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Wiley

Preprints posted in the last 90 days, ranked by how well they match Small's content profile, based on 78 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
Critical reassessment of lipophilic dye labeling reveals negligible incorporation into small extracellular vesicles derived form serum-free cultured cells

Ji, Y.; Ji, Q.; Ji, J.; Shentu, Y.; Zhou, l.; Wu, J.; Shao, Q.; Xu, W.; Zhang, C.; Shen, M.; Xie, Q.

2026-07-08 bioengineering 10.64898/2026.07.04.722344 medRxiv
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Lipophilic dyes are widely used to track extracellular vesicles (EVs), yet their labeling efficiency toward bona fide small EVs (sEVs) remains poorly defined. Here, we critically reassess this efficiency using a serum-free HEK293F system that generates endogenously fluorescent protein-tagged sEVs (sEVs-FPT) as an unambiguous positive reference, thereby minimizing interference from co-isolated, dye-labelable non-vesicular extracellular particles (NVEPs). Two orthogonal methods, nanoflow cytometry and fluorescence microscopy, were employed for cross-validation. We found that PKH26, PKH67, and DiD labeled <0.5% of sEVs-FPT, regardless of vesicle heterogeneity. In vivo tracking confirmed that dye-derived signals were far weaker than FPT signals and strikingly failed to colocalize with them. Preliminary mechanistic evidence indicates that this failure is due to an inability of sEVs to actively internalize dye aggregates. Our findings raise serious concerns about the validity of lipophilic dye-based EV tracking and call for a critical reevaluation of the relevant literature.

2
In Vitro Fertilization using Magnetotactic Sperm Cells

Ribeiro, C.; Striggow, F.; Nauber, R.; Hebenstreit, F.; Schoen, J.; Medina-Sanchez, M.

2026-04-27 bioengineering 10.64898/2026.04.23.720095 medRxiv
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In vitro fertilization (IVF) is essential for many couples facing infertility, e.g. in cases of low sperm count (oligospermia), where natural fertilization is unlikely. Medical microrobotics, making use of microscopic devices designed to perform targeted tasks inside the body under imaging guidance and controlled actuation, represents a promising strategy to guide sperm cells toward the oocyte. This approach may significantly reduce the time, invasiveness, and patient burden of conventional IVF, with long-term potential for in vivo assisted reproduction. Here, we report the first successful in vitro fertilization (IVF) using magnetically functionalized spermatozoa, termed magnetotactic sperm cells (MSCs), as a step toward in vivo microrobotic guidance of sperm cells for targeted artificial insemination. We present a protocol for the preparation of MSCs for their use in IVF, resulting in samples largely free of non-functionalized sperm cells (99.69% purity). We systematically evaluate the effect of particle functionalization on sperm health, including acrosome integrity, DNA fragmentation, mitochondrial membrane potential, oxidative stress, and epithelial interactions, and observe no adverse effects. Notably, MSCs showed improved mitochondrial membrane integrity compared to the control samples after two hours of incubation. Using MSCs, we successfully performed complete IVF cycles that resulted in embryos developing to the blastocyst stage at a comparable rate as non-functionalized sperm cells of the same concentration. Lower concentrations of non-functionalized sperm cells (comparable to those remaining in the MSC sample after purification) did not result in any development of embryos to blastocysts. To facilitate manipulation and translation, we implemented automated image-based recognition, magnetic manipulation, and pre-clustering routines that increased guidance efficiency and are compatible with standard IVF workflows. Together, these results demonstrate that magnetic functionalization can be applied without compromising key sperm quality metrics and can enable directed sperm guidance for assisted oocyte fertilization. This work provides a practical framework for integrating microrobotic sperm manipulation into assisted-reproduction workflows and supports further development toward automated in vitro and eventual in vivo applications.

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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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Stereochemical identity of lipid nanoparticles modulates protein expression via internal lipid organization

Aschmann, D.; Knol, R. a.; Wijngaarden, S.; Escalona-Rayo, O.; Freire, R. V. M.; Bertram, K.; Tekkali, I.; Bunzel, G.; Fontein, B. L.; Dharan, A.; Pfister, I.; Zhang, Y.; Keijer, T.; Reek, J. N. H.; Voets, I.; Sluetter, B.; kros, A.

