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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 217 records · Page 12

Understanding the stability of a plastic‐degrading Rieske iron oxidoreductase system

Abstract Rieske oxygenases (ROs) are a diverse metalloenzyme class with growing potential in bioconversion and synthetic applications. We postulated that ROs are nonetheless underutilized because they are unstable. Terephthalate dioxygenase (TPA DO PDB ID 7Q05 ) is a structurally characterized heterohexameric α 3 β 3 RO that, with its cognate reductase (TPA RED ), catalyzes the first intracellular step of bacterial polyethylene terephthalate plastic bioconversion. Here, we showed that the heterologously expressed TPA DO /TPA RED system exhibits only ~300 total turnovers at its optimal pH and temperature. We investigated the thermal stability of the system and the unfolding pathway of TPA DO through a combination of biochemical and biophysical approaches. The system's activity is thermally limited by a melting temperature ( T m ) of 39.9°C for the monomeric TPA RED , while the independent T m of TPA DO is 50.8°C. Differential scanning calorimetry revealed a two‐step thermal decomposition pathway for TPA DO with T m values of 47.6 and 58.0°C (Δ H = 210 and 509 kcal mol −1 , respectively) for each step. Temperature‐dependent small‐angle x‐ray scattering and dynamic light scattering both detected heat‐induced dissociation of TPA DO subunits at 53.8°C, followed by higher‐temperature loss of tertiary structure that coincided with protein aggregation. The computed enthalpies of dissociation for the monomer interfaces were most congruent with a decomposition pathway initiated by β‐β interface dissociation, a pattern predicted to be widespread in ROs. As a strategy for enhancing TPA DO stability, we propose prioritizing the re‐engineering of the β subunit interfaces, with subsequent targeted improvements of the subunits.

59 BASIC BIOLOGICAL SCIENCES↗

Tetranucleotide frequencies differentiate genomic boundaries and metabolic strategies across environmental microbiomes

Microbiomes are constrained by physicochemical conditions, nutrient regimes, and community interactions across diverse environments, yet genomic signatures of this adaptation remain unclear. Metagenome sequencing is a powerful technique to analyze genomic content in the context of natural environments, establishing concepts of microbial ecological trends. Here, we developed a data discovery tool-a tetranucleotide-informed metagenome stability diagram-that is publicly available in the integrated microbial genomes and microbiomes (IMG/M) platform for metagenome ecosystem analyses. We analyzed the tetranucleotide frequencies from quality-filtered and unassembled sequence data of over 12,000 metagenomes to assess ecosystem-specific microbial community composition and function. We found that tetranucleotide frequencies can differentiate communities across various natural environments and that specific functional and metabolic trends can be observed in this structuring. Our tool places metagenomes sampled from diverse environments into clusters and along gradients of tetranucleotide frequency similarity, suggesting microbiome community compositions specific to gradient conditions. Within the resulting metagenome clusters, we identify protein-coding gene identifiers that are most differentiated between ecosystem classifications. We plan for annual updates to the metagenome stability diagram in IMG/M with new data, allowing for refinement of the ecosystem classifications delineated here. This framework has the potential to inform future studies on microbiome engineering, bioremediation, and the prediction of microbial community responses to environmental change. IMPORTANCE: Microbes adapt to diverse environments influenced by factors like temperature, acidity, and nutrient availability. We developed a new tool to analyze and visualize the genetic makeup of over 12,000 microbial communities, revealing patterns linked to specific functions and metabolic processes. This tool groups similar microbial communities and identifies characteristic genes within environments. By continually updating this tool, we aim to advance our understanding of microbial ecology, enabling applications like microbial engineering, bioremediation, and predicting responses to environmental change.

Kellom, Matthew↗

Relating Oxidative Protein Damage to Antioxidant Status in Health and Disease (Full Technical Report for 24-LW-026)

This two-year project evaluated how dietary antioxidants influence oxidative damage in cancer using complementary analytical and in-vivo approaches. We initially developed a protein oxidation labeling workflow and a parallel accelerator and molecular mass spectrometry (PAMMS) quantification method, but ultimately discontinued the labeling strategy due to unresolved separation challenges; PAMMS was instead leveraged to quantify radiolabeled catechol in rat plasma as a methodological benchmark. The biological study used a genetically engineered murine model (GEMM) for breast cancer (n = 40; four groups of 10: cancer/high antioxidant diet, cancer/normal diet, healthy/high-antioxidant diet, healthy/normal diet). In lieu of the abandoned labeling assay, untargeted metabolomics profiled plasma across groups, revealing widespread treatment-dependent changes in metabolites.

