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Nature Nanotechnology

Springer Science and Business Media LLC

Preprints posted in the last 30 days, ranked by how well they match Nature Nanotechnology's content profile, based on 30 papers previously published here. The average preprint has a 0.05% match score for this journal, so anything above that is already an above-average fit.

1
Programmable DNA Origami Caps for Site-Selective Functionalization of Microtubule Tips and Lattice Defects

Carey-Morgan, H.; Palestina-Romero, B.; Atabay, A.; Bath, J.; Turberfield, A.; Krieg, E.; Diez, S.

2026-05-11 bioengineering 10.64898/2026.05.08.722927 medRxiv
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Microtubules are central components of cytoskeletal transport systems and have been widely repurposed as active elements in motor-driven nanodevices. However, site-specific functionalization of stabilized microtubules remains a fundamental challenge, as the tubulin lattice presents chemically indistinguishable binding sites along its length. Here we report a strategy for selective end-functionalization of stabilized microtubules using DNA origami nanostructures. By coupling DNA origami to Fab fragments targeting acetylated -tubulin Lys40 within the microtubule lumen, and exploiting steric exclusion of the origami from the lattice interior, binding is confined to accessible sites at microtubule ends and lattice defects. Using a six-helix bundle origami as a minimal construct, we demonstrate selective tip labelling of gliding microtubules without perturbing kinesin-driven motility. The same structures additionally mark lattice defects, enabling dynamic visualization of defect sites during transport. Furthermore, we show that tip-bound origami can hybridize with complementary DNA strands to capture cargo from surfaces in motion, establishing programmable, end-specific loading. This approach introduces a generalizable route to spatially controlled functionalization of cytoskeletal filaments, enabling new capabilities in molecular transport, nanoscale assembly, and the study of microtubule integrity and repair.

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Membrane sialylation orchestrates cellular gateways: A spatiotemporal analysis of cellular transport using DNA nanocages via membrane charge modulation

Prakash, G.; Parmar, B.; Dave, H.; Dhanasekaran, S.; Bhatia, D. D.

2026-05-08 bioengineering 10.64898/2026.05.05.722926 medRxiv
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Negatively charged DNA nanostructures, such as tetrahedral nanocages, are internalized by cells despite the electrostatic repulsion from the anionic cell membrane, and, paradoxically, cancer cells, which carry intrinsically higher negative charge due to overexpression of sialic acids on their cell surface, show markedly higher uptake than normal cells. This contradiction exposes a fundamental gap in our understanding of how these anionic nanostructures overcome this repulsion. Using chemical modulation of cell-surface sialylation in RPE1 cells to create three groups with altered sialylation levels, together with inhibitor-based dissection of endocytic pathways, we demonstrate that an increase in cell surface sialylation governs the uptake of DNA tetrahedra not through electrostatics but by structurally remodeling the cell membrane via rearrangement of the GM1 lipid raft microdomain, recruiting caveolae-mediated endocytosis as an additional pathway alongside clathrin-mediated endocytosis, thereby increasing the intake of the nanostructure. These findings reframe tumor hyper-sialylation as a determinant of the uptake of anionic nanostructures, such as DNA tetrahedra, and as a targetable parameter for rational optimization of DNA-based nanotherapeutics against cancer. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/722926v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@10eede7org.highwire.dtl.DTLVardef@124dd56org.highwire.dtl.DTLVardef@13f5355org.highwire.dtl.DTLVardef@780ecf_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Falafel-Style Wrapping of AuNPs for DNA Origami Barcodes

Youssef, S.; Swope, T.; Schmidt, T. L.; Goncalves, D. P. N.

