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Biology subjects

Suzuki, Y.

Publications and source records attributed to Suzuki, Y..

At least 55 records · Page 3Linked to original sources

Genomic Insights into Ceftazidime Resistance in Burkholderia pseudomallei: Discovery of A172T Mutation, and Palindromic GC-Rich Repeat Sequences Facilitating penA Duplication and Amplification.

Ceftazidime (CAZ) resistance in Burkholderia pseudomallei, the causative agent of melioidosis, complicates treatment in endemic regions. This study identified a novel A172T mutation and other known penA mutations as critical contributors to CAZ resistance in a large Thai strain collection. Frequent gene duplication and amplification (GDA) of penA, likely driven by Palindromic GC-Rich Repeat Sequences (PGCRRS), highlights the urgent need for rapid diagnostics and optimized treatment strategies to manage this life-threatening disease effectively.

microbiology↗

Misclassification in memory modification in AppNL-G-F knock-in mouse model of Alzheimers disease

Alzheimers disease (AD), the leading cause of dementia, could potentially be mitigated through early detection and interventions. However, it remains challenging to assess subtle cognitive changes in the early AD continuum. Computational modeling is a promising approach to explain a generative process underlying subtle behavioral changes with a number of putative variables. Nonetheless, internal models of the patient remain underexplored in AD. Determining the states of an internal model between measurable pathological states and behavioral phenotypes would advance explanations about the generative process in earlier disease stages beyond assessing behavior alone. In this study, we assumed the latent cause model as an internal model and estimated internal states defined by the model parameters being in conjunction with measurable behavioral phenotypes. The 6- and 12-month-old AppNL-G-F knock-in AD model mice and the age-matched control mice underwent memory modification learning, which consisted of classical fear conditioning, extinction, and reinstatement. The results showed that AppNL-G-F mice exhibited a lower extent of reinstatement of fear memory. Computational modeling revealed that the deficit in the AppNL-G-F mice would be due to their internal states being biased toward overgeneralization or overdifferentiation of their observations, and consequently the competing memories were not retained. This deficit was replicated in another type of memory modification learning in the reversal Barnes maze task. Following reversal learning, AppNL- G-F mice, given spatial cues, failed to infer coexisting memories for two goal locations during the trial. We concluded that the altered internal states of AppNL-G-F mice illustrated their misclassification in the memory modification process. This novel approach highlights the potential of investigating internal states to precisely assess cognitive changes in early AD and multidimensionally evaluate how early interventions may work.

neuroscience↗

Global loss of responsiveness in key regulator metabolites and elevated enzyme proteins as metabolic dysregulation in skeletal muscle and liver of obese mice during starvation

Starvation induces complex metabolic adaptations in skeletal muscle, a key tissue for maintaining energy homeostasis; however, these adaptations are largely impaired in obesity. How obesity alters global metabolic adaptations to starvation in skeletal muscle remains unclear. Here, we analyzed the metabolic adaptations on a trans-omics scale during starvation in skeletal muscle from wild-type (WT) and leptin-deficient obese (ob/ob) mice. We measured multi-omics data during starvation and constructed global trans-omics networks in WT and ob/ob mice. We found that starvation induces "responsiveness" in WT mice, characterized by increases or decreases in key regulator metabolites, including ATP and AMP, as well as enzyme proteins, leading to global regulation of metabolic pathways, which was lost in ob/ob mice. In contrast, during starvation, ob/ob mice exhibit "difference" in comparison to WT mice, manifested by the persistently elevated expression of metabolic enzymes. These features were similarly found in liver, another key metabolic organ. Thus, global loss of responsiveness and elevated enzyme proteins are systemic features of metabolic dysregulation in ob/ob mice.