2026-06-09 pharmacology and toxicology 10.64898/2026.06.05.730351 medRxiv
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Stereochemistry plays a crucial role in how molecules interact with complex physiological environments, affecting pharmacokinetics, pharmacodynamics, efficacy, and toxicity. Although these effects are well studied for small-molecular drugs, they are largely overlooked for supramolecular assemblies used in drug delivery. Even for lipid nanoparticles (LNPs)--the most advanced RNA delivery platform--stereochemical effects are rarely investigated and, when considered, are typically limited to the ionizable lipid rather than the overall stereochemical identity of the LNP. Here we separate the ionizable lipid cKK-E12 into its two stereoisomers (trans: R,S/S,R; cis: R,R/S,S), which are normally used as a mixture. LNPs containing the cis isomer exhibit improved physicochemical properties, stability, and protein expression. By systematically varying the stereochemistry of the ionizable lipid, phospholipid, and cholesterol, we reveal stereochemistry-dependent differences in uptake and protein expression across six cell lines and in vivo in zebrafish embryos and mice. AI-assisted cryo-TEM analysis and SAXS link enhanced protein expression to structural differences, demonstrating control over internal lipid phases (lamellar and inverse hexagonal), influencing sample uniformity, and identifying stereochemical identity as a key determinant of functional RNA delivery.

5
DNA Double-decker Ring Scaffolded Nanodisc for Self-assembly of Membrane Protein into Lipid Bilayer

Aye, S. L.; Fadaei, F.; Gomibuchi, Y.; Suzuki, Y.; Prakash, P. S.; Chandrasekhar, S.; Yasunaga, T.; Schmidt, T.-L.; Sato, Y.

2026-05-21 bioengineering 10.64898/2026.05.19.726119 medRxiv
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Membrane models of scaffolded discoidal lipid bilayers called nanodiscs have proven to be a valuable tool for the study of membrane proteins in a native environment. DNA-scaffolded membrane model has emerged as an alternative tool for membrane protein studies. Taking advantage of the designability of DNA nanostructure, we created a double-decker double-stranded DNA ring (DDring) to self-assemble DNA-based nanodiscs (DNA-ND). The DDring is 17 nm wide and 4 nm high, and equipped with 28 alkyl chains on the inside that can interact with each hydrophobic leaflet of the lipid bilayer. We further demonstrate the functionality of DNA-ND membrane model with the assembly of membrane proteins. DDrings are suited to neutral or cationic charged phospholipids and detergents. This study provides more insights into the potential use of DNA- assisted nanodiscs for membrane protein characterization.

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Sulfo-DIBMA encapsulation uniquely preserves signalling-competent active states of the class B1 GPCRs, calcitonin gene-related peptide and parathyroid hormone 1 receptors, in native-like nanodiscs

Khwaja, F. N.; Gunner, J.; Thacker, E.; Abdolhay, Y.; Logan, R.; Kitchen, P.; Veprintsev, D.; Wheatley, M.; Poyner, D.; Ayub, H.

2026-05-15 pharmacology and toxicology 10.64898/2026.05.13.724797 medRxiv
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Class B1 G-protein-coupled receptors (GPCRs), such as the calcitonin gene-related peptide (CGRP) receptor and parathyroid hormone 1 (PTH1) receptor, require native lipid interactions to maintain signalling-competent conformations. However, conventional detergents disrupt these environments. Amphipathic copolymers offer a detergent-free alternative, yet the field still lacks a clear understanding of which polymer architectures best preserve active-state GPCR pharmacology, limiting their broader translational utility. Here, we examine how distinct copolymer chemistries influence the functional integrity of class B1 GPCRs by comparing SMA 2000, DIBMA-12, and the electroneutral sulfo-DIBMA. Using NanoLuciferase bioluminescence resonance energy transfer (NanoBRET) ligand-binding, competition, and mini-G-protein recruitment assays on nanodisc-encapsulated receptors, we show that all three copolymers maintain high-affinity extracellular ligand binding but differ markedly in their ability to preserve intracellular signalling. Despite lower receptor extraction efficiency, only sulfo-DIBMA support mini-Gs engagement at the CGRP receptor and enable G-protein-dependent allosteric modulation at the PTH1 receptor, including conserved ligand affinity and prolonged residence time. These data reveal that polymer charge and backbone chemistry, rather than extraction yield, determine whether native-like nanodiscs retain the conformational landscape required for active-state signalling. Controlling non-specific ligand binding to the copolymer is a key requirement for a successful assay. Our findings identify sulfo-DIBMALP as a particularly superior environment for preserving native signalling behaviour in class B1 GPCRs, highlighting copolymer chemistry as an important determinant in detergent-free membrane protein studies. HIGHLIGHTSO_LISulfo-DIBMA encapsulated nanodiscs preserve active-state conformation of human calcitonin gene-related peptide receptor and parathyroid hormone 1 receptor. C_LIO_LIAll three copolymers (SMA 2000, DIBMA-12 and sulfo-DIBMA) preserve extracellular ligand binding but only sulfo-DIBMA preserves intracellular functional competence, including mini-Gs recruitment and G-protein-dependent allosteric modulation. C_LIO_LICopolymer chemistry, particularly the electroneutral, aliphatic nature of sulfo-DIBMA, may influence the preservation of signalling-competent states in two class B1 GPCRs by minimising charge-driven perturbations during solubilisation. C_LIO_LISulfo-DIBMALP provides a novel platform for studying dynamic membrane proteins with potential to provide mechanistic insights and facilitate drug discovery programmes in the future. C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/724797v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@12db163org.highwire.dtl.DTLVardef@d8efb3org.highwire.dtl.DTLVardef@610dbaorg.highwire.dtl.DTLVardef@1cc3ce4_HPS_FORMAT_FIGEXP M_FIG C_FIG