2026-05-20 biophysics 10.64898/2026.05.18.725969 medRxiv
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The ability to encode and reliably read nanoscale information is increasingly important for multiplexed biomolecular detection and super-resolution imaging. DNA origami provides a uniquely programmable platform for arranging structural and functional elements with nanometer precision, enabling the creation of identifiable nanoscale patterns. In this context, DNA origami-based barcodes that incorporate gold nanoparticles (AuNPs) to encode either origami geometry or the identity of specific biological targets within defined nanoparticle patterns have been paired with transmission electron microscopy imaging for decoding. However, surface-bond AuNPs may detach during handling, purification, or biological incubation, leading to misidentification or decoding errors in barcode analysis. Here we report a rational design for the controlled encapsulation of AuNPs within DNA origami tubes to enhance nanoparticle retention and structural integrity. We engineered curvature-inducing modifications in a flat rectangular DNA origami scaffold to promote inward folding and confinement of AuNPs. These barcodes can be further functionalized on the outer surface with bioactive aptamers and/or fluorescence dyes, enabling targeted interactions with cells and optical readout. Programable dimerization further expands multiplexing capacity. This design provides a robust framework for structurally stable origami barcodes and advances the development of high-resolution, multiplexed labeling and diagnostic platforms. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=60 SRC="FIGDIR/small/725969v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@686c1aorg.highwire.dtl.DTLVardef@1914c4eorg.highwire.dtl.DTLVardef@28ad47org.highwire.dtl.DTLVardef@8847ca_HPS_FORMAT_FIGEXP M_FIG C_FIG

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An extracellular vesicle biogenesis-inspired engineering platform for efficient protein delivery and therapeutic base editing

Xie, S.; Yang, Q.; Ilahibaks, N.; Qu, K.; Yao, B.; Vader, P.; Brans, M. A. D.; Snijders Blok, C.; Gunnarsson, A.; Doevendans, P. A.; Xiao, J.; Schiffelers, R.; Lei, Z.; Sluijter, J.

2026-05-18 bioengineering 10.64898/2026.05.18.721905 medRxiv
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Efficient and controllable delivery of genome-editing proteins remains a central challenge for therapeutic translation of gene-editing technologies. Extracellular vesicles (EVs) offer an attractive non-viral delivery modality due to their biocompatibility and large capacity for cytosolic cargo delivery. Yet, rational strategies to achieve controlled and programmable protein loading are still lacking. Here, we present NEO-TOP-EVs, an EV biogenesis-guided engineering platform that systematically integrates key features of three design principles inspired by vesicle formation: 1) PI(4,5)P2-mediated plasma membrane targeting, 2) ESCRT-dependent membrane scission, and 3) self-assembly-driven cargo clustering for enabling efficient encapsulation of genome-editing ribonucleoproteins. Together, the NEO design increased cargo incorporation and enhanced functional delivery of gene editing modalities under particle-normalized conditions. Using NEO-TOP-EVs, we achieve efficient delivery of Cas9 and adenine base editor ribonucleoproteins without nucleic acid templates. In an in vitro proof-of-concept, delivery of an adenine base editor targeting proprotein convertase subtilisin/kexin type 9 (PCSK9) induces efficient splice-site disruption, resulting in reduced PCSK9 expression and enhanced LDL receptor activity. Proof-of-concept in vivo experiments provide preliminary evidence of functional Cre protein delivery to the liver. Together, these findings establish NEO-TOP-EVs as a modular platform for protein-based genome editing, demonstrating how biogenesis-informed EV engineering yields functional protein delivery at levels relevant to therapeutic development.

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Sequentially Self-Assembled Supramolecular Nanocomplexes Enable Systemic Cas9 RNP Delivery and In Vivo Tumor Genome Editing

Matsuo, T.; Honda, Y.; Chino, T.; Nomoto, T.; Osakabe, Y.; Miura, Y.; Nishiyama, N.

2026-05-12 bioengineering 10.64898/2026.05.08.723716 medRxiv
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In vivo genome editing with CRISPR-Cas9 ribonucleoproteins (RNPs) holds substantial therapeutic promise, yet rapid bloodstream clearance and the absence of delivery systems capable of systemic tumor targeting have hindered its clinical translation. Herein, a supramolecular ternary complex platform is reported in which Cas9/sgRNA RNPs are co-assembled with tannic acid (TA) and phenylboronic acid (PBA)-conjugated polymers through sequential self-assembly, producing [~]30 nm core-shell ternary complexes that protect RNPs from enzymatic degradation and dissociate selectively at endosomal pH. Upon intravenous administration in subcutaneous tumor-bearing mice, these ternary complexes exhibit prolonged blood circulation and preferential tumor accumulation, achieving 37.2% gene editing at tumor sites compared with only 1.5% for free RNPs. The platform successfully knocks out previously undruggable oncogenes including mutant KRAS and polo-like kinase 1 (PLK1), markedly suppressing tumor growth in vivo. By integrating sequential supramolecular self-assembly with stimuli-responsive cargo release, this strategy establishes a generalizable framework for systemically administered in vivo CRISPR therapeutics.

