Biology subjects

Liu, D.

Publications and source records attributed to Liu, D..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

The m6A reader protein YTHDF2 facilitates HTLV-1 infectious and mitotic propagation by stabilizing Tax RNA

N6-methyladenosine (m6A) is one of the important RNA modifications that affect RNA abundance and function and has also been implicated in viral infection. In this study, we identify a number of m6A modification sites within human T-cell leukemia virus type 1 (HTLV-1) RNAs, particularly in the RNA of the Tax oncogene. We demonstrate that YTH domain family, member 2 (YTHDF2), a key m6A reader protein that binds m6A-modified RNAs and influences RNA metabolism, is required for HTLV-1 replication in both de novo and persistently infected cells. Mechanistically, YTHDF2 interacts with and stabilizes Tax RNA in an m6A-dependent manner, thereby promoting Tax-driven HTLV-1 replication. Importantly, YTHDF2 activates oncogenic cellular pathways and promotes proliferation in HTLV-1 infected cells, aligning with the functions of Tax. Overall, our findings characterize YTHDF2 as a host factor critical to HTLV-1 RNA metabolism and viral propagation, offering novel insights into the understanding of HTLV-1 life cycle and the development of targeted interventions. Importancem6A is an RNA modification that plays crucial roles in physiological and pathological conditions; however, its roles in HTLV-1 infection are poorly understood. In this study, we identify that m6A modification is widely present in HTLV-1 RNAs including Tax. We demonstrate that YTHDF2, a prominent m6A reader protein, enhances the stability of Tax RNA, thereby promoting both de novo and persistent HTLV-1 replication. Our findings position YTHDF2 as an essential factor for HTLV-1 persistence and suggest it as a potential therapeutic target for viral clearance.

microbiology↗

bioRxiv2025

Synthetic Modular Cyanobacterial Consortium Enables Carbon-Negative Production of Glycerol and Derivatives

Cyanobacteria offer a direct route for converting solar energy and CO2 into valuable chemicals, yet the metabolic burden of complex heterologous pathways often limits their productivity and stability. Here, we present a modular co-culture strategy that uses glycerol as an efficient mediator metabolite to link cyanobacterial carbon fixation with downstream bioconversion. We first engineered Synechococcus elongatus UTEX 2973 (Syn2973) for high-level glycerol biosynthesis by optimizing synthase selection, eliminating competing pathways, and improving CO2-supply conditions, achieving a production of 14.53 g{middle dot}L-1. In parallel, we constructed glycerol conversion modules in Syn2973 and Gluconobacter oxydans enabling production of 1,3-propanediol (1,3-PDO), 3-hydroxypropionic acid, and dihydroxyacetone, with exogenous glycerol yielding up to 30.07 g{middle dot}L-1 1,3-PDO. Integrating the two modules resulted in a fully autotrophic co-culture that produced all three target chemicals directly from CO2, including semi-continuous 1,3-PDO production at 6.02 g{middle dot}L-1{middle dot}day-1, corresponding to a net carbon fixation efficiency of 3.43 kg CO2 eq/kg 1,3-PDO.

synthetic biology↗

bioRxiv2025

IgG-Bridging-Seeded Synergistic Aggregation of SARS-CoV-2 Spikes Underlies Potent Neutralization by A Low-Affinity Antibody

Mechanistic studies of viral neutralization typically prioritize high-affinity antibodies, relegating low-affinity binders to the sidelines. We report P5-1C8, a Class 1 SARS-CoV-2 antibody that exemplifies this underexplored "low-affinity yet high-potency" phenotype, retaining strong neutralization of Omicron JN.1 despite markedly weakened trimer binding (KD = 225 nM; IC50 = 0.06 nM). Structural and biophysical analyses reveal that P5-1C8 engages WT and BA.1 spikes through canonical intra-spike bivalency, but with JN.1 it induces aggregation. Using virion-like nanoparticles displaying multiple spikes, we show that IgG remains bound with no detectable dissociation and triggers pronounced aggregation. Coarse-grained molecular dynamics delineate the stepwise pathway in which weak IgG-spike contacts seed aggregation via transient inter-spike bridging. Together, these findings establish the first mechanistic framework demonstrating how weak-binding antibodies can nonetheless achieve potent neutralization through higher-order aggregation, thereby expanding the conceptual landscape of antibody function and opening new directions for antibody evaluation and design. Graphical AbstractLow-affinity antibodies are frequently disregarded in discovery pipelines. This work reports P5-1C8, a Class 1 SARS-CoV-2 antibody with weak trimer binding (KD-to-IC50 > 3,700-fold) yet potent neutralization of Omicron JN.1. Structural, biophysical, functional and coarse-grained simulations collectively demonstrate that transient inter-spike IgG bridging seeds higher-order aggregation, which in turn drives neutralization and provides a mechanistic framework. O_FIG O_LINKSMALLFIG WIDTH=199 HEIGHT=200 SRC="FIGDIR/small/691454v1_ufig1.gif" ALT="Figure 1000"> View larger version (79K): org.highwire.dtl.DTLVardef@1d4f132org.highwire.dtl.DTLVardef@1274400org.highwire.dtl.DTLVardef@e186a6org.highwire.dtl.DTLVardef@4f1870_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Antibacterial Activity of the Natural Product Elaiophylin against Streptococcus suis and its Biofilm Eradication Effect