7
In vitro virus-like particle assembly follows two distinct, competing pathways

Wang, X.;Luo, H.;Liu, S.;Gerstweiler, L.

2026-06-19 Molecular Biology 10.64898/2026.06.18.733309 medRxiv
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1.Virus-like particles (VLPs) formed from the murine polyomavirus major capsid protein VP1 are widely used as vaccine antigens and are being explored as nucleic acid and drug delivery vehicles. However, the factors controlling distinct VP1 capsid morphologies remain unclear. We investigated in vitro VP1 assembly with tRNA across NaCl concentrations of 0.15-1.0 M and tRNA mass ratios of 1:1-1:80 (w/w) using SEC-HPLC, transmission electron microscopy, and dynamic light scattering. Two competing assembly pathways were identified. At low ionic strength ([&le;]0.15 M NaCl), nucleic acid-templated assembly produced compact, tRNA-filled T=1 VLPs ([~]28-30 nm). Assembly was maximal at tRNA ratios of 1:10-1:20, whereas excess or insufficient tRNA reduced yields. Increasing NaCl to 0.30 M lowered T=1 yields by 68-97%, and no T=1 particles were detected at [&ge;]0.5 M NaCl. Conversely, high ionic strength ([&ge;]0.5 M NaCl) promoted template-independent formation of hollow T=7 VLPs ([~]55-60 nm). T=7 assembly was inhibited by tRNA and was highest without nucleic acid. At 1.0 M NaCl, reducing the tRNA ratio from 1:40 to 1:80 increased T=7 yield more than 11-fold, while removing tRNA produced the greatest assembly efficiency. Kinetic analyses further showed that VP1 concentration and ionic strength regulate nucleation and assembly rate in the template-driven pathway. These findings show that electrostatic interactions govern pathway selection between tRNA-templated T=1 assembly and salt-driven T=7 self-assembly, providing practical guidance for controlling capsid morphology and cargo loading in VLP-based applications.

8
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.

9
Influence of Physicochemical Parameters on the in vitro Stability of DNA Tetrahedral Nanostructures

Viroja, J.; Rajput, K.; Jain, S.; Bhatia, D. D.

2026-05-13 bioengineering 10.64898/2026.05.10.724064 medRxiv
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Tetrahedral DNA nanostructures (TDNs) are promising nanocarriers due to their structural precision, biocompatibility, and efficient cellular uptake. However, their stability under physiological conditions remains a key challenge. In this study, TDNs were synthesized via a one-pot thermal annealing method and characterized using native PAGE, dynamic light scattering (DLS), and zeta potential analysis, confirming uniform size ([~]13 nm) and negative surface charge. Their stability was systematically evaluated across different biological media (DMEM complete, serum-free DMEM, and E3), temperatures (4 {degrees}C, 25 {degrees}C, and 37 {degrees}C), and pH conditions (4.0, 7.0, and 8.5) over 24 h. Results revealed rapid degradation in serum-containing medium, increased instability at higher temperatures, and reduced stability under acidic conditions, while serum-free, lower-temperature, and neutral to mildly basic environments enhanced structural integrity. These findings highlight the strong environmental dependence of TDN stability and provide insights for optimizing their design for biomedical applications.