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Mirror-Image L-DNA Nanocubes for Stable and Targeted Multimodal Drug Delivery

Farkaly, T.; Wu, S.; Dantsu, Y.; Tapash, A.; Zhang, W.

2026-05-22 biochemistry 10.64898/2026.05.20.726533 medRxiv
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Nucleic acid nanostructures provide programmable architectures for molecular delivery but remain limited by rapid nuclease degradation, poor in vivo persistence and inefficient intracellular cargo release. Here we report a mirror-image L-DNA nanocube as a biologically persistent and modular therapeutic delivery platform. The nanocube self-assembles from synthetic L-DNA oligonucleotides into a structurally defined architecture that exhibits substantially enhanced resistance to enzymatic degradation and prolonged stability under physiological conditions compared with the corresponding D-DNA nanostructure. Surface functionalization with folic acid enables selective tumour targeting in vitro and in vivo. The L-DNA nanocube supports the delivery of chemically distinct therapeutic cargos, including doxorubicin, a bortezomib prodrug and MCL1-targeting small interfering RNA (siRNA). In tumour-bearing mice, L-DNA nanocube-mediated delivery improves therapeutic efficacy while reducing systemic toxicity relative to free drug and D-DNA nanocube controls. For siRNA delivery, we engineer a pH-responsive release mechanism that promotes endosomal escape and cytosolic cargo localization, as visualized by cryo-electron tomography, resulting in efficient gene silencing. Together, these results establish mirror-image nucleic acid nanostructures as a class of biologically functional nanomaterials for programmable intracellular therapeutic delivery.

7
Sequence-Defined Digital Bottlebrush Polymers for Programmable Oligonucleotide Delivery

Lin, J.; Sun, T.; Wei, Y.; Xue, C.; Xu, G.; Chen, P.; Wang, Y.; Yang, S.; Cavazos, C.; Shen, C.; Wang, A.; Wang, A.; Zhang, K.

2026-05-13 bioengineering 10.64898/2026.05.09.723525 medRxiv
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Oligonucleotide therapeutics hold transformative potential, yet their clinical translation is hindered by delivery barriers, including rapid renal/hepatic clearance and poor organ specificity. Bottlebrush polymers conjugates have emerged as a promising vector to address these limitations, but conventional architectures with uniform backbones can only achieve an unmodifiable, rigid biodistribution profile. Here, we report a library of sequence-defined "digital" bottlebrush polymers, precisely engineered with controlled placements of chemical motifs that modify physiochemical properties - including lipids, cholesterol, and cationic groups - along a polyphosphodiester backbone. Systematic evaluation of the digital bottlebrush polymer library reveals distinct structure-property relationships and enables organ-biased systemic delivery to several traditionally difficult-to-reach tissues, including muscle and skin. In a mouse model of rheumatoid arthritis, a single dose of a spleen-homing polymer-conjugated antisense oligonucleotide targeting TNF- achieves potent knockdown and drives full functional recovery. These findings establish a versatile design framework for tailoring bottlebrush polymers to specific therapeutic applications.

8
Decoupling Fabrication from Encoding: DNA-Addressable Template Microparticles for Large, User-Defined Optical Barcode Libraries

Eguchi, A.; Iwamoto, Y.; Narita, H.; Tokuda, H.; Martin, A. M.; Ota, S.