systems biology↗

Circadian PERIOD proteins sculpt themammalian alternative splicing landscape

Mammalian circadian oscillators are driven by a transcription-translation feedback loop where CLOCK:BMAL1 activity is repressed by the PER:CRY complex. While transcriptional regulation by PER is well established, the role of circadian feedback in co- and post- transcriptional processes remains unclear. Here, we used Nanopore long-read direct RNA sequencing (dRNAseq) and quantitative mass spectrometry (qMS) to uncover a critical function of PERs in alternative splicing (AS) regulation in the liver. Our expanded long-read transcriptome revealed significant changes in rhythmic expression of annotated transcripts, novel isoforms of known genes, and previously unannotated genes, with widespread perturbations in Per1-/-;Per2-/- (PerKO) livers. Rhythmic AS events were restricted to a distinct subset of transcripts, and splicing entropy - a metric of AS complexity - displayed oscillations in only a limited number of pathways, primarily those associated with glucose homeostasis and cellular responses to insulin. In PerKO livers, however, we detected increased isoform complexity and altered splicing entropy across a broad range of pathways linked to cell growth, morphogenesis, ER-associated degradation (ERAD), insulin response and histone methylation. Biochemical analyses and qMS data indicate that these changes are not due to mis-expression of splicing factors, but rather stem from altered nuclear abundance and chromatin retention of a few Serine-Arginine-rich splicing factors (SRSFs). In particular, SRSF3 acts proximal to the core-clock by defining both the period and amplitude of cellular rhythms. Our findings highlight a critical role for PER proteins in shaping the circadian liver proteome by integrating rhythmic transcription with the regulation of a complex and dynamic splicing landscape.

physiology↗

Phased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia

The selection of a reference sequence in genome analysis is critical, as it serves as the foundation for all downstream analyses. Recently, the pangenome graph has been proposed as a data model that incorporates haplotypes from multiple individuals. Here we present JaSaPaGe, a pangenome graph reference for Saudi Arabian and Japanese populations, both of which have been significantly underrepresented in previous genomic studies. We constructed JaSaPaGe from high-quality phased diploid assemblies which were made utilizing PacBio high-fidelity long reads, Nanopore long reads, and Hi-C short reads of 9 Saudi and 10 Japanese individuals. Quality evaluation of the pangenome graph by variant calling showed that our pangenome outperformed earlier linear reference genomes (GRCh38 and T2T-CHM13) and showed comparable performance to the pangenome graph provided by the Human Pangenome Reference Consortium (HPRC), with more variants found in Japanese and Saudi samples using their population-specific pangenomes. This pangenome reference will serve as a valuable resource for both the research and clinical communities in Japan and Saudi Arabia.

genomics↗

Microthrombi-growth in ADAMTS13 deficiency exacerbated ulcerative colitis via mucosal and endothelial dysfunction

BackgroundUlcerative colitis (UC) is a chronic inflammatory bowel disease characterized by mucosal inflammation and ulceration, with systemic immune dysregulation exacerbating disease progression. While the accumulation of von Willebrand factor (VWF), normally digested by a disintegrin-like and metalloproteinase with thrombospondin type 1 motif 13 (ADAMTS13) from ultra-large multimers to small molecules, has been implicated in UC pathogenesis, the association between aberrant microthrombus formation and colitis remains unclear. MethodsPlasma and inflamed colonic tissues from UC patients were analyzed. In the experimental colitis model, we employed an intravital imaging technique to reveal real-time structural dynamics of the mucus layer and the mucosal vasculature. Dextran sulfate sodium (DSS)-induced colitis in wild-type and ADAMTS13-deficient mice was evaluated for disease progression, mucus layer disruption, leukocyte recruitment, and thrombus formation in mucosal vessels using intravital multiphoton excitation microscopy within single-cell spatial resolution. ResultsUC patients exhibited significantly reduced plasma ADAMTS13 activity correlating with disease severity and excessive VWF deposition in inflamed colonic tissues. In DSS-induced colitis mice, ADAMTS13 deficiency showed heightened disease activity and increased mucosal erosion in histochemical analysis compared to wild-type mice. A novel methodology established in this study using intravital microscopy successfully appraised colonic mucus barrier integrity by visualizing fluorescent dextran penetration from the colonic lumen to the crypts. ADAMTS13 deficiency accelerated mucus layer disruption, leukocyte adhesion, and microthrombi formation, particularly close to crypt epithelium regions. Vessel-specific analyses demonstrated that obstructive microthrombi were most prominent in the mucosal layer, contributing to local ischemia and mucosal erosion. Therapeutical usage of recombinant human ADAMTS13 alleviated microthrombus formation, improved mucosal integrity, and mitigated colitis severity in wild-type and ADAMTS13-deficient mice. ConclusionsObstructive thrombi formed in mucosal vessels due to impaired ADAMTS13 activity appeared essential in the disease progression of UC. Advanced intravital imaging provided novel insights into single-cell resolution UC pathogenesis.