10
Predicting Supramolecular Self-Assembly of Peptide Structures with AlphaFold3

Sklar, C.; Huh, S.; Chen, S.; Gray, J. J.

2026-04-30 bioengineering 10.64898/2026.04.28.720402 medRxiv
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Self-assembled peptide-based nanostructures have diverse applications in the pharmaceutical and materials fields, but accurately predicting their self-assembly behavior without time-intensive organic synthesis and characterization remains a significant challenge. Here, we assess the effectiveness of AlphaFold3 (AF3), a deep learning model for protein structure prediction, in modeling peptide-based nanostructures and the interactions driving supramolecular self-assembly. We designed amphiphilic peptides composed of alternating hydrophobic residues (valine, leucine, isoleucine, phenylalanine) and hydrophilic residues (glutamic acid), varying both sequence length and residue order. Using AF3s multimer mode, we modeled assemblies with copy numbers ranging from 10 to 1000, generating diverse morphologies such as micelles and nanotubes. We qualitatively analyzed hydrophobic regions, secondary structures, and intermolecular interactions, while also calculating radii of gyration, packing scores, and aspect ratios using PyRosetta. Our results indicate that AF3 predicts morphologies consistent with hydrophobic driving forces and steric constraints. Increased hydrophobicity correlates with smaller radii of gyration, while higher copy numbers correspond to smaller aspect ratios (more compact structures). Longer hydrophobic segments lead to disordered structures, whereas longer hydrophilic segments promote organization. While AF3 captures systemic trends consistent with biophysical principles, comparisons to literature reveal discrepancies driven by charge effects and secondary structure bias, including an overemphasis on helical propensity (e.g., alanine-rich sequences) and sensitivity to terminal charge repulsion. Additionally, since AF3 is predisposed to predict a single assembled entity rather than higher-order assemblies such as multiple micelles or fibers, finding the optimal copy number for the best prediction requires system-specific iteration. These limitations highlight the need for complementary approaches with controlled chemical potential and environmental conditions, though qualitative agreement with experimental trends in morphology and compactness supports AF3s utility for initial structure generation. Our findings highlight AF3s potential as a user-friendly design tool for structure generation in peptide design, aiding the efficient development of functional self-assembled peptide nanomaterials.

11
Investigating nanostructure and -mechanics of contracting actin stress fibers by scanning ion conductance microscopy

Zhang, Y.; Takahashi, Y.; Lin, Y.-R.; Shevchuk, A.; Korchev, Y.; Franz, C. M.

2026-07-07 biophysics 10.64898/2026.07.01.735957 medRxiv
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Scanning ion conductance microscopy (SICM) provides gentle, non-contact cell surface imaging, but it has not been used to investigate intracellular structures because the plasma membrane restricts nanopipette access. Here, we combined SICM with microsonication-based cell de-roofing to expose intracellular actin stress fibers (SFs) in U2OS cells for nanotopographical and -mechanical characterization. Importantly, the de-roofing conditions preserved actomyosin contractility, allowing analysis of SF structural and biomechanical changes during ATP-induced contraction. Resting SFs displayed an average height of 203{+/-}38 nm and width of 357{+/-}73 nm, and a complex surface architecture characterized by regularly spaced long-range height modulations (~500 nm periodicity; Wq ~25 nm) and smaller irregular corrugations (Ra ~19.2 nm). ATP stimulation reduced SF height and width by ~39% and ~15%, respectively, while largely preserving surface corrugation patterns. During contraction, some SFs separated into two longitudinal strands. High-resolution SICM imaging also revealed filamentous crosslinks mechanically coupling neighboring SFs, and nanomechanical measurements demonstrated local stiffening during contraction. These findings provide new insight into the structural and mechanical regulation of SF contraction and highlight the potential of SICM combined with cell de-roofing as a powerful platform for studying dynamic intracellular processes at nanometer resolution.

12
TRPA1 channel activation by synthetic lipid nanoparticles

Milici, A.; Startek, J. B.; Bultynck, G.; Talavera, K.