2026-05-13 bioengineering 10.64898/2026.05.10.723434 medRxiv
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Optical barcodes for pooled high-throughput screening must support large libraries while remaining decodable in a single imaging step. Existing approaches often trade design control for manufacturability: deterministic barcodes often require per-code redesign of particle fabrication, whereas stochastic combinatorial barcodes are difficult to generate as predefined batches. Here we introduce a chemically programmable barcoding architecture that decouples particle fabrication from barcode assignment. Using a contact-free multilaminar flow lithography platform with all-around three-dimensional sheathing, we continuously fabricate a universal hydrogel scaffold containing five spatially segregated DNA-addressable domains at rates >106 particles/h. Chosen barcode identities are subsequently written on demand onto the same template batch by domain-selective DNA hybridization. Single-domain measurements resolved 64 candidate optical states, indicating an experimentally informed theoretical upper bound of 645 {approx} 1.1 x 109 barcodes. We further implemented a predefined 59,049-code library by split-pool labeling, achieving an 88% recovery of decoded beads at a stringent posterior threshold (>0.95). After 11 days, >7,800 beads were correctly re-identified at >0.95 accuracy in matched fields of view. This strategy provides a highly scalable, chemically programmable route to build large, user-defined optical barcode libraries with single-image optical readout and longitudinal traceability.

9
Acoustofluidic Active Flow Sculpting Enables Dynamic, Reconfigurable Cross-Sectional Patterning

Sahin, M. A.; Stoecklein, D.; Park, J.; Destgeer, G.

2026-05-13 bioengineering 10.64898/2026.05.10.724179 medRxiv
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Microstructures created with flow lithography exhibit distinct functionality depending on the shape and composition of the precursor fluids, enabling applications from tissue engineering to anti-counterfeiting. However, current techniques rely on static nozzle geometries or passive hydrodynamic focusing, which commit to a fixed structure and limit dynamic reconfiguration of material architecture during fabrication. Here, we introduce ActiSculpt, an acoustofluidic platform that replaces in-channel physical structures with programmable, electronically driven acoustic streaming. By exploiting the interplay between laminar stability and acoustic streaming, we decouple deterministic fluid deformation from chaotic mixing, achieving a continuous cross-sectional displacement sensitivity of ~15 m/V. We demonstrate the generation of a diverse library of hydrogel particles whose cross-sectional moments of inertia are tunable up to 5.5-fold, establishing a direct, geometry-mediated link between acoustic parameters and the moments that govern bending and torsional rigidity. We further demonstrate continuous fiber fabrication in which acoustic parameters are varied in real time, encoding structural variation along the fibers length. The result is a platform that overcomes the one-device, one-geometry constraint of existing techniques, enabling not only on-demand reconfiguration between fabrication runs but also real-time control of material architecture. This spatiotemporal control establishes a new design axis for soft-material manufacturing.

10
T-cell Receptor (TCR) targeting with Multivalent T-cell Engagers

Paul, D.; Kulkarni, A.; Rodriguez, F.; Dahlberg, D.; Rozumalski, L.; Wagner, C. R.

2026-05-20 immunology 10.64898/2026.05.17.725710 medRxiv
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T-cell engagers (TCEs) for cancer immunotherapy have traditionally relied on high affinity single chain fragment variable (scFv) domains to target CD3, specifically the {varepsilon} chain, for the activation of T-cells. Despite their clinical success, there have been reports of TCEs driving systemic toxicity, non-specific T-cell activation, on-target off-tumor effects, and severe inflammation due to cytokine release. To address these limitations, we designed multivalent TCEs using Chemically Self-Assembled Nanorings (CSANs) that target the /{beta} constant region of the T-cell receptor (TCR) in the TCR/CD3 complex using a moderate affinity TCR nanobody (TCRVHH). Nanobodies offer superior physical and chemical properties over scFvs- including higher solubility, stability and lower production cost- making them increasingly popular as structural units of TCEs. We compared the efficacy and safety profile of this moderate affinity, nanobody-based TCR binder against high affinity CD3scFv based CSANs across EGFR and PSMA expressing solid tumor models. While the CD3scFv CSANs offered potent cytotoxicity, they also induced antigen independent T-cell activation bypassing the requirement of tumor crosslinking for cytotoxicity. In contrast the TCRVHH CSANs required strict antigen engagement to trigger cytotoxicity, significantly reducing non-specific T-cell activation and thus enhancing the safety profile. Although the initiation of cytotoxicity was kinetically slower than the CD3scFv counterpart, TCRVHH CSANs achieved comparable end point cytotoxicity across multiple antigen densities, as well as in 3D tumor spheroids. Through this study we demonstrate the applicability of nanobodies as T-cell targeting domains, enhanced specificity and safety of moderate affinity T-cells binders and the diversification of T-cell targeting epitopes without compromising the efficacy of TCEs.

