM. Quantitative live cell imaging on destabilized eGFP reporter cell line combined with systematic variation of LNPs lipid composition and N/P ratio allowed deconvolution of the interplay between siRNA packing, cell internalization and silencing and its dependance on lipid composition and electrostatics. Our findings surprisingly revealed that low-order particles while encapsulating modest RNA, they mediate more efficient knockdown of the destabilized eGFP reporter than their high-order counterparts. Guided by these findings we predicted and experimentally validated that tuning composition and N/P ratio to favor less compact siRNA packing enhances silencing potency. This framework offers actionable guiding for the rational optimization of LNP formulations for RNA therapeutics.

The delivery of nanotherapeutics to specific tissues relies on bespoke targeting strategies or invasive surgeries. Conversely, adeno-associated viruses (AAVs) can target specific tissues following intravenous injections. Here we show that cell-targeting properties of AAVs could be broadly conferred to nanomaterials. We develop a strategy to couple AAV capsids to nanoparticles that is invariant of viral serotype or nanomaterial chemistry and permits control over stoichiometry of the AAV-nanoparticle chimeras. The chimeras selectively escort nanoparticles into cell classes governed by AAV serotypes. When applied to magnetic nanoparticles, the AAV-nanoparticle chimeras enable magnetically localized gene delivery. In vivo, we show that leveraging the brain-targeting AAV serotype CAP-B10 achieves nanoparticle delivery to the parenchyma with [~]10% efficiency (% injected dose/g[brain]) while avoiding accumulation in the liver. The enhanced delivery efficiency and tissue specificity highlight the potential of AAV-chimeras as a versatile strategy to escort broad classes of nanotherapeutics to the brain and beyond.

Incorporation of colloidal quantum emitters into silicon-based photonic devices would enable major advances in quantum optics. However, deterministic placement of individual sub-10 nm colloidal particles onto micron-sized photonic structures with nanometer-scale precision remains an outstanding challenge. Here, we introduce Cavity-Shape Modulated Origami Placement (CSMOP) that leverages the structural programmability of DNA origami to precisely deposit colloidal nanomaterials within lithographically-defined resist cavities. CSMOP enables clean and accurate patterning of origami templates onto photonic chips with high yields. Soft-silicification-passivation stabilizes deposited origamis, while preserving their binding sites to attach and align colloidal quantum rods (QRs) to control their nanoscale positions and emission polarization. We demonstrate QR integration with photonic device structures including waveguides, micro-ring resonators, and bullseye photonic cavities. CSMOP therefore offers a general platform for the integration of colloidal quantum materials into photonic circuits, with broad potential to empower quantum science and technology.

Proteins exist in diverse biochemical states, including oligomers, complexes, heterogeneous proteoforms and shed fragments that encode functional and regulatory information. Yet, these molecular states remain difficult to resolve with existing analytical techniques, which typically require labelling, immobilisation or amplification and collapse this information into a single readout. Here, we introduce a modular platform that integrates programmable DNA nanostructures with single-molecule mass photometry for rapid, label-free and multiplexed protein analysis in native and complex media, without washing, enrichment or immobilisation, making native biochemical states observable directly in serum and plasma. DNA nanostructures act as nanosensors whose mass and mobility on supported lipid bilayers provide orthogonal identifiers for target identity and biochemical state, thereby decoupling recognition from readout. We define the analytical specificity and response window, demonstrate quantitative affinity determination, and resolve oligomeric and proteoform differences under native conditions. The nanosensors are rapidly reprogrammable to new targets, support multiplexed detection with internal controls for non-specific interactions, and enable selective resetting via strand displacement. Together, these capabilities establish nanoscale programmability as a route to state-resolved single-molecule protein profiling adaptable to both diagnostic and mechanistic applications.