physiology↗

CGC1, a new reference genome for Caenorhabditis elegans

The original 100.3 Mb reference genome for Caenorhabditis elegans, generated from the wild-type laboratory strain N2, has been crucial for analysis of C. elegans since 1998 and has been considered complete since 2005. Unexpectedly, this long-standing reference was shown to be incomplete in 2019 by a genome assembly from the N2-derived strain VC2010. Moreover, genetically divergent versions of N2 have arisen over decades of research and hindered reproducibility of C. elegans genetics and genomics. Here we provide a 106.4 Mb gap-free, telomere-to-telomere genome assembly of C. elegans, generated from CGC1, an isogenic derivative of the N2 strain. We used improved long-read sequencing and manual assembly of 43 recalcitrant genomic regions to overcome deficiencies of prior N2 and VC2010 assemblies, and to assemble tandem repeat loci including a 772-kb sequence for the 45S rRNA genes. While many differences from earlier assemblies came from repeat regions, unique additions to the genome were also found. Of 19,972 protein-coding genes in the N2 assembly, 19,790 (99.1%) encode products that are unchanged in the CGC1 assembly. The CGC1 assembly also may encode 183 new protein-coding and 163 new ncRNA genes. CGC1 thus provides both a completely defined reference genome and corresponding isogenic wild-type strain for C. elegans, allowing unique opportunities for model and systems biology.

genomics↗

Priming Epigenetic Landscape at Gene Promoters through Transcriptional Activation in Mammalian Germ Cells

In mammalian germ cells, a cycle of erasing and resetting epigenetic information is crucial for sex-specific gametogenesis and early embryogenesis. Specific chromatin states at promoters allow genes to be expressed at the appropriate time during germ cell development, however, the mechanism that establishes such characteristic chromatin states remains unclear. Here, we show that, in mouse male embryonic germ cells, promoters of developmental and housekeeping genes are selectively protected from de novo DNA methylation, coinciding with their transient upregulation and genome-wide erasure of H3K27me3. Importantly, a specific level of H3K4me3 density at the promoters serves as a potent probe that distinguishes between hypo- and hyper-DNA methylation states. Subsequent restoration of H3K27me3 contributes to establishing bivalent chromatin states that prime genes for activation at later developmental stages. These findings reveal a molecular framework shaping the epigenetic landscape at promoters with long-term effects beyond germ cell development.

genomics↗

Tertiary lymphoid structure as a therapeutic target of Crohns disease: modulation by TNFα blockade

Inflammatory diseases, such as Crohns disease (CD), are primarily treated with therapies aimed at alleviating inflammation. Notably, biological agents like TNF inhibitors have transformed the management of these conditions. Previous research has indicated that TNF inhibitors affect the cells in the lamina propria. However, this study demonstrates that infliximab, a type of TNF inhibitor, reduces the presence of tertiary lymphoid structures (TLS) and alleviates inflammation of CD by targeting follicular dendritic cells and macrophages within these structures. TLS could also be a potential target for various biological agents used to treat inflammatory diseases beyond CD. Furthermore, our study suggests that the status of TLS may serve as a predictor for the response to TNF inhibitor treatment. Our research could pave the way for new treatment strategies and the advancement of personalized medicine for inflammatory diseases.

immunology↗

Characterization of the Kaposi's sarcoma-associated herpesvirus terminase complex component ORF29

Kaposis sarcoma-associated herpesvirus (KSHV) belongs to the gammaherpesvirinae subfamily. In the lytic phase of herpesviruses, viral capsids are formed in the nucleus of the host cell and the replicated viral genome is packaged into capsids. The herpesviral genome is replicated as a precursor head-to-tail concatemer consisting of tandemly repeated genomic units, and each genomic unit is flanked by terminal repeats (TRs). The herpesvirus terminase complex packages one genomic unit into a capsid, by cleavage of the TRs in a precursor genome. Although the terminase complexes of alpha- and beta-herpesviruses are well characterized, in KSHV, the terminase complex is poorly understood. KSHV ORF7, ORF67.5, and ORF29 are thought to be components of the terminase complex. We previously reported that ORF7- or ORF67.5-deficient KSHV formed immature soccer ball-like capsids and failed to cleave the TRs, resulting in decreased virion production. Moreover, ORF7 interacted with ORF29 and ORF67.5. However, ORF29 and ORF67.5 did not interact with each other. Thus, although ORF7 and ORF67.5 are important for KSHV terminase function, the function of ORF29 remains largely unknown. Here, we constructed ORF29-deficient BAC16 and analyzed its virological properties. ORF29 was essential for virion production and TR cleavage. Numerous immature soccer ball-like capsids were observed in ORF29-deficient KSHV-harboring cells. The N-terminal region of ORF29 was important for its interaction with ORF7, although full-length ORF29 was required for effective complexation of the KSHV terminase. Furthermore, ORF29 preferentially interacted with itself rather than with ORF7. Thus, our data shows that ORF29 functions as a fundamental terminase component. IMPORTANCESince the role of ORF29 in the KSHV terminase complex remains unknown, we constructed ORF29-deficient KSHV. Our results demonstrated that ORF29 functions as a component of the KSHV terminase and is critical for capsid formation, TR cleavage, and terminase complexation. Moreover, ORF29 robustly interacted with itself. In HSV-1, a terminase complex containing UL15, UL28, and UL33 forms a trimer, and six trimers assemble into a hexameric ring. The HSV-1 genome passes through this ring and undergoes TR cleavage and genome packaging into a capsid. The self-interaction of ORF29 may be involved in the multimerization of a terminase complex or formation of the KSHV terminase ring. In addition, a novel KSHV protein, which we refer to as ORF29.5, was expressed during the lytic state. ORF29.5 mRNA shares the same stop codon with the ORF29 mRNA. Moreover, a part of the ORF29.5 coding region may overlap with the C-terminal ORF29 coding region.