11
Bacterial Swarming-Guided Biomineralization Enables Pattern Formation in Engineered Living Materials

Chaithanya, K. V.; Kumar, U.; Pushpavanam, K.

2026-05-08 bioengineering 10.64898/2026.05.05.722913 medRxiv
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Engineered living materials (ELMs) harness the adaptive and self-replicating capabilities of biological systems to create functional materials for sensing, catalysis, and biomineralization. While most ELM strategies rely on static microbial assemblies, the role of bacterial motility in structuring living materials remains unexplored. Here, for the first time, we demonstrate how swarming motility in Escherichia coli MG1655 can be induced to guide spatio-temporally organized calcium phosphate mineralization. The mineralized calcium phosphate is characterized by scanning electron microscopy and elemental analysis. By systematically varying phosphate sources and their concentrations in calcium-rich media, we observe the emergence of regularly spaced concentric mineralized patterns. The previously undocumented observation of the concentric patterns was rationalized through a continuum model that captures the spatiotemporal coupling between swarm expansion and mineral deposition. The model shows that this coupling can generate recurrent front arrest and restart, leading to concentric ring formation. Finally, we show that altering the phosphate species results in distinct mineral morphologies. Together, this work establishes a novel framework for integrating bacterial swarming with biomineralization, enabling dynamic and programmable pattern formation in ELMs.

12
Two-Dimensional Phase Separation of DNA Nanomotifs Anchored to Lipid Bilayers

Ramnarain, V.; Vazquez, A.; Labale, S.; Di Cicco, A.; Nakazawa, K.

2026-05-21 biophysics 10.64898/2026.05.19.724116 medRxiv
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Spatial organization and temporal regulation of membrane components are essential for achieving complex functions in artificial cells, such as cell division and signalling. DNA-based molecular tools provide a powerful means to control biomolecular interactions with high precision. Here, we investigate the phase behavior of cholesterol-modified, star-shaped DNA nanomotifs anchored to the lipid bilayers of giant unilamellar vesicles (GUVs), by using fluorescence confocal microscopy and cryo-electron microscopy. These motifs spontaneously anchor to the lipid bilayers via hydrophobic interactions and exhibit distinct spatial organization depending on their sticky end sequences. Motifs with complementary sticky end sequences interact and distribute uniformly, while orthogonal motifs with different sticky end sequences segregate into isolated gel-like domains with limited lateral mobility. Notably, the phase separation of motifs does not require lipid phase separation, indicating that DNA-driven organization can take place independently of lipid phase separation. The behavior of this system is governed by the interplay of three key parameters: (i) hydrophobic anchoring via cholesterol, (ii) electrostatic repulsion between negatively charged DNA nanomotifs, and (iii) sticky end interactions. The observed two-dimensional phase separation of orthogonal DNA nanomotifs at the GUV interface presents a novel strategy for controlling lateral membrane organization in GUV systems. This approach would offer flexibility in membrane composition and enables molecular positioning, thereby achieving a high degree of organization on the surface in artificial cell models.

13
Nature-inspired nanodiscs for lesion-targeted delivery reprogram macrophages and attenuate established abdominal aortic aneurysms

He, Z.; Huang, Y.; Wang, Y.; Ren, Q.; Xu, J.; Wang, Q.; Guo, L.-W.; Bao, H.

2026-05-16 bioengineering 10.64898/2026.05.13.724870 medRxiv
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Abdominal aortic aneurysm (AAA) is a life-threatening vascular disease characterized by chronic inflammation and immune dysregulation, with lesional macrophages playing a pivotal role in disease progression. However, effective and safe delivery of immune modulators to macrophages at the site of AAA remains a major clinical challenge. To address this unmet need, we report a nature-inspired nanodisc platform based on high-density lipoproteins for targeted delivery to lesional macrophages, further engineered with a multi-component targeting strategy incorporating an aneurysm-homing peptide and phosphatidylserine lipids. Nanodiscs encapsulating an anti-inflammatory protein kinase R-like endoplasmic reticulum kinase (PERK) inhibitor remarkably attenuated progression of established AAA in an elastase-induced mouse model. Using a combination of in vivo biodistribution and immune profiling approaches, we demonstrate that nanodisc-assisted PERK inhibitor delivery selectively reprograms the local immune microenvironment and attenuates pathological inflammation in AAA disease models. Notably, a single administration achieves sustained therapeutic efficacy with favorable safety profiles, effectively limiting the progression of established AAA in a clinically relevant setting. This work presents a new avenue of designer nanomedicines for targeted immunomodulation and maybe broadly applicable for a wide range of vascular and immune-mediated pathologies.