59 BASIC BIOLOGICAL SCIENCES↗

Role of Ribosomal Protein bS1 in Orthogonal mRNA Start Codon Selection

In many bacteria, the location of the mRNA start codon is determined by a short ribosome binding site sequence that base pairs with the 3'-end of 16S rRNA (rRNA) in the 30S subunit. Many groups have changed these short sequences, termed the Shine-Dalgarno (SD) sequence in the mRNA and the anti-Shine-Dalgarno (ASD) sequence in 16S rRNA, to create "orthogonal" ribosomes to enable the synthesis of orthogonal polymers in the presence of the endogenous translation machinery. However, orthogonal ribosomes are prone to SD-independent translation. Ribosomal protein bS1, which binds to the 30S ribosomal subunit, is thought to promote translation initiation by shuttling the mRNA to the ribosome. Thus, a better understanding of how the SD and bS1 contribute to start codon selection could help efforts to improve the orthogonality of ribosomes. Here, we engineered the Escherichia coli ribosome to prevent binding of bS1 to the 30S subunit and separate the activity of bS1 binding to the ribosome from the role of the mRNA SD sequence in start codon selection. We find that ribosomes lacking bS1 are slightly less active than wild-type ribosomes in vitro. Furthermore, orthogonal 30S subunits lacking bS1 do not have an improved orthogonality. Our findings suggest that mRNA features outside the SD sequence and independent of binding of bS1 to the ribosome likely contribute to start codon selection and the lack of orthogonality of present orthogonal ribosomes.

59 BASIC BIOLOGICAL SCIENCES↗

Action at a distance: The remarkable coupling of CO 2 uptake to electron transfer in specialized cyanobacterial NDH-1 complexes

Cyanobacteria achieve highly efficient photosynthesis using a CO 2 -concentrating mechanism relying on specialized Type I (NDH-1) complexes. Among these, NDH-1 3 and NDH-1 4 catalyze redox-coupled hydration of CO 2 to bicarbonate, supporting carbon fixation in carboxysomes. The mechanism of coupling electron transfer to CO 2 -hydration by these variant NDH-1 complexes remains unknown. We engineered a Synechococcus PCC7942 strain that expresses exclusively the high flux/low affinity NDH-14 complex, enabling the observation of the coupling of CO 2 hydration to cyclic electron flow in isolation from the other NDH-1 isoforms normally present in cells. We found that inhibition of the CupB protein by the carbonic anhydrase inhibitor ethoxzolamide (EZ) suppressed CO 2 uptake, slowed photosystem I rereduction, and abolished proton pumping as probed by acridine orange fluorescence. These effects were absent in strains lacking Cup proteins, confirming specificity. The results demonstrate that CO 2 hydration and electron transfer through NDH-14 are tightly coupled via proton translocation across the thylakoid membrane. These findings provide direct evidence for the bidirectional interaction in bioenergetic coupling between the plastoquinone reduction and the CO 2 uptake at the distal Zn-site over a span of ~150 Å and support a proton-removal hypothesis involving the proton transfer pathways from the Zn-site of CO2 hydration to an energetically coupled proton loading site evolutionarily repurposed from the ancestral proton pumping mechanism to enable energetic CO 2 uptake.

59 BASIC BIOLOGICAL SCIENCES↗

Magnetic resonance control of spin-correlated radical pair dynamics in vivo

Magnetic fields can influence reactions involving spin-correlated radical pairs (SCRPs). This provides a mechanism by which both static and time-varying magnetic fields can affect living systems at the biomolecular level. However, an engineered SCRP system conferring magnetic sensitivity to a non-native biochemical process in a multicellular organism has not yet been demonstrated. Here, in this study, we demonstrate control of SCRP dynamics using magnetic resonance in a live transgenic animal. We show that the emission of various red fluorescent proteins (RFPs), in the presence of a flavin cofactor, can be modified by a combination of static and radiofrequency magnetic fields applied near the electron spin resonance frequency. This effect was measured at room temperature both in vitro and in the nematode Caenorhabditis elegans, genetically modified to express the RFP mScarlet. These observations suggest that the magnetic field effects measured in RFP-flavin systems are due to quantum-correlated radical pairs with a coherence time larger than 4 ns. Our experiments demonstrate that radiofrequency magnetic fields can influence dynamics of reactions involving SCRPs in vivo, potentially enabling new methods for remotely controlling biomolecular processes, such as gene expression, and suggest broader potential for quantum tools in biology.