microbiology↗

Downregulation of astrocytic C3 production alleviates neuronal mitochondrial dysfunction in tauopathy models

Neuronal mitochondrial dysfunction is associated with cognitive decline in neurodegenerative disorders such as Alzheimers Disease (AD). In this study, multiple pieces of evidence proved that phosphorylated tau (p-Tau) caused mitochondrial swelling and dysfunction in neurons. In a novel in vitro newborn neurons culture system, we discovered mitochondrial swelling and dysfunction were associated with increased p-Tau, leading to necroptosis activation, which was induced by Complement C3 (C3) produced from activated astrocytes. In the in vivo tauopathy mouse models, the effects of astrocytic C3 on tau-associated mitochondrial dysfunction and necroptosis were also discovered in hippocampal newborn neurons, and we directly showed that p-Tau aggregation was associated with mitochondria swelling in the hippocampal neurons by electron microscopy analysis. In addition, we proved the ability of compound anserine, which can block Tak1-Ikk dependent NF-{kappa}B activation, to further down-regulate astrocytic C3 production and alleviate neuronal mitochondrial dysfunction in vitro and in vivo, respectively. Down-regulation of astrocyte C3-production by anserine could also rescue mortality as well as cognitive and motor functions. Our findings first reported the contribution of p-Tau on neuronal mitochondrial dysfunction and proposed the therapies that down-regulate astrocytic C3 production have a potential role in alleviating this neurotoxic effect.

neuroscience↗

Single-nucleus transcriptional and chromatin accessibility analyses of maturing mouse Achilles tendon uncover the molecular landscape of tendon stem/progenitor cells

Tendons and ligaments are crucial connective tissues linking bones and muscles, yet achieving full functional recovery after injury remains challenging. We investigated the characteristics of tendon stem/progenitor cells (TSPCs) by focusing on the declining tendon repair capacity with growth. Using single-cell RNA sequencing on Achilles tendon cells from 2-and 6-week-old mice, we identified Cd55 and Cd248 as novel surface antigen markers for TSPCs. Combining single-cell RNA sequencing with single-nucleus RNA and ATAC sequencing analyses revealed that Cd55 and Cd248 positive fractions in tendon tissue represent TSPCs, as confirmed by their expression of established TSPC markers, with this population decreasing at 6 weeks. We also identified candidate upstream transcription factors regulating these fractions. Functional analyses of isolated CD55/CD248 positive cells demonstrated high clonogenic potential and tendon differentiation capacity, forming functional tendon-like tissue in vitro. This study establishes CD55 and CD248 as novel TSPC surface antigens, potentially advancing tendon regenerative medicine and contributing to the development of new treatment strategies for tendon and ligament injuries.

developmental biology↗

Expression of endogenous Anopheles gambiae microRNAs using an Anopheles gambiae densovirus (AgDNV) intronic expression system