14
Programmable DNA Protonuclei Reveal Environmental Context on Protein Phase Separation

Fritzen, J.; Samanta, A.; Kuhr, N. S.; Preuss, A.; Sternburg, E.; Stelzl, L.; Michels, J.; Dormann, D.; Walther, A.

2026-05-08 synthetic biology 10.64898/2026.04.07.716875 medRxiv
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Understanding protein phase separation in cellular environments remains a major challenge, as ex vivo assays often fail to capture the influence of environmental context - such as crowding, multimodal interactions, and the dynamic properties of the cytosol or nucleus. Here, we introduce programmable DNA-based protonuclei (PN) as nucleus-inspired compartments to probe phase separation of the neurodegeneration-linked protein FUS. We show that FUS partitioning and condensate formation are highly sensitive to nucleic acid sequence, spatial confinement, and viscoelastic properties of the PN core. Notably, classical test-tube affinity assays fail to predict protein behavior within the crowded and multivalent PN environment. By tuning DNA crosslinking, we modulate condensate dynamics and suppress liquid-to-solid transitions of FUS - a hallmark of disease. These findings demonstrate that multivalent, confined environments fundamentally reshape protein-nucleic acid interactions and phase behavior. The PN platform complements test-tube assays and complex cellular settings and enables to dissect nuclear condensates under controllable conditions.

15
Amphiphilic Peptide Fusion Promotes Endocytic Uptake of Nanodiscs

Pizarro, B. S.; Reinhardt, T. G.; Semenske, J. A.; Ji, Z.; Jacobs, C. O.; Zeno, W. F.

2026-05-12 bioengineering 10.64898/2026.05.08.723726 medRxiv
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A major limitation across nanoparticle delivery platforms is sequestration within endosomal compartments, which restricts access to intracellular targets despite efficient cellular uptake. Here, we show that peptide architecture can be used to control intracellular trafficking and reduce endosomal accumulation in lipid-protein nanocarriers. Specifically, we fuse R6W3 (RRWWRRWRR), an amphipathic cell penetrating peptide, to the N- or C- terminus of the nanodisc scaffold proteins and systematically evaluate its impact on membrane interactions and cellular behavior. Structural and biophysical characterization confirms that R6W3 incorporation preserves nanodisc assembly and protein-lipid interactions, enabling direct attribution of functional differences to peptide-driven interfacial effects. R6W3-functionalized nanodiscs exhibit enhanced binding and cellular uptake, with N-terminal fusion producing the strongest interfacial interactions. In live cells, R6W3-functionalization increases endocytic activity, evidenced by increased formation of clathrin-coated pits and intracellular colocalization with clathrin-coated vesicles. Notably, R6W3-funtionalized nanodiscs display reduced accumulation in early endosomes relative to unmodified nanodiscs, indicating decreased endosomal sequestration following endosomal uptake. These trafficking differences translate to functional outcomes, as doxorubicin-loaded, R6W3-functionalized nanodiscs achieve greater cytotoxicity than unmodified controls at equivalent concentrations. Together, these results establish peptide architecture as a design parameter for controlling intracellular trafficking and overcoming endosomal bottlenecks, providing a broadly applicable strategy for improving nanocarrier- based delivery systems.

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Intracellular photonic crystals in photosynthetic sea slugs form via a kidney-mediated biomineralisation pathway

Humphrey, S.; He, X.; Raguin, E.; Haataja, J. S.; Priemel, T.; Schmitt, C. N. Z.; Brodie, J.; Greer, H. F.; Wangpraseurt, D.; Nelmes, L.; Fratzl, P.; Jesus, B.; Ogawa, Y.; Vignolini, S.