The multidrug resistance (MDR) problem in Streptococcus suis(S. suis) is becoming increasingly severe, necessitating the development of novel antibacterial agents and strategies. In this study, seven Elaiophylin derivatives were isolated from Streptomyces sp. WS-30248, and the antibacterial activity and mechanism of action of the principal compound, Elaiophylin, against S. suis were systematically evaluated for the first time. Through comprehensive approaches including in vitro efficacy assays, biofilm inhibition and eradication tests, bacterial membrane integrity analysis, reactive oxygen species (ROS) level detection, and a mouse infection model, Elaiophylin was found to exhibit significant antibacterial activity against multiple clinically MDR S. suis strains. Its minimum inhibitory concentration (MIC) was as low as 0.5 g/mL, and complete bactericidal activity was achieved within 24 hours at 4xMIC. The compound effectively inhibited and eradicated bacterial biofilms, directly killing embedded cells within the biofilm matrix. Mechanistic studies revealed that Elaiophylin functions through multiple synergistic pathways, including disruption of bacterial membrane integrity and induction of massive ROS accumulation, thereby interfering with the proton motive force (PMF), depleting intracellular ATP, and blocking energy metabolism. In the mouse infection model, the Elaiophylin-treated group showed a significantly increased survival rate of 60% and effectively reduced bacterial loads in tissues. This study demonstrates that Elaiophylin is a highly promising natural candidate drug with multi-target synergistic effects, offering a new strategy to combat MDR S. suis and biofilm-associated infections.

microbiology↗

bioRxiv2025

sept-1/zina-1 is an Ancient Toxin-Antidote System in Caenorhabditis elegans

The toxin-antidote (TA) systems, consisting of two tightly linked genes acting as a postzygotic distorter, are found in several eukaryotic organisms, including three androdioecious Caenorhabditis species. However, the evolutionary history of such TA systems remains poorly understood. We report an ancient C. elegans TA system identified in the highly divergent Hawaiian strain XZ1516. The maternal toxin SEPT-1 induces a rod-like larval arrest phenotype in progeny that do not carry the antidote ZINA-1, which has ten zinc finger motifs. Interestingly, zina-1 is pseudogenized in most non-Hawaiian strains, while sept-1 evolves from a toxic to a non-toxic form through sequence divergence. Phylogenetic studies found that sept-1/zina-1 is the most ancestral TA system among the three known ones, and its loss preceded the rise of sup-35/pha-1. These two maternal TAs do not coexist in the same strain but have overlaps with the paternal TA peel-1/zeel-1, which is the latest one to propagate.

evolutionary biology↗

bioRxiv2025

Distinctive Functionality of Semantic Hubs: Evidence from Semantic Dementia

Semantic cognition relies on a distributed network with multiple candidate hub regions that bind multimodal conceptual information. While the anterior temporal lobe (ATL) is widely regarded as a core semantic hub, the roles of other candidate regions--such as the fusiform gyrus (FFG) and posterior middle temporal gyrus (pMTG)--remain debated, particularly regarding verbal and non-verbal semantic processing within the same sensory modality. This study examined 33 patients with semantic dementia and 20 healthy controls using a comprehensive behavioral battery (word and picture versions of the Pyramid and Palm Trees Test and a word-picture verification task) combined with multimodal neuroimaging, including voxel-based morphometry, diffusion-weighted imaging, and resting-state fMRI. Partial correlation and commonality analyses revealed that (1) the left ATL selectively underpins abstract verbal semantic processing, (2) the left FFG contributes to general semantic processing across verbal and non-verbal stimuli, (3) and the left pMTG plays a critical role in integrating verbal and non-verbal semantic information. White matter tracts linking the left ATL and FFG to the right ATL significantly predicted semantic integration performance, underscoring the importance of inter-hemispheric structural connectivity. Functional measures in contralateral regions, including amplitude of low-frequency fluctuation (ALFF) in the right FFG and degree centrality (DC) in the right pMTG, also predicted integration outcomes, suggesting compensatory network reorganization. These findings highlight functional specialization among semantic hubs and underscore the importance of multimodal, cross-hemispheric approaches for understanding the neural architecture of semantic representation.