2026-05-05 pharmacology and toxicology 10.64898/2026.05.03.722497 medRxiv
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TRPA1 is a polymodal ion channel receptor known for its role in nociception. TRPA1 can be activated by local mechanical perturbations in the surrounding plasma membrane (PM) by molecules that insert in the lipid bilayer. Here, we tested whether TRPA1 function can be modulated by lipid nanoparticles (LNPs) while interacting with the target cell plasma membrane. We found that LNP induce irregular Ca2+ transients in heterologous and native TRPA1-expressing cells, which may reflect stochastic LNP-PM interactions. By using different cell types and applying selective and non-selective TRPA1 inhibitors, we revealed that the cytosolic [Ca2+] is elevated transients arise as a result through multiple mechanisms: TRPA1-dependent Ca2+ influx, TRPA1-independent Ca2+ influx, and Ca2+ mobilization from the endoplasmic reticulum. Our results describe a novel, non-canonical TRPA1 activation mechanism by LNPs, that may be relevant in the context of the development of cancer and nasal vaccines.

13
Microfluidic Core-Shell Encapsulation Enables Scalable Generation of Apical-Out Intestinal Spheroids

Ota, S.; SHUKLA, P.; Otaki, N.; Taylor, E. J.; Hattori, K.

2026-06-10 bioengineering 10.64898/2026.06.10.731294 medRxiv
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Apical-out intestinal spheroids provide direct access to the lumen-facing epithelial surface, making them attractive three-dimensional models for studying epithelial barrier function, nutrient uptake, and luminal exposure. However, existing polarity-reversal methods typically require releasing spheroids from surrounding ECM gels and culturing them in suspension, which can compromise matrix-derived cues, promote fusion, increase size heterogeneity, and limit scalability. Here, we develop a microfluidic core-shell encapsulation strategy to scalably produce apical-out intestinal spheroids within uniform hydrogel microcapsules. These microcapsules consist of a Matrigel core surrounded by an agarose shell. Flow-focusing microfluidics first confines Caco-2 cells in Matrigel cores that provide instructive extracellular matrix cues, and particle-templated emulsification subsequently encloses each core within an inert agarose shell that prevents spheroid fusion and preserves batch uniformity. The method generated >100,000 microcapsules per experiment, with a mean shell diameter of 117 {micro}m, a coefficient of variation below 9%, and >90% single-spheroid formation efficiency. The resulting spheroids established apical-basolateral polarity, organised tight junctions, formed a dextran-excluding epithelial barrier, and exhibited fatty-acid uptake. This core-shell strategy provides an experimentally tractable platform for scalable intestinal epithelial modelling and may be extensible to other epithelial microtissue systems. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=42 SRC="FIGDIR/small/731294v2_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@16dc3forg.highwire.dtl.DTLVardef@d5d947org.highwire.dtl.DTLVardef@1abe79forg.highwire.dtl.DTLVardef@f39239_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Peptide additives reprogram the lipid nanoparticle corona and enhance gene delivery in a serum-free environment for lung epithelium

Hu, J.; Papah, M. B.; Ramirez, A.; Alapati, D.; Sullivan, M. O.

2026-07-13 bioengineering 10.64898/2026.07.10.737795 medRxiv
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Lipid nanoparticles (LNPs) have become a clinical standard for systemically-administered nucleic acid drugs and vaccines, but the LNP pipeline for locally-delivered LNP therapies remains much less mature. Local delivery in lung represents a particularly compelling application space for DNA-LNP therapeutics, as local gene therapies could support sustained epithelial recovery and functional restoration in various lung diseases. However, locally-delivered DNA-LNPs face multiple barriers, including the limited availability of serum components that often support conventional LNP activity, and the additional delivery barriers posed by the nucleus. We generated hybrid peptide-lipid nanoparticles (hpLNPs) for pulmonary DNA delivery by using a core-shell assembly strategy to incorporate short histone-derived peptides, selected for their DNA-transport capacity, into a clinically inspired LNP formulation. In parallel, we evaluated serum pre-coating of LNPs as a strategy to boost hpLNP activity in the serum-poor airway environment. A peptide:DNA amine/phosphate (N/P) ratio of 0.9 was identified as the highest feasible ratio to permit peptide incorporation into hpLNPs while preserving DNA encapsulation efficiency at >90%, retaining hpLNP colloidal stability, and preserving the overall pKa for LNPs. At N/P = 0.9, hpLNPs showed markedly enhanced DNA delivery in alveolar lung cells, achieving up to a 17-fold increase in transgene expression compared to peptide-free LNPs. Transgene expression levels varied depending on serum concentration, with expression peaking in the presence of 6% serum. Furthermore, serum pre-coating was necessary to enable in vivo hpLNP activity following intratracheal administration in mice, yielding robust local GFP expression. Mechanistic studies in exosome-free serum revealed that peptide incorporation in the hpLNPs enhanced transgene delivery by increasing nanoparticle interactions with serum exosome components, resulting in significant enhancements to hpLNP uptake. Together, these findings identify nanoparticle- serum interactions as a critical determinant of LNP-mediated pulmonary DNA delivery and establish peptide incorporation and serum pre-coating as promising strategies to enable robust, localized gene transfer in serum-free environments.