2026-05-08 biophysics 10.64898/2026.05.07.723475 medRxiv
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Sea slugs in the Sacoglossa superorder are some of the few animals capable of photosynthesising by isolating and maintaining functional chloroplasts within their body1,2. While this ability allows some species in this superorder, such as Elysia viridis, to appear green, camouflaging themselves within their surroundings3,4, this species is marked by extremely bright, coloured regions. Here, we show that these animals produce a yet undiscovered class of photonic structure consisting of intracellular mixed amorphous CaCO3 and calcite spherical nanoparticles organised in non-closed-packed face-centred cubic (FCC) lattices and photonic glasses5. By mapping the distribution of the cells containing such architectures, we suggest that their colour is linked both to their function and to their biological formation via the animals renal system. Using a combination of different optical methods and cryo-electron microscopy, we reveal that the biomineralisation pathway proceeds through stages of calcium ion concentration in the kidney, transport via internal vessels, and precipitation from a dense liquid-like precursor, culminating in the formation of monodisperse nanoparticles, which are the building blocks of these photonic structures.

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Modular Albumin-Chaperoned NIR-II Nanofluorophores Enables Pan-Ovarian Cancer Imaging Across Multiscale Tumor Models

Vasquez, I.; Nash, L.; Shahriar, M. T.; Megahed, M.; Cao-Xue, J.; De Leon, I.; Xu, C.; Bickel, U.; Raghavan, S. A.; Srivastava, I.

2026-05-11 bioengineering 10.64898/2026.05.06.717945 medRxiv
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Ovarian cancer remains the most lethal gynecological malignancy, primarily due to late-stage diagnosis and the challenges of achieving complete cytoreduction. While fluorescence image-guided surgery (FIGS) offers intraoperative visualization, current clinical agents are limited by insufficient brightness, rapid photobleaching, and poor molecular selectivity, particularly in the near-infrared window. Here, we report the rational modular design of ultrabright NIR-II semiconducting polymer (SP) nanofluorophores for high-fidelity ovarian cancer imaging. By nanoconfining of a representative hydrophobic SP within a functional albumin matrix induces a "chaperone" effect that suppresses aggregation-induced quenching and shifts emission in the NIR-II window (1000-1250 nm). This platform integrates a dual-receptor targeting strategy, leveraging intrinsic albumin-receptor interactions (GP60 and SPARC) alongside folate receptor alpha (FR) functionalization. This synergistic approach enables pan-ovarian cancer imaging by ensuring high-affinity binding across diverse tumor phenotypes, regardless of heterogeneous receptor expression. Across a multiscale validation framework, the nanofluorophores demonstrate efficient receptor-mediated endocytosis in 2D cultures and deep interstitial penetration in 3D tumor spheroids. Furthermore, microfluidic tumor-on-chip models incorporating endothelial-like fenestrations confirm controlled extravasation and targeting under physiological shear stress. 3D bioprinted tumor phantoms and ex vivo porcine ovary tissues further confirm that BSA-FA@SP2 provides superior lesion delineation and signal-to-background ratios compared to indocyanine green, a clinical standard. Importantly, the nanofluorophores exhibit excellent hemocompatibility, with minimal hemolysis and negligible complement activation, indicating a non-immunogenic, stealth profile. Collectively, this work establishes albumin-shielded NIR-II nanofluorophores as a robust platform for precision intraoperative pan-ovarian imaging and advances the translational potential of nanotechnology-enabled surgical oncology.

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In vitro evolution of DNA operators enables multivalency protein-DNA interactions: towards programmable transcription factor regulation

Adler, N. A.; Antelo, G. T.; Villarruel Dujovne, M.; Rondon, J. J.; Le, M. T.; Giedroc, D. P.; Peinetti, A. S.; Capdevila, D. A.