neuroscience↗

bioRxiv2025

MotifAE Reveals Functional Motifs from Protein Language Model: Unsupervised Discovery and Interpretability Analysis

Protein language models (pLMs) learn sequence patterns at evolutionary scale, but these patterns remain inaccessible within these "black box" models. To discover them, we developed MotifAE, an unsupervised framework based on the sparse autoencoder (SAE) architecture that projects pLM embeddings into an interpretable, sparse latent space. MotifAE introduces an additional smoothness loss to encourage coherent feature activation, which markedly improves the identification of known functional motifs compared to the standard SAE. The sequence patterns captured by MotifAE exhibit rich diversity, align with known functional motifs, and are reflected in the models weight space. Beyond short motifs, MotifAE also captures structural domains, with latent feature activation scores correlating with residue importance for different domain functions. By aligning MotifAE features with experimental data, we further identified features associated with domain folding stability. These features enable the prediction of a stability-specific fitness landscape that improves stability prediction and supports the engineering of domains with enhanced stability. Overall, MotifAE provides a general framework for systematic sequence pattern discovery and interpretation, with the potential to advance protein function analysis, mutation effect interpretation, and rational protein engineering.

bioinformatics↗

bioRxiv2025

SUGP1 associates Y-box protein to regulate piRNA biogenesis in Bombyx mori

PIWI-interacting RNAs (piRNAs) are critical for transposon silencing and genome integrity, as well as gene expression regulation and antiviral immunity in metazoans, yet the molecular mechanisms governing their biogenesis remain incompletely understood. The participation of the splicing-associated process in piRNA biogenesis has been emphasized in multiple species, but the key factors and mechanisms remain elusive. Here, we identified SUGP1 (SURP and G-Patch Domain Containing 1) in BmE (a unique model cell system with a complete piRNA biogenesis pathway) as a key splicing factor that functions in piRNA biogenesis. Through CRISPR-Cas9-mediated gene knockdown in cultured cells combined with RNA-seq, small RNA-seq, and IP-mass spectrometry (IP-MS), our results reveal that SUGP1 deficiency disrupts piRNA accumulation, alters mature piRNA length distributions, and activates transposon expression. Immunofluorescence and Western blot (WB) analyses further demonstrate that SUGP1 interacts with Y-box protein (YBP), which is key regulators of RNA metabolism. Functional validation in Drosophila SUGP1-RNAi lines highlights evolutionary conserved and species-specific roles of SUGP1 in piRNA maturation. Collectively, our data uncover a dual role for silkworm SUGP1 in coordinating YBP-dependent piRNA biogenesis, thus elucidating a novel mechanistic framework for piRNA pathway regulation. Our work also underscores the silkworm as a unique model for studying non-canonical piRNA biogenesis mechanisms, with implications for treating transposon dysregulation-linked diseases. Author summaryDisruption of piRNA synthesis leads to abnormal consequences such as transposon de-repression, posing a significant threat to genomic stability. It is therefore essential to in-depth analysis of the piRNA biosynthetic mechanism. Previous studies have highlighted the involvement of splicing-related processes in piRNA biosynthesis, yet key factors and mechanisms remain poorly understood. This study employed the silkworm cell system, which possesses a complete piRNA biosynthetic pathway. Utilizing CRISPR-Cas9-mediated gene knockout technology combined with RNA sequencing, small RNA sequencing, and immunoprecipitation-mass spectrometry (IP-MS), we discovered that SUGP1 deficiency disrupts piRNA accumulation, alters the length distribution of mature piRNAs, and activates transposon expression. Furthermore, immunofluorescence and Western blot analyses confirmed an interaction between SUGP1 and Y-box proteins (YBPs), key regulators of RNA metabolism. Functional validation using Drosophila SUGP1-RNAi lines revealed that SUGP1 plays dual roles in piRNA maturation. Our study reveals that the silkworm scissor-related factor SUGP1 has dual functions in coordinating YBP-dependent piRNA biosynthesis.