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Extreme Hydrophobicity of Cytotoxic Drugs Enables Design of Next Generation Antibody-Drug Conjugates Nanotherapeutics

Khyade, A.; Sharma, A.; Sandanaraj, B.

2026-05-04 pharmacology and toxicology 10.64898/2026.04.29.721383 medRxiv
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Antibody and protein-drug conjugates (XDCs) have emerged as promising cancer therapeutics, yet their clinical utility remains constrained by dose-limiting toxicities and narrow therapeutic windows. These safety challenges stem primarily from two factors: premature payload release during systemic circulation, and poor physicochemical properties inherent to the hydrophobic cytotoxic drugs they carry. Prior strategies attempted to address these limitations by appending water-soluble tags to reduce overall conjugate hydrophobicity, but achieved only modest improvements. As a result, the hydrophobic nature of cytotoxic payloads has remained a persistent obstacle in XDC development. Here, we report a fundamentally different chemical strategy that reframes this liability as a design opportunity. Rather than masking drug hydrophobicity, we exploit it as the driving force for self-assembly of facially amphiphilic protein-drug conjugates with programmable drug moieties (PDCs). In this architecture, the hydrophobic cytotoxic drug and the hydrophilic protein serve as the core and shell, respectively, spontaneously assembling into monodisperse, well-defined spherical protein nanotherapeutics of controlled size. This design principle transforms a longstanding physicochemical challenge into a functional engineering tool, enabling precise nanostructure formation without sacrificing potency. In vitro studies confirm that the resulting nanotherapeutics effectively kill cancer cells, establishing a strong foundation for further therapeutic development.

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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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Liquid crystalline mesophase spacing as a quantitative predictor of release kinetics for co-loaded hydrophilic and hydrophobic payloads

Dasaro, S.; Sawant, S.; Stern, A.; Johnson, L.; Fretz, C.; Salim, M.; Kirby, N.; Boyd, B.; Wilson, B.; Duncan, G.; Zhou, Q. T.; Ristroph, K.

2026-06-29 bioengineering 10.64898/2026.06.26.734853 medRxiv
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Liquid crystalline mesophases exhibit structurally programmable internal architectures that enable co-loading of chemically orthogonal molecules within a single composite material. Realizing the potential of these materials for drug delivery requires a quantitative understanding of how tuning the composition affects internal mesophase architecture and consequently performance metrics such as payload release. Here, Flash NanoPrecipitation with hydrophobic ion pairing is used to prepare nanocarriers containing liquid crystalline mesophases co-encapsulating two compounds from widely different chemical classes: hydrophilic polymyxin B (logP -6) with one of four hydrophobic co-core materials (logP 7-11), achieving >75% encapsulation efficiency and up to 32% and 50% mass loadings for polymyxin and co-core. Synchrotron SAXS is used to quantify characteristic mesophase repeat spacing, which is found to be tunable as a function of composition. A strong correlation between d-spacing and polymyxin release rate is presented. Co-core chemistry and weight fraction jointly govern mesophase architecture, and repeat distance emerges as a structural metric linking these to the hydrophilic payload release kinetics. Mucus diffusivity and antibacterial efficacy are assessed as independent performance metrics, and results corroborate the release behavior. These findings establish a quantitative framework connecting material composition, mesophase architecture, and functional performance that can be applied toward rational co-formulation design. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=86 SRC="FIGDIR/small/734853v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1d722eborg.highwire.dtl.DTLVardef@135adb7org.highwire.dtl.DTLVardef@11fe29eorg.highwire.dtl.DTLVardef@571165_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOToC Graphic TextC_FLOATNO Flash NanoPrecipitation yields liquid crystalline nanocarriers co-encapsulating with high efficiency payloads with widely distinct physicochemical properties. Synchrotron SAXS establishes characteristic repeat spacing as a quantitative structural metric directly governing hydrophilic release kinetics, providing a rational design framework linking mesophase architecture to functional performance across a range of payload structures. C_FIG

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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.