2026-05-04 synthetic biology 10.64898/2026.05.02.721436 medRxiv
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In vitro transcription (IVT) systems regulated by allosteric transcription factors (aTFs) are central to emerging cell-free biosensing and synthetic biology platforms, yet their performance is often limited by suboptimal protein-DNA interactions and the need for well-characterized regulatory elements. Here, we report an in vitro evolution strategy to engineer DNA operator sequences that enables tunable aTF-DNA interactions without requiring prior detailed knowledge of the native operator or regulatory mechanism. Using a SELEX-based approach with integrated positive and counter-selection steps, we evolved non-natural operators for the sulfane sulfur-responsive transcriptional repressor SqrR. The selected sequences preserve ligand-responsive allostery, with some sequences exhibiting enhanced binding affinity and reducing transcriptional leakage. Notably, we identify operator with binding behaviors consistent with cooperative recruitment of multiple SqrR dimers, suggesting that sequence architecture can modulate aTF-DNA interactions beyond affinity alone. Incorporation of these operators into IVT circuits improves transcriptional control and dynamic range, enabling the development of ROSALIND-based sensors for sulfane sulfur species, achieving sensitive and selective detection in a fully cell-free format. More broadly, this work establishes operator evolution as a programmable strategy to optimize transcription factor-DNA interactions and expand the design space of transcription-based biosensors, including for systems lacking well-characterized genetic components.

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Super-Resolution Macrophage Imaging via Ultrasound Localization Microscopy and Blinking Nanodroplets

Gotshal Zahavi, S.; Bismuth, M.; Bercovici, T.; Ilovitsh, T.

2026-05-11 bioengineering 10.64898/2026.05.07.723418 medRxiv
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Tracking immune cells deep within living tissue remains a fundamental challenge due to the diffraction-limited resolution of ultrasound imaging and the inability to resolve dense cellular populations. Here, we introduce an intracellular super-resolution ultrasound imaging framework based on stochastic phase-changing nanodroplets (NDs) and ultrasound localization microscopy (ULM). We engineer [~]170 nm perfluorocarbon NDs that undergo reversible, stochastic liquid-gas transitions under acoustic excitation, generating temporally sparse "blinking" signals. Leveraging the intrinsic endocytic activity of macrophages, these NDs are internalized, enabling intracellular contrast generation independent of vascular flow. We validate this approach across imaging scales, from controlled phantoms and in vitro systems to in vivo tumor models, demonstrating robust intracellular blinking, high cell viability, and consistent super-resolution reconstruction in dense cellular environments. The stochastic blinking of internalized NDs provides the temporal separation required to localize individual sources, overcoming a central limitation of conventional ULM. Following systemic administration, ND-labeled macrophages are tracked in vivo after homing to the liver, where super-resolution ULM resolves cellular distributions with a spatial resolution of 26.3 {+/-} 3.2 {micro}m, corresponding to a 6.1-fold improvement over diffraction-limited imaging. This work establishes a previously unexplored paradigm for ultrasound-based intracellular super-resolution imaging, enabling non-invasive visualization of immune cell organization in deep tissue. By introducing spatiotemporally programmable intracellular contrast, this approach expands ultrasound beyond vascular imaging toward functional cellular imaging, with broad implications for immunology, diagnostics, and cell-based therapies.

20
Covalent tumor anchoring spatially orchestrates antitumor immunity

Li, Q.; Chen, H.; Zhang, P.; Cao, L.; Yu, B.; Wang, L.

2026-05-14 synthetic biology 10.64898/2026.05.13.724746 medRxiv
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Protein immunotherapies can elicit potent tumor rejection, but reversible target engagement, incomplete tumor retention, and systemic leakage often erode spatial control. Here, we develop covalently anchored tumor immunotherapeutic proteins (CATIPs), a modular platform that uses proximity-enabled covalent chemistry to immobilize immune cues on tumor-cell surfaces after intratumoral administration. CATIPs combine tumor-targeting nanobodies with payloads for T cell engagement, co-stimulation, and cytokine support. In human PBMC-reconstituted NSG mice, CATIPs completely eradicated treated EGFR-positive tumors, outperforming matched non-covalent proteins while limiting redistribution, systemic T cell activation, cytokine release, xGVHD-associated morbidity, and on-target, off tumor toxicity. In immunocompetent melanoma models, CATIPs remodeled the tumor microenvironment, expanded antigen-specific CD8+ T cells, induced antigen-restricted abscopal control, and generated durable protection against local and metastatic rechallenge. CATIP-engineered tumor cells further functioned as whole-cell vaccines. Thus, covalent tumor anchoring converts local protein delivery into tumor-surface immune programming, enabling systemic, tumor-specific, durable antitumor immunity while limiting systemic immunopathology.