molecular biology↗

bioRxiv2025

A scalable proteogenomic framework for dissecting phospho-signaling pathways in primary immune cells

Signaling networks modulated by post-translational modifications orchestrate cellular responses to external cues. Traditional approaches to study these pathways lack the throughput to systematically capture the causal architecture of these signaling pathways at scale. Here, we present an integrated proteogenomic framework that combines saturating genetic perturbations with high-throughput proteomics to systematically map cytokine-induced signaling in primary human T cells. Supporting this framework is simplePhos, a streamlined, low-input phosphoproteomics workflow that enables scalable, time-resolved analysis without the requirement for specialized equipment or robotics. We extensively validate the simplePhos pipeline by applying inflammatory stimuli, including type I and II interferons, lipopolysaccharide, and Sendai virus to primary T cells and myeloid cells, establishing foundational datasets in these treatment contexts. Ultimately, using type I interferon signaling in genetically modified T cells as a model, we demonstrate that combined application of genetic alterations and proteomic analyses can map key signaling nodes in primary immune cells. This represents a powerful strategy to mechanistically interrogate phospho-signaling networks in human immune cells, with broad applications in translational immunology and therapeutic development.

systems biology↗

bioRxiv2025

Human brains construct individualized global rankings from identical few-shot local learning

Ranking--a ubiquitous relational structure--enables humans to organize complex information and overcome cognitive load, yet in real-world settings it is often inferred from sparse, few-shot learning of local pairwise relationships. How the human brain performs relational inference under such limited evidence remains unknown. We hypothesized that under few-shot learning, relational inference is shaped by inductive biases, such that individuals actively impose structured global relationships--often idiosyncratic--to constrain and unify limited local information. In a preregistered behavioral study combined with magnetoencephalography (MEG) recordings, we show that even after identical few-shot local pair learning, individuals construct stable and self-consistent, yet idiosyncratic, global rankings that diverge from the ground-truth order--a phenomenon not readily explained by classical computational models of transitive inference. MEG recordings further reveal that frontoparietal neural representations are reorganized to reflect each individuals subjective ranking rather than those of others. Together, these findings highlight the constructive and generative nature of human cognition: under sparse samples and limited computational resources, the human brain actively infers and imposes relational structure.

neuroscience↗

bioRxiv2025

Multiomic profiling of a unique in-transit melanoma cohort identifies melanoma differentiation as predictor of tumor progression and therapy response

Melanoma patients with in-transit metastasis (ITM), a stage of disease where melanoma has metastasized to sites in between the primary lesion and draining lymph node, vary significantly in their clinical outcomes, but the biology driving differential outcomes in ITM is poorly understood. To elucidate the mechanisms of differential outcomes, we utilized multimodal molecular profiling (WES, RNA-seq, highly multiplexed immunofluorescence, spatial transcriptomics) in 1) evolutionary analysis of longitudinal tumor samples and 2) identifying prognostic tumor intrinsic and microenvironmental features in a unique cohort of patients with unresectable ITM. Among other findings, we observed a persistent dedifferentiated AXL/NGFR clonal lineage pre-existing and following immune checkpoint blockade in in-transit and distant metastases. Concordantly, we found that low pigmentation and high T cell exhaustion signatures were independently associated with distant progression. Our findings highlight tumor cell state and immune dysfunction as key predictors and potential biomarkers of metastatic risk in ITM. STATEMENT OF SIGNIFICANCEWhat drives distant progression in melanoma is unclear. Analyzing tumor and immune features in a rare in-transit melanoma patient cohort, we identify biological signals highlighting how immune and tumor states observable in pre-distant metastasis melanomas shape long-term outcomes, and nominate potential prognostic biomarkers.

cancer biology↗

bioRxiv2025

A deep learning and co-conservation framework enable discovery of non-canonical Cas proteins

CRISPR-Cas systems are central to prokaryotic adaptive immunity, widely harnessed for biotechnology. Yet, their vast and uncharacterized diversity, especially non-canonical variants, impedes full exploitation. Here we present BioPrinCRISPR, a class-agnostic computational framework leveraging gene co-conservation, protein domain co-occurrence, and embedding similarity to identify and characterize CRISPR-Cas systems across prokaryotic genomes. Applying BioPrinCRISPR to over one million bacterial genomes, we uncovered extensive canonical and uncharacterized systems, revealing a rich landscape of atypical Cas proteins and novel domain architectures. Notably, we identified recurrent fusion proteins with unique enzymatic combinations, suggesting roles in regulatory control or nucleic acid remodeling. Experimental validation of two divergent Cas13an-like effectors demonstrated RNA knockdown capacity in human cells, confirming our frameworks predictive power. These findings expand the functional repertoire of CRISPR-associated proteins and highlight unexplored modes of microbial immunity. BioPrinCRISPR thus stands as a powerful tool for comprehensively mapping CRISPR-Cas diversity, offering new insights into prokaryotic defense and facilitating discovery of novel candidates for next-generation genome engineering. An accompanying interactive web platform was also developed to facilitate data exploration.

synthetic biology↗

bioRxiv2025

Programming Microbe-Computer Interaction for Customized Life-Nonlife and Cross-Life Communication

This extension of human-computer interaction (HCI) paradigm to the non-intelligent microbe-computer interaction (MCI) is attractive for building generalized life-nonlife communication. Main challenges lie in how to construct biohybrid interface within individual MCI unit and thereafter program cross-life communication based on these MCI units. Here, we propose the design and construction of opto-interfaced MCI unit composed of engineered microbes and computer terminals, for enabling quantifiable transduction between microbial signals and digital signals. These units were able to serve as biohybrid sensors, actuators and transceivers, supporting biomonitoring, bio-actuation and microbe-centric bidirectional operations. Based on these functional units, we established programmable cross-life communication architectures capable of unicast, multicast, and logic-gate-driven communication with temporal dynamic control. The architectures were validated in biomedical scenarios including tumor hypoxia biomarking, epidermal heavy metal detoxification, and colitis intervention, demonstrating robust performance in closed-loop diagnostic-therapeutic applications. Additionally, we integrated MCI with an unmanned surface vessel for environmental monitoring, highlighting its cross-domain potential. Collectively, we provide a scalable strategy for building customized life-nonlife and cross-life communication, which is expected as an important complement to internet of things (IoT).

synthetic biology↗

bioRxiv2025

Harnessing the CD2 axis to broaden and enhance the efficacy of CAR T cell therapies

Patients with T-cell lymphomas and leukemias have overall poor outcomes due to the lack of targeted and effective treatments, particularly in the relapsed and refractory settings. Development of chimeric antigen receptor (CAR) T-cells against T-cell neoplasms is limited by a lack of discriminating T-cell antigens that allow for effective anti-tumor responses while preventing CAR T-cell fratricide. We hypothesized that targeting CD2, a pan-T-cell antigen, using anti-CD2 CAR T-cells engineered without CD2 expression (CART2), would support CAR T-cell manufacturability and preclinical efficacy. Optimized CD2-knockout CART2, generated using CRISPR-Cas9, eradicated primary patient-derived CD2+ hematological neoplasms in vitro and in vivo, secreted effector cytokines, and exhibited adequate proliferative capacity. Nevertheless, CD2 has a key costimulatory function, and its deletion could lead to CAR T-cell dysfunction. Therefore, we tested the role of the CD2:CD58 axis in CAR T-cells, using the anti-CD19 CART models. We demonstrate that CD2 loss attenuates CART19 efficacy by reducing avidity for tumor antigen, co-stimulation, and ultimately in vivo activity. Analogously, we show that tumor CD58 loss reduces CART19 efficacy. To overcome this issue, we developed a novel PD-1:CD2 switch receptor that rescues intracellular CD2 signaling, particularly when PD-L1 is engaged, resulting in improved in vivo outcomes. Collectively, we studied the role of CD2 both as a target for CAR T cell therapy and as a critical costimulatory protein, whose signaling can be rescued using the PD-1:CD2 switch receptor. This receptor can be incorporated into CAR T-cells and provides an effective strategy to overcome CD2-signaling deficiencies.

cancer biology↗

bioRxiv2025

Discrete interneuron subsets participate in GluN1/GluN3A excitatory glycine receptor (eGlyR)-mediated regulation of hippocampal network activity throughout development and evolution.