Anopheles gambiae densovirus (AgDNV) is a highly species-specific parvovirus that reaches high titers in adult Anopheles gambiae mosquitoes with few transcriptomic effects and no significant fitness effects. Given these characteristics, AgDNV has been proposed as a viral vector for basic research and mosquito control. Previous work created an AgDNV co-expression system with a wild-type AgDNV helper plasmid and a transducing enhanced green fluorescent protein (EGFP) expressing plasmid that can be used to co-transfect cells to generate infectious recombinant transducing AgDNV virions. Generated virions infect the An. gambiae midgut, fat body, and ovaries, yet this viral vector system is limited in the size of transgenes that can be expressed due to capsid packaging limitations. Considering these size constraints, we created an artificial intron within the EGFP gene of the transducing construct that can express small pieces of genetic material such as microRNAs (miRNAs), microRNA sponges, or other small sequences. Placement of this intron in EGFP created a fluorescent reporter such that incorrect splicing produces a frameshift mutation in EGFP and an early stop codon whereas correct splicing results in normal EGFP expression and co-transcription of the intronic genetic cargo. A selection of miRNAs with predicted or demonstrated importance in mosquito immunity and reproduction with expression localized to the fat body or ovaries were chosen as intronic cargo, construct expression and splicing evaluated, and the impact of miRNA expression on putative miRNA targets was measured in vitro and in vivo. While the intron was correctly spliced in cells and mosquitoes, miRNA delivery resulted in inconsistent changes to miRNA and target gene transcript levels--possibly due to organ-specific miRNA expression or miRNA-target gene sequence mismatch. However, with optimization this viral vector and developed intron have potential as an expression tool within An. gambiae mosquitoes or cells.

microbiology↗

Giant extrachromosomal element "Inocle" potentially expands the adaptive capacity of the human oral microbiome

Survival strategy of bacteria is expanded by extrachromosomal elements (ECEs). However, their genetic diversity and functional roles for adaptability are largely unknown. Here, we discovered a novel family of intracellular ECEs using 56 saliva samples by developing an efficient microbial DNA extraction method coupled with long-read metagenomics assembly. Even though this ECE family was not hitherto unidentified, our global prevalence analysis using 476 salivary metagenomic datasets elucidated that these ECEs reside in 74% of the population. These ECEs, which we named, "Inocles", are giant plasmid-like circular genomic elements of 395 kb in length, having Streptococcus as a host bacterium. Inocles encode a series of genes that contribute to intracellular stress tolerance, such as oxidative stress and DNA damage, and cell wall biosynthesis and modification involved in the interactions with oral epithelial cells. Moreover, Inocles exhibited significant positive correlations with immune cells and proteins responding to microbial infection in peripheral blood. Intriguingly, we examined and found their marked reductions among 68 patients of head and neck cancers and colorectal cancers, suggesting its potential usage for a novel biomarker of gastrointestinal cancers. Our results suggest that Inocles potentially boost the adaptive capacity of host bacteria against various stressors in the oral environment.

genomics↗

Robust and highly efficient transformation method for a minimal Mycoplasma cell

Mycoplasmas have been widely investigated for their pathogenicity, as well as for genomics and synthetic biology. Conventionally, transformation of mycoplasmas was not highly efficient, and due to the low transformation efficiency, large amounts of DNA and recipient cells were required for that purpose. Here we report a robust and highly efficient transformation method for the minimal cell JCVI-syn3B, which was created through streamlining of the genome of Mycoplasma mycoides. When the growth states of JCVI-syn3B were examined in detail by focusing on such factors as pH, color, absorbance, CFU, and transformation efficiency, we found that the growth phase after the lag phase can be divided into three distinct phases, of which the highest transformation efficiency was observed during the early-exponential growth phase. Notably, we attained the transformation efficiency up to 4.4 x 10-2 transformants per cell per g plasmid DNA. We developed a method to obtain several hundred to several thousand transformants with less than 0.2 mL of cultured cells and 10 ng of plasmid DNA. Moreover, we established a transformation method using frozen stock of transformation-ready cells. These procedures and information could simplify and enhance the transformation process of minimal cells, facilitating advanced genetic engineering and biological research using minimal cells. IMPORTANCEMycoplasmas are parasitic and pathogenic bacteria for many animals. They are also useful bacteria to understand cellular process of life and for bioengineering because of their simple metabolism, small genomes and cultivability. Genetic manipulation is crucial for these purposes, but transformation efficiency in mycoplasmas is typically quite low. Here we report a highly efficient transformation method for the minimal genome mycoplasma JCVI-syn3B. Using this method, transformants can be obtainable only 10 nanograms of plasmid DNA, which is around one-thousandth amount required for traditional mycoplasma transformations. Moreover, we established a convenient method using frozen stocks of transformation-ready cells. These improved methods play a crucial role in further studies using minimal cells.

microbiology↗

Arterial spin labelling perfusion MRI analysis for the Human Connectome Project Lifespan Ageing and Development studies

The Human Connectome Project Lifespan studies cover the Development (5-21) and Aging (36-100+) phases of life. Arterial spin labelling (ASL) was included in the imaging protocol, resulting in one of the largest datasets collected to-date of high spatial resolution multiple delay ASL covering 3,000 subjects. The HCP-ASL minimal processing pipeline was developed specifically for this dataset to pre-process the image data and produce perfusion estimates in both volumetric and surface template space. Applied to the whole dataset, the outputs of the pipeline revealed significant and expected differences in perfusion between the Development and Ageing cohorts. Visual inspection of the group average surface maps showed that cortical perfusion often followed cortical areal boundaries, suggesting differential regulation of cerebral perfusion within brain areas at rest. Group average maps of arterial transit time also showed differential transit times in core and watershed areas of the cerebral cortex, which are useful for interpreting haemodynamics of functional MRI images. The pre-processed dataset will provide a valuable resource for understanding haemodynamics across the human lifespan.

neuroscience↗

Modular photostable fluorescent DNA blocks dissect the effects of pathogenic mutant kinesin on collective transport

Intracellular transport is driven by teams of various motor proteins. Advances in DNA nanotechnology have enabled the programmable linkage of different types of motor proteins. In this study, we developed a modular, photostable, fluorescence-labeled tiny DNA origami block (FTOB) for extended observation of collective transport by selected motor combinations. The FTOB is designed as a 4-helix bundle ([~]8.4 nm) with densely accumulated fluorescent dyes, minimizing blinking and photobleaching. By designing a pair of connector DNAs, FTOBs are heterodimerized following motor protein attachment using the ALFA-tag/nanobody system. Our system examined the impact of a pathogenic mutant kinesin on its collective movement with wild-type kinesin, clearly observing two distinct behaviors: the teams velocity was generally governed by the slower mutant but occasionally surged to levels comparable to that of a single wild-type motor. Our photostable, robust, modular FTOB system could serve as a versatile tool for precisely dissecting cooperative cargo transport.

bioengineering↗

Nanoscale visualization of Drosophila E-cadherin ectodomain fragments and their interactions using DNA origami nanoblocks

The adhesive function of cell surface proteins can be visually assessed through direct observation; however, the underlying structures that mediate adhesion typically remain invisible at the nanoscale level. This hinders knowledge on the diversity of molecular architectures responsible for cell-cell adhesion. Drosophila E-cadherin (DE-cadherin), a classical cadherin with a unique domain structure, demonstrates adhesive function; however, it lacks a structural model that explains its adhesion mechanism. In this study, we present a novel application of DNA origami technology to create a cell-free, flat environment in which full DE-cadherin ectodomains are anchored using SNAP-tags and biotin-streptavidin interactions. DNA origami was assembled into a 120 nm long block, bearing 5 or 14 biotin:streptavidin sites that were evenly spaced on one lateral face. DE-cadherin ectodomain fragments were attached via biotinylated SNAP-tags. These decorated DNA origami nanoblocks were subjected to transmission electron and high-speed atomic force microscopy, which revealed a hinge-like site that separated the membrane-distal and -proximal portions of the DE-cadherin ectodomain, suggesting a role in mechanical flexibility. We also observed interactions between DE-cadherin ectodomains via their membrane-distal portions on single DNA origami nanoblocks. We reconstituted an adhesion-like process via pairing DNA origami nanoblocks using DE-cadherin ectodomain interactions. Homophilic associations of functional DE-cadherin ectodomains between the paired DNA origami nanoblocks were visualized at the nanoscale, displaying strand-like molecular configurations, likely representing the extracellular cadherin repeats without regular arrays of structural elements. This study introduces a DNA origami-based platform for reconstituting and visualizing cadherin ectodomain interactions, with potential applications for a broader range of adhesion molecules. HighlightsO_LIDNA origami technology was applied to perform a structure-function study of cadherin. C_LIO_LIDNA origami nanoblocks decorated with DE-cadherin ectodomains were observed by TEM/HS-AFM. C_LIO_LIA hinge-like site that separated the membrane-distal and -proximal portions of the DE-cadherin ectodomain was revealed. C_LIO_LIAn adhesion-like process was mimicked via pairing two nanoblocks using DE-cadherin ectodomain interactions. C_LIO_LIHomophilic associations of DE-cadherin ectodomains between the nanoblocks were visualized at the nanoscale level. C_LI

molecular biology↗