Biology subjects

Zeng, X.

Publications and source records attributed to Zeng, X..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Designing AAV Capsid Protein with viability-guided Diffusion Model

Adeno-associated virus (AAV) capsids have shown great promise as delivery vectors for gene therapy. However, the natural properties of AAV capsids impose significant limitations on their efficacy. While capsid library screening and directed evolution have facilitated the development of improved vectors, current methods for generating AAV libraries frequently yield nonviable variants that fail to assemble or package DNA. Here, we propose a viability-guided diffusion model AAVDiffusion for de novo viable AAV capsid design. AAVDiffusion iteratively denoises Gaussian vectors into vectors of AAV capsid protein sequences, yielding intermediate latent variables. By leveraging the continuous nature of these latent variables, AAVDiffusion integrates an additional viability classifier that applies gradient updates to enhance the generation of viable AAV sequences. Through extensive computational tests, AAVDiffusion exhibits superior performance in generating viable AAV sequences. Furthermore, 196 AAV candidates were identified through a selection workflow, with the potential to cross the blood-brain barrier, thereby offering safer and more effective gene therapies for brain diseases. AAVDiffusion offers a powerful and efficient computational method for designing viable AAV capsids, advancing the development of AAV vectors for gene therapy.

bioinformatics↗

bioRxiv2026

Interorganelle competition for linoleic acid underlies steatotic liver pathology

Lipid droplets (LDs) are traditionally viewed as protective organelles that sequester potentially cytotoxic lipids. However, whether and how LD biogenesis in pathological contexts actively rewires interorganelle lipid homeostasis to drive organelle dysfunction and disease progression remains unexplored. Here, we identify the adipocyte-enriched protein calsyntenin 3{beta} (CLSTN3B) as a critical promoter of metabolic dysfunction-associated steatotic liver disease (MASLD). CLSTN3B, an ER-LD contact protein previously shown to support LD maturation in adipocytes, is robustly induced in mouse hepatocytes by peroxisome proliferator-activated receptor {gamma} (PPAR{gamma}) in response to dietary caloric overload. CLSTN3B drives LD biogenesis and neutral lipid storage by stabilizing hemifusion-like ER-LD membrane bridges via its arginine-rich segment. These bridges preferentially recruit cone-shaped linoleoylated phosphatidic acid (PA), diverting linoleic acid (LA) into triacylglycerides (TAGs) rather than mitochondrial cardiolipin (CL), leading to disrupted cristae architecture, deficient ETC supercomplex assembly, elevated electron leak, and oxidative stress. Hepatocyte-specific CLSTN3B deletion impairs LD formation, reduces TAG accumulation, enhances fatty acid oxidation, restores CL maturation, and mitigates oxidative stress, collectively attenuating MASLD progression. Consistently, hepatic CLSTN3B expression correlates with fibrosis severity and progression in human MASLD. These findings position LDs as active regulators of interorganelle lipid partitioning and establish CLSTN3B as a key determinant of mitochondrial vulnerability, providing a general framework for how dysregulated organelle interfaces shape disease.

cell biology↗

bioRxiv2025

Mitochondrial membrane junction-mediated ATP channeling drives activity-dependent glucose metabolism

Neurons and brown adipocytes rely on rapid ATP production from accelerated glucose metabolism to sustain bursts of activity upon stimulation, a process known as activity-dependent glucose metabolism. The first committed step in this pathway, the hexokinase I (HK1)-catalyzed phosphorylation of glucose, consumes ATP, raising the question of how this reaction can be accelerated when cytosolic ATP becomes limiting during stimulation. We identify Cell Cycle Exit and Neuronal Differentiation protein 1 (CEND1), expressed in both cell types, as a critical regulator of this process. Loss of CEND1 impairs activity-dependent glucose utilization, ATP generation, and stimulation-evoked activity both in vitro and in vivo. Mechanistically, CEND1 assembles a complex with HK1, voltage-dependent anion channel 1 (VDAC1), and adenine nucleotide translocase 1 (ANT1) at hemifusion-like membrane junction between the outer/inner mitochondrial membrane, channeling mitochondrially derived ATP directly to HK1. These findings uncover a previously unrecognized mechanism that sustains activity-dependent glucose metabolism, with broad implications for energy homeostasis in specialized cell types.

physiology↗

bioRxiv2025

End-to-end high-throughput single-cell proteomics via SPRINT and dual-spray LC-MS

Single-cell proteomics (SCP) enables direct measurement of protein heterogeneity but remains constrained by throughput and limited applicability to primary tissues. Here, we present an integrated workflow developed to address both challenges. We engineered SPRINT, an AI-powered bioprinting platform that prepares more than 10,000 single cells per day, over tenfold faster than existing systems, while maintaining stability and enabling identification of over 6,000 proteins from individual HeLa cells. To expand analytical capacity, we further designed a dual-spray tandem direct injection (TDI) LC system that parallelizes non-analytical steps with peptide separation, doubling MS utilization efficiency and enabling 168 label-free SCP runs per day without sensitivity loss. Together with optimized tissue-dissociation protocols, this integrated workflow enabled creation of the first mouse tissue-derived SCP atlas, profiling >1,000 single cells across six organs. These advances establish SCP as a scalable platform ready for broad biological and biomedical applications.

systems biology↗

bioRxiv2025

An Electromechanical Relay-like Multi-enzymatic System Gates c-di-GMP-Dependent Cell Fate in a Cyanobacterium

Cyclic-di-GMP is a ubiquitous bacterial second messenger that regulates diverse cellular processes. Although many bacteria harbor multiple enzymes for metabolism, the mechanisms underlying coordinated regulation remain unclear. Using the cyanobacterium Anabaena PCC 7120, we generate mutant strains with varying numbers of c-di-GMP metabolic genes deleted, including cdg0 (all degradation genes deleted) and cdgmax (all synthesis genes deleted). We found that cyclic-di-GMP is essential for both cell viability and size regulation. Quantitative analysis identified two critical physiological thresholds: one for maintaining normal cell size and a lower, lethal threshold required for survival. The 16 cyclic-di-GMP metabolic enzymes function as an electromechanical-like dual relay system, where different enzyme groups maintain cyclic-di-GMP homeostasis or activate SOS-like alarm responses when cyclic-di-GMP concentrations drop below the lethal threshold. These regulatory effects are mediated by the cyclic-di-GMP receptor CdgR, depending on the fraction of apo-CdgR form. This dual-threshold system enables dynamic cellular adaptation while preventing lethal consequences, representing a fundamental growth-survival trade-off strategy in living organisms.

microbiology↗

bioRxiv2025

A human iPSC-derived motor neuron-myogenic cell coculture platform to evaluate neuromuscular junction innervation after axon injury and in Spinal Muscular Atrophy

Traumatic nerve injury is challenging as motor neurons with damaged axons repair slowly, which can lead to muscle degeneration, while in Spinal Muscular Atrophy (SMA), muscle innervation is reduced. While pro-regenerative or neuroprotective compounds have been identified, their specific ability to enhance or restore neuromuscular junction (NMJ) function in patients remains unclear due to a lack of in vitro human models that track axon growth, NMJ innervation and muscle function. We developed a human iPSC-derived motor neuron-myogenic coculture platform that enables real-time monitoring of axon growth NMJ innervation and axon regeneration and muscle activity following axonal injury, and for SMA-derived motor neurons. We identified spontaneous synchronized GCaMP6f muscle activity as a useful functional marker of NMJ formation. Using this platform, we show that blebbistatin, a pro-regenerative non-muscle myosin II (NMII) inhibitor differentially regulates growth cone dynamics in injured versus uninjured motor neurons, resulting in enhanced NMJ reinnervation. This highlights the therapeutic potential of developing pro-regenerative compounds to promote NMJ innervation. We also confirm that NMJ function is reduced in SMA type 0 (prenatal onset) and type I (pediatric onset) patient-derived motor neurons in the coculture. This human stem cell-based framework can be used, therefore, to evaluate pro-regenerative compounds for axon injury and neuroprotective one for neurodevelopmental and neurodegenerative disorders.

neuroscience↗

bioRxiv2025

Asymmetry in hydrophobicity induces electric potential in non-charged protein condensates