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Tunable Rigid Spikes on Virus-Like Porous Silica Enable Mechanistically Controlled Nanovaccine Platforms

Pang, C.; Wang, J.; Montaser, A.; Ma, S.; Leinonen, H.; Hu, G.; Lehto, V.-P.; Fan, L.; Xu, W.

2026-04-29 bioengineering 10.64898/2026.04.26.720861 medRxiv
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Virus-like particles represent an emerging and promising vaccine platform. However, these particles are inherently mechanically soft and have limited control over particle surface architecture, thereby constraining their immunological control. Herein, we report the rational design of bioinspired virus-like porous silica (VLPSi) nanoparticles (NPs) with tunable and mechanically rigid spike architectures that function dually as antigen delivery carriers and immune adjuvants. Using ovalbumin (OVA) as a model antigen, we systematically elucidate the spiky structure-function relationship in antigen delivery and immune response. VLPSi NPs exhibit good biocompatibility, sustained antigen release, and markedly enhanced cellular uptake and endosomal escape compared with soft spike and spherical counterparts. Mechanistic investigations combining molecular dynamics simulations and proteomic analyses reveal that rigid spike architectures reduce the energetic barrier for cellular internalization and concurrently activate dual pathways involving endosomal Toll like receptors and calcium signaling. Consequently, VLPSi with long spikes elicit significantly enhanced humoral and cellular immune responses, outperforming the particles with shorter spikes, spherical shape as well as clinically used alum adjuvant. To demonstrate translational potential, bioinspired antibacterial vaccines were produced by loading Staphylococcus aureus surface protein rEsxB. The VLPSi-based vaccine elicited robust protective immunity to achieve complete (100%) survival following lethal challenge without detectable adverse effects, whereas traditional Alum-adjuvanted formulation conferred only minimal protection, with a survival rate of 10%. Collectively, this work establishes VLPSi with tunable spikes as a mechanistically controlled platform for next generation vaccines. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=145 SRC="FIGDIR/small/720861v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@1f6c13eorg.highwire.dtl.DTLVardef@1090d07org.highwire.dtl.DTLVardef@1364926org.highwire.dtl.DTLVardef@fc68ab_HPS_FORMAT_FIGEXP M_FIG C_FIG

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A Polymeric Nanoparticle System for the Delivery of CRISPR/Cas9 Components into Arabidopsis Pollen

Yang, Q.;Adair, L.;Jones, B.;Muellner, M.

2026-06-19 Plant Biology 10.64898/2026.06.17.733037 medRxiv
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Efficient and heritable genome editing in plants remains constrained by transformation bottlenecks and reliance on tissue culture-based regeneration. Targeting the male germline offers a promising alternative for DNA-free genome modification. Here, we report a polymeric nanoparticle platform for the delivery of RNA-based CRISPR/Cas9 components into Arabidopsis thaliana pollen, establishing a foundation for sperm transfection-assisted genome editing (STAGE)-like approaches in plants. Poly(2-dimethylaminoethyl methacrylate) (PDMAEMA)-based polyplexes were designed to independently encapsulate Cas9 mRNA and ATTO 550-labeled guide RNA, forming nanoparticles with hydrodynamic diameters of [~]146 nm and condensed cores of 20-30 nm. Following internalization and cytosolic release, Cas9 mRNA translation enabled the nuclear localization of ATTO 550-labeled gRNA, as confirmed by confocal imaging and fluorescence lifetime (TauSense) analysis. Fluorescent signals corresponding to the CRISPR RNPs were detected in both vegetative and sperm cell nuclei, with higher accumulation in the vegetative nucleus. Together, these results demonstrate the feasibility of RNA-mediated delivery and intracellular assembly of CRISPR/Cas9 RNPs in plant male gametophytes. By bypassing tissue culture and DNA integration, this nanoparticle-based approach establishes a framework for a more efficient mechanism for introducing heritable genome modifications in plants. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=91 SRC="FIGDIR/small/733037v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@170f7a5org.highwire.dtl.DTLVardef@1929c6forg.highwire.dtl.DTLVardef@5c4a94org.highwire.dtl.DTLVardef@1243cc8_HPS_FORMAT_FIGEXP M_FIG C_FIG