Decades of studies implicating GluN3A N-methyl-D-aspartate receptor (NMDAR) subunits in physiological and pathological function have largely been interpreted through direct regulation of conventional glutamatergic NMDARs. However, emerging evidence indicates that GluN3A frequently assembles with GluN1 forming unconventional glutamate-insensitive NMDARs that operate as native excitatory glycine receptors (eGlyRs). Here we demonstrate that hippocampal somatostatin and neurogliaform interneurons (Sst-INs and NGFCs) express functional eGlyRs from early postnatal through adult ages. In the developing hippocampus eGlyR-mediated excitation of NGFCs with ambient glycine dramatically increases GABAergic tone, with consequences for the generation of giant depolarizing potentials (GDPs). In the mature hippocampus, eGlyR- mediated excitation of Sst-INs regulates sharp wave ripples (SWRs). Finally, we reveal evolutionary conservation of hippocampal Sst-IN eGlyRs and eGlyR- mediated SWR regulation in non-human primates confirming functional eGlyR availability for therapeutic potential in higher species. Our findings underscore that eGlyR mediated regulation of cell and circuit excitability through both cell autonomous and cell non-autonomous mechanisms must be considered to understand GluN3A roles in brain development, plasticity, and disease.

neuroscience↗

bioRxiv2025

From Correlation to Causation: Cell-Type-Specific Gene Regulatory Networks in Alzheimer's Disease

INTRODUCTIONAlzheimers disease (AD) involves complex regulatory disruptions across multiple brain cell types, yet a comprehensive understanding of the intracellular causal mechanisms remains unclear. METHODSWe presented an integrative analysis framework using single-nucleus transcriptomic with matched subject-level genotype data from 272 human AD in the Religious Orders Study and the Rush Memory and Aging Project (ROSMAP) study, and constructed causality-based, cell-type-specific gene regulatory networks (GRNs). RESULTSOur method identifies regulatory genes from both transcription factors (TFs) and non-TFs, thereby capturing a complete and accurate causal regulatory map across different brain cell types. This work revealed both established and novel regulations, pathways, and cell-type-unique hub genes in AD. Beyond constructing transcriptome-wide GRNs, we quantitatively assessed hub genes and distinguished those with regulatory or responsive roles. DISCUSSIONOur study provides a comprehensive mapping of cell-type-specific causal GRNs in AD, providing a powerful resource for dynamic pathway exploration, hypothesis generation, and functional interpretation.

neuroscience↗

bioRxiv2025

Loss of the tumor suppressor PTEN activates cell-intrinsic interferon signaling to drive immune resistance

Loss of the tumor suppressor PTEN is strongly associated with a lack of response to immune checkpoint blockade therapies in cancer patients, but the underlying mechanisms are not fully understood. We have developed a transformation model where knocking out PTEN in human mammary epithelial cells drives dependence on the p110{beta} subunit of PI3K and, notably, elicits a robust induction of endogenous retroviral elements (ERVs) and activation of the interferon signaling. This constitutive cell-intrinsic interferon response, hallmarked by hyperactivated STAT1, is also observed in human tumors with a PTEN-low status. We further find that PTEN deficiency renders cancer cells resistant to the cytotoxic effects of immune cells and interferon-{gamma}. Notably, PTEN loss also results in a dependency on an activated DNA damage response pathway, leading to an exquisite vulnerability to CDK12 inhibition. Our study suggests an interferon adaptation model in which tumors driven by PTEN deficiency inherently activate the interferon response, enabling them to adapt to interferon cytotoxicity and gain resistance to immunotherapies.

cancer biology↗

bioRxiv2025

DNA Data Storage Architecture via Ligation of Dynamic DNA Bytes

The explosive growth of digital data is overwhelming conventional storage media, creating an urgent need for more efficient solutions. DNA offers immense potential for digital data storage, yet most systems remain static and archival. Here, we present a modular DNA storage architecture based on dynamic DNA bytes (DynaBytes)-- pre-fabricated DNA segments that can be ligated into reconfigurable information units. Utilizing core, functional and control DynaBytes, we stored 210,776 bits (26,347 bytes) of digital information organized within a file-system, and demonstrated CRUD (Create-Read-Update-Delete)-like operations, hierarchical access and nanopore-based realtime retrieval. Robust data recovery was achieved under [~]100x error-prone sequencing using streamlined error correction and fuzzy decoding. By relying on in vitro ligation of standardized components, DynaBytes reduces cost, scales efficiently, and allows interactive, rewritable storage. These features advance DNA storage beyond passive archiving toward a reconfigurable framework, opening new possibilities for dynamic, practical and large-scale DNA-based data systems.

synthetic biology↗