The capacity of biomolecular condensates to establish and modulate electrochemical equilibria is emerging as an important functioning mechanism in cellular biochemistry. However, the physical chemistry basis of the electric potentials arising from biomacromolecular phase transitions remains unclear. Here, we show that asymmetry in hydrophobicity, which is a generalizable feature in condensate system, can directly encode an electric potential gradient between the dilute and the dense phases. We demonstrate that using a non-charged intrinsically disordered protein, ion-dependent kosmotropic effect can encode measurable pH and interphase potential gradients into condensate. All-atom molecular dynamics simulations further reveal that the distinct intrinsic transfer free energy of ions defines the ion partitioning capability of condensates via favorable interactions with protein backbones. The simulation also shows the existence of both interfacial and interphase electric potentials. These built-in potentials modulate the partitioning and reactivity of charged solutes, enabling non-enzymatic, potential-dependent chemistry within condensates. Our findings identify hydrophobic asymmetry as a simple and generalizable mechanism for charging biological matter, linking water activity and ion energetics to the emergent electrochemistry of condensates.

biophysics↗

bioRxiv2025

Multi-platform framework for mapping somatic retrotransposition in human tissues

Mobile element insertions (MEI) shape the human genome in both germline and somatic tissues. While inherited MEIs are well characterized, mapping somatic MEIs (sMEI) in non-cancer tissues remains challenging due to their low allelic fraction and repetitive nature. We established an integrative framework for sMEI analysis leveraging modern sequencing technologies and analytical innovations. We first benchmarked sMEI detection and demonstrated advantages of long-read and MEI-targeted sequencing for ultra-low-frequency events using a mixture of well-established cell lines. We then showed that haplotype phasing and donor-specific assemblies refine sMEI detection, effectively distinguishing from germline and false signals in in-silico tumor-normal mixtures. We further developed a source-tracing strategy based on internal sequence variation, expanding the catalogue of active source elements beyond traditional transduction-based methods. Applying this framework to donor tissues, we identified 18 rare somatic L1 insertions, revealing structural and source diversity. Our work provides a foundational framework and biological insight into sMEIs.

genomics↗

bioRxiv2025

Machine learning behavioral analysis reveals cervical instability as an early biomarker of Amyotrophic Lateral Sclerosis

Early detection of neuromuscular disorders is a major clinical challenge, with most diagnoses only occurring after considerable motor neuron degeneration has already taken place. The central problem for early diagnosis of neuromuscular diseases is the subtlety of early symptoms and where to look for them. Without defined behavioral markers, the earliest stages of disease go undetected, delaying intervention and limiting neuroprotective therapeutic evaluation. Here, we present a machine learning (ML) based framework that identifies subtle postural alterations in freely behaving animals. Using longitudinal pose data from SOD1G93A mice, a widely used Amyotrophic Lateral Sclerosis (ALS) mouse model, we focused on postural states in idle periods, behavioral states usually overlooked in disease monitoring. Our analyses revealed consistent deviations in posture and a feature analysis pinpointed cervical instability during adolescence as a key distinguishing feature. We validated these findings through two independent behavioral assays engaging cervical musculature: rearing and wet-dog shakes, both of which showed significant impairments in male SOD1G93A mice as early as 3 weeks of age, many weeks earlier than conventional muscle function assays. This approach establishes an unbiased, non-invasive, scalable strategy for detecting early-stage neuromuscular dysfunction, and provides a foundation both for clinical behavioral biomarker development in ALS and related disorders and will enable evaluation of early neuroprotective interventions.

neuroscience↗

bioRxiv2025

Injured SSTR2+ nociceptor axons in neuromas drive chronic spontaneous neuropathic pain

Spontaneous pain is a common but poorly understood consequence of peripheral nerve injury1-3, including injuries that lead to the formation of neuromas4,5. We developed a chronic neuroma model for measuring spontaneous pain-related behaviours in mice, which revealed that limb flicks - emerging predominantly 2 months post-injury - reflect spontaneous paroxysmal pain. Ectopic activity of injured dorsal root ganglia (DRG) sensory neurons whose axonal endings terminate within the neuroma drives this spontaneous pain. In vivo imaging showed that a subset of small-diameter DRG sensory neurons are the source of spontaneous neural signals emanating from the neuroma, and these spontaneously active neurons are distinct from the intact larger diameter sensory neurons that mediate stimulus-evoked mechanical allodynia from spared nerves. Cell-type-specific gain- and loss-of-function studies identified a genetically- and functionally-defined subtype of small-diameter C-fibre nociceptors whose injured axons in neuromas drive spontaneous limb flicks/neuropathic pain. These findings establish the neurobiological basis of spontaneous pain enabling targeted pain management strategies and define a cellular and mechanistic separation between spontaneous and evoked neuropathic pain.