Burd, Shaun C. [Stanford Univ., CA (United States)↗

Systematic identification of transcriptional activation domains from non-transcription factor proteins in plants and yeast

Transcription factors can promote gene expression through activation domains. Whole-genome screens have systematically mapped activation domains in transcription factors but not in non-transcription factor proteins (e.g., chromatin regulators and coactivators). To fill this knowledge gap, we employed the activation domain predictor PADDLE to analyze the proteomes of Arabidopsis thaliana and Saccharomyces cerevisiae. We screened 18,000 predicted activation domains from >800 non-transcription factor genes in both species, confirming that 89% of candidate proteins contain active fragments. Our work enables the annotation of hundreds of nuclear proteins as putative coactivators, many of which have never been ascribed any function in plants. Analysis of peptide sequence compositions reveals how the distribution of key amino acids dictates activity. Finally, we validated short, "universal" activation domains with comparable performance to state-of-the-art activation domains used for genome engineering. Our approach enables the genome-wide discovery and annotation of activation domains that can function across diverse eukaryotes.

59 BASIC BIOLOGICAL SCIENCES↗

Bacterial microcompartments as a next-generation metabolic engineering tool: utilizing nature's solution for confining challenging catabolic pathways

Advancements in synthetic biology have facilitated the incorporation of heterologous metabolic pathways into various bacterial chassis, leading to the synthesis of targeted bioproducts. However, total output from heterologous production pathways can suffer from low flux, enzyme promiscuity, formation of toxic intermediates, or intermediate loss to competing reactions, which ultimately hinder their full potential. The self-assembling, easy-to-modify, protein-based bacterial microcompartments (BMCs) offer a sophisticated way to overcome these obstacles by acting as an autonomous catalytic module decoupled from the cell's regulatory and metabolic networks. More than a decade of fundamental research on various types of BMCs, particularly structural studies of shells and their self-assembly, the recruitment of enzymes to BMC shell scaffolds, and the involvement of ancillary proteins such as transporters, regulators, and activating enzymes in the integration of BMCs into the cell's metabolism, has significantly moved the field forward. These advances have enabled bioengineers to design synthetic multi-enzyme BMCs to promote ethanol or hydrogen production, increase cellular polyphosphate levels, and convert glycerol to propanediol or formate to pyruvate. These pioneering efforts demonstrate the enormous potential of synthetic BMCs to encapsulate non-native multi-enzyme biochemical pathways for the synthesis of high-value products.

59 BASIC BIOLOGICAL SCIENCES↗

Expression of a Bacterial Trehalose 6-Phosphate Synthase Gene otsA in Camelina sativa Seeds Promotes the Channelling of Carbon Towards Oil Accumulation

Improving seed oil yield is essential for developing Camelina sativa as a sustainable biofuel crop. Fatty acid synthesis depends on the production of acetyl-CoA from photosynthetically derived sugars. Trehalose 6-phosphate (T6P), a proxy for sucrose availability, can link sugar status to plant growth and development. Synthesised by trehalose 6-phosphate synthase (TPS) from UDP-glucose and glucose-6-phosphate, T6P plays a regulatory role in metabolism. Our previous studies on Arabidopsis transgenic lines constitutively expressing the E. coli otsA (encoding TPS) showed increased T6P levels and seed triacylglycerol, along with stunted growth. In the present study we express otsA in camelina under the control of a seed-specific Phaseolin promoter. Seeds of the resulting transgenic lines accumulated high levels of T6P, and a 15%–20% increase in total fatty acids and triacylglycerol compared to wild-type. Molecular analysis showed the transgenic seeds had reduced SnRK1 activity, elevated WRI1 protein levels, and increased the levels of WRI1 and its target genes, along with enhanced rates of fatty acid synthesis that increased seed weights relative to wild type. Notably, the increase in oil did not affect seed protein levels but did reduce the soluble metabolite fraction. Crucially, seed-specific expression of otsA mitigated the growth defects associated with constitutive otsA expression, and the transgenic lines showed normal seed development and germination. These findings demonstrate that targeted T6P modulation via seed-specific otsA expression is an effective metabolic engineering strategy to boost oil production in camelina and potentially in other oilseed crops and bioenergy crops such as energycane, sorghum and miscanthus.

59 BASIC BIOLOGICAL SCIENCES↗

Rational engineering to enhance C8-fatty acid biosynthesis in Picosynechococcus sp. PCC 7002

Medium-chain fatty acids (e.g., C8-C14) are important biofuel precursors that can be produced from CO2 by cyanobacteria and other photoautotrophs. However, cyanobacteria naturally direct a relatively small fraction of fixed carbon to lipid synthesis, primarily producing long-chain membrane-bound fatty acids. We investigated whether mitigating kinetic bottlenecks within the fatty acid biosynthesis (FAB) pathway could enhance flux to free fatty acid (FFA) production in Picosynechococcus sp. PCC 7002. Previous in vitro studies proposed that the FAB initiating enzyme FabH is the primary rate-controlling enzyme in PCC 7002. We hypothesized that enhancing fatty acid initiation could increase in vivo FFA production while shifting the kinetic bottleneck further downstream in the pathway. We enabled C8-FFA accumulation by knocking out the native acyl-acyl carrier protein synthetase gene (aas) and expressing the highly active Cuphea palustris-derived mutant thioesterase CpFatB1.2-M4-287 (CupTE), which selectively catalyzes C8 chain termination. We then expressed the diatom-derived Chaetoceros sp. GSL56 FabH ortholog (chKASIII), to enhance initiation, and a medium-chain selective E. coli ketosynthase ecFabF[I108F] (ecFabF∗), to enhance elongation. When expressed individually or in combination with ecFabF∗, chKASIII slowed growth and decreased net carbon fixation rates relative to the parental Δaas-CupTE strain. However, co-expression of chKASIII, ecFabF∗, and CupTE redirected a larger fraction of fixed carbon toward FFA production, increasing relative carbon flux to C8-FFA and decreasing the projected minimum selling price by four-fold. This work demonstrates how systems metabolic engineering can be applied to enhance C8-FFA production in cyanobacteria while highlighting the unpredictable physiological consequences of host metabolic burden.

09 BIOMASS FUELS↗

Heterogeneous Multilayer Nanopores via Chemically Tuned Dielectric Breakdown for Single‐Molecule Sensing

Solid-state nanopores are powerful platforms for single-molecule sensing, yet their performance is often constrained by fabrication complexity, noise, and limited control over surface properties. Here we report a direct method to fabricate heterogeneous multilayer nanopores using chemically tuned controlled dielectric breakdown (CT-CDB). We integrate hBN, MoS 2 , or graphene atop a silicon nitride membrane to form five distinct bilayer and tri-layer architectures, with bare SiN x nanopore as a control. CT-CDB achieves pore formation reproducibly through material-stacks with high efficiency, good pore size control, and strong yield, validated by various characterizations. Transferrin protein translocation experiments, supported by simulations, reveal that multilayer configurations modulate protein conformations, ionic current blockade and dwell time distributions, reflecting combined effects of membrane type, interfacial chemistry, and local electric field gradients. A supervised machine learning framework is implemented to assist identifying multilayer structure effects embedded in signal signatures, with over 96% accuracy. This work presents a modular and scalable framework for functional nanopore engineering with complex structural integration, thereby expanding the potential of 2D materials in single-molecule sensing applications.

2D materials↗

Effects of process intensification on homogeneity of an IgG1:κ monoclonal antibody during perfusion culture

The pharmaceutical industry employs various strategies to improve cell productivity. These strategies include process intensification, culture media improvement, clonal selection, media supplementation and genetic engineering of cells. However, improved cell productivity has inherent risk of impacting product quality attributes (PQA). PQAs may affect the products’ efficacy via stability, bioavailability, or in vivo bioactivity. Variations in manufacturing process may introduce heterogeneity in the products by altering the type and extent of N-glycosylation, which is a PQA of therapeutic proteins. We investigated the effect of different cell densities representing increasing process intensification in a perfusion cell culture on the production of an IgG1-κ monoclonal antibody from a CHO-K1 cell line. This antibody is glycosylated both on light chain and heavy chain. Our results showed that the contents of glycosylation of IgG1-κ mAb increased in G0F and fucosylated type glycans as a group, whereas sialylated type glycans decreased, for the mAb whole protein. Overall, significant differences were observed in amounts of G0F, G1F, G0, G2FS1, and G2FS2 type glycans across all process intensification levels. G2FS2 and G2 type N-glycans were predominantly quantifiable from light chain rather than heavy chain. It may be concluded that there is a potential impact to product quality attributes of therapeutic proteins during process intensification via perfusion cell culture that needs to be assessed. Since during perfusion cell culture the product is collected throughout the duration of the process, lot allocation needs careful attention to process parameters, as PQAs are affected by the critical process parameters (CPPs).

59 BASIC BIOLOGICAL SCIENCES↗

Atomic view of photosynthetic metabolite permeability pathways and confinement in synthetic carboxysome shells

Carboxysomes are protein microcompartments found in cyanobacteria, whose shell encapsulates rubisco at the heart of carbon fixation in the Calvin cycle. Carboxysomes are thought to locally concentrate CO 2 in the shell interior to improve rubisco efficiency through selective metabolite permeability, creating a concentrated catalytic center. However, permeability coefficients have not previously been determined for these gases, or for Calvin-cycle intermediates such as bicarbonate (HCO$^–_3$), 3-phosphoglycerate, or ribulose-1,5-bisphosphate. Starting from a high-resolution cryogenic electron microscopy structure of a synthetic β-carboxysome shell, we perform unbiased all-atom molecular dynamics to track metabolite permeability across the shell. The synthetic carboxysome shell structure, lacking the bacterial microcompartment trimer proteins and encapsulation peptides, is found to have similar permeability coefficients for multiple metabolites, and is not selectively permeable to HCO$^–_3$ relative to CO 2 . To resolve how these comparable permeabilities can be reconciled with the clear role of the carboxysome in the CO 2 -concentrating mechanism in cyanobacteria, complementary atomic-resolution Brownian Dynamics simulations estimate the mean first passage time for CO 2 assimilation in a crowded model carboxysome. Despite a relatively high CO 2 permeability of approximately 10 -2 cm/s across the carboxysome shell, the shell proteins reflect enough CO 2 back toward rubisco that 2,650 CO 2 molecules can be fixed by rubisco for every 1 CO 2 molecule that escapes under typical conditions. The permeabilities determined from all-atom molecular simulation are key inputs into flux modeling, and the insight gained into carbon fixation can facilitate the engineering of carboxysomes and other bacterial microcompartments for multiple applications.

59 BASIC BIOLOGICAL SCIENCES↗

Development of modular expression across phylogenetically distinct diazotrophs

Diazotrophic bacteria can reduce atmospheric nitrogen into ammonia enabling bioavailability of the essential element. Many diazotrophs closely associate with plant roots increasing nitrogen availability, acting as plant growth promoters. These associations have the potential to reduce the need for costly synthetic fertilizers if they could be engineered for agricultural applications. However, despite the importance of diazotrophic bacteria, genetic tools are poorly developed in a limited number of species, in turn narrowing the crops and root microbiomes that can be targeted. Here, we report optimized protocols and plasmids to manipulate phylogenetically diverse diazotrophs with the goal of enabling synthetic biology and genetic engineering. Three broad-host-range plasmids can be used across multiple diazotrophs, with the identification of one specific plasmid (containing origin of replication RK2 and a kanamycin resistance marker) showing the highest degree of compatibility across bacteria tested. We then demonstrated modular expression by testing seven promoters and eleven ribosomal binding sites using proxy fluorescent proteins. Finally, we tested four small molecule inducible systems to report expression in three diazotrophs and demonstrated genome editing in Klebsiella michiganensis M5al.

59 BASIC BIOLOGICAL SCIENCES↗

Applications of Decellularized Plant Tissues in Regenerative Medicine and Tissue Engineering

The development of biomaterials capable of supporting complex tissue growth remains a central challenge in regenerative medicine and tissue engineering, particularly in replicating the structural, mechanical, and transport functions of native extracellular matrices. While decellularized animal tissues have demonstrated significant success as scaffolds for tissue engineering, they are still constrained by cost, immunogenicity, and ethical concerns. In recent years, decellularized plant tissues have emerged as a compelling alternative scaffold platform due to their inherent vascular architectures, ethical sourcing, tunable mechanical properties, cytocompatibility, and sustainability. This review summarizes current strategies for the decellularization of plant tissues, including chemical, enzymatic, and physical approaches, and discusses how these methods preserve plant cell wall structure while removing immunogenic components. Advances in surface loading and functionalization, including protein coatings, oxidation, nanoparticle incorporation, peptide conjugation, and bioactive molecule loading, have further enhanced cell adhesion, differentiation, biodegradability, and immunomodulation. Recent applications of decellularized plant scaffolds in cardiac, skeletal muscle, bone, nerve, and wound healing contexts are reviewed, highlighting proof-of-concept successes and remaining challenges. Beyond therapeutic applications, plant-derived scaffolds have also enabled physiologically relevant in vitro models for vascular biology, mechanotransduction, cancer, metabolic tissues, and drug response studies. Collectively, these advances position decellularized plant tissues as versatile, low-cost, and ethically favorable biomaterials with growing relevance for both regenerative medicine and tissue modeling.

59 BASIC BIOLOGICAL SCIENCES↗

Structural and biochemical basis for regiospecificity of the flavonoid glycosyltransferase UGT95A1

Glycosylation is a predominant strategy plants use to fine-tune the properties of small molecule metabolites to affect their bioactivity, transport, and storage. It is also important in biotechnology and medicine as many glycosides are utilized in human health. Small molecule glycosylation is largely carried out by family 1 glycosyltransferases. Here, we report a structural and biochemical investigation of UGT95A1, a family 1 GT enzyme from Pilosella officinarum that exhibits a strong, unusual regiospecificity for the 3'-O position of flavonoid acceptor substrate luteolin. We obtained an apo crystal structure to help drive the analyses of a series of binding site mutants, revealing that while most residues are tolerant to mutations, key residues M145 and D464 are important for overall glycosylation activity. Interestingly, E347 is crucial for maintaining the strong preference for 3'-O glycosylation, while R462 can be mutated to increase regioselectivity. The structural determinants of regioselectivity were further confirmed in homologous enzymes. Our study also suggests that the enzyme contains large, highly dynamic, disordered regions. We showed that while most disordered regions of the protein have little to no implication in catalysis, the disordered regions conserved among investigated homologs are important to both the overall efficiency and regiospecificity of the enzyme. This report represents a comprehensive in-depth analysis of a family 1 GT enzyme with a unique substrate regiospecificity and may provide a basis for enzyme functional prediction and engineering.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Modeling Protein–Protein and Protein–Ligand Interactions by the ClusPro Team in CASP16

ABSTRACT In the CASP16 experiment, our team employed hybrid computational strategies to predict both protein–protein and protein–ligand complex structures. For protein–protein docking, we combined physics‐based sampling—using ClusPro FFT docking and molecular dynamics—with AlphaFold (AF)‐based sampling, followed by AF‐based refinement. Our method produced numerous high‐accuracy complex models, including cases where AF alone failed, underscoring the critical role of physics‐based sampling alongside deep learning‐based refinement. For protein–ligand docking, we integrated the ClusPro LigTBM template‐based approach with a machine learning‐based confidence model for rescoring. The method preserves conserved interaction fragments derived from homologous complexes, followed by local resampling using physics‐based sampling and a diffusion model. Our template‐based strategy achieved a mean lDDT‐PLI of 0.69 across 233 targets, which was highly competitive. These results demonstrate that combining physics‐based modeling with AI‐driven refinement can significantly enhance the accuracy of both protein–protein and protein–ligand structure predictions.

Ashizawa, Ryota [Department of Applied Mathematics↗

DNA-PAINT Imaging with Hydrogel Imprinting and Clearing

Hydrogel-embedding is a versatile technique in fluorescence microscopy, offering stabilization, optical clearing, and the physical expansion of biological specimens. DNA-PAINT is a super-resolution microscopy approach based on the diffusion and transient binding of fluorescently labeled oligos, but its feasibility in hydrogels has not yet been explored. In this study, we demonstrate that polyacrylamide hydrogels support sufficient diffusion for effective DNA-PAINT imaging. Using acrydite-anchored oligonucleotides imprinted from patterned DNA origami nanostructures and microtubule filaments in fixed cells, we find that hydrogel embedding preserves docking strand positioning at the nanoscale. Sample clearing via protease treatment had minor structural effects on the microtubule structure and enhanced diffusion and accessibility to hydrogel-imprinted docking strands. Our work demonstrates promising potential for diffusion and binding-based fluorescence imaging applications in hydrogel-embedded samples.

DNA origami↗