neuroscience↗

bioRxiv2025

Unifying spatial and episodic representations in the hippocampus through flexible memory use

A key question in neuroscience is why the hippocampus is essential for episodic memory in humans, while dominantly exhibiting spatial representations in a number of other species. Some accounts suggest that spatial representation is the primary hippocampal function. Here, we propose that the primary function is storing and retrieving episodic memories, and spatial representations emerge due to this memory function. To demonstrate this, we adopt a computational model that autonomously learns to store information in memory and retrieve it to solve a variety of tasks. In memory tasks, the model develops associations and categorical representations akin to concept cells. In navigation tasks, the model forms representations of the spatial structure, performs geometric computations, and even learns representations of unique events similar to recently discovered barcodes. Our model predicts that the hippocampus represents any task-relevant variable, if the animal learns the task, suggesting that space is not special for the hippocampus.

neuroscience↗

bioRxiv2025

PD-1 signaling is essential for the early accumulation of HBV-specific CD8+ T cells during HBV infection

Background & AimsProgrammed cell death Protein 1(PD-1) is one of the key inhibitory receptors that regulates CD8 T cell exhaustion during chronic viral infection. However, the role of PD-1 in modulating effector T cell differentiation and function during early phase of hepatitis B virus (HBV) infection remains poorly defined. MethodsUsing adoptive transfer of wild-type or PD-1 KO HBV-specific TCR transgenic (C93-TCRtg) CD8 T cells, flow cytometry, and transcriptome sequencing, we systematically profiled early PD-1 dynamics in splenic and intrahepatic T cells and evaluated how PD-1 deficiency shapes anti-HBV T cell responses in acute self-resolving (AR) and chronic (CH) HBV mouse models. ResultsAcute HBV infection induced sustained PD-1 upregulation on intrahepatic/splenic CD8 T cells, which predominantly exhibited an effector phenotype. PD-1 cells displayed enhanced proliferation, cytotoxicity, and effector cytokine production compared to PD-1- counterparts. Adoptive transfer of PD-1 KO C93-TCRtg CD8 T cells resulted in significantly impaired early expansion in both spleen and liver during acute infection, accompanied by reduced granzyme B expression while maintaining IFN-{gamma}, TNF-, or IL-2 production. Transcriptomic analysis revealed that PD-1 deficiency was associated with the upregulation of apoptosis gene signatures. In chronic HBV infection, PD-1 KO cells failed to expand long-term and exhibited exacerbated exhaustion evidenced by a loss of IFN-{gamma} production. ConclusionsPD-1 is essential for the early expansion and survival of HBV-specific CD8 T cells during acute infection and does not suppress their effector cytokine function. Its absence impairs proliferation and promotes exhaustion of HBV-specific CD8 T cell in chronic infections. Impact and implicationsOur study redefines PD-1s role in acute HBV infection. Rather than merely constraining effector function, PD-1 is essential for the early expansion and survival of HBV-specific CD8+ T cells, acting as a safeguard against activation-induced apoptosis. The context-dependent functions position PD-1 as a critical rheostat calibrating the magnitude and quality of the antiviral CD8+ T cell response, with significant implications for immunotherapeutic strategies targeting this pathway in hepatitis B.

immunology↗

bioRxiv2025

Higher-order Residue Interactions Encode Diversified Physical Properties of Biomolecular Condensates

Biomolecular condensates often formed by proteins containing extended intrinsic disordered regions (IDPs) can coordinate versatile cellular processes. The biological functions of condensates are attributed to a variety of physical properties, including viscoelasticity, interfacial tension and saturation concentration. Comprehensive understanding of biological functions of protein condensates and the corresponding sequence encoding requires unified interpretation of the diverse physical properties by a single model. Here we report the diversified physical properties of condensate and the interactions between constituent IDPs can be interpreted on the basis of higher-order residue interactions. These findings are based on s-scale atomistic molecular dynamics simulations of three homogeneous IDP condensates (FUS PLD, ARF6 PLD, LAF-1 RGG) combined with the reported simulation trajectories of two heterogeneous condensates. In all interacting IDPs, there are residue interactions between finite motifs (3[~]5 residues) that organize in a highly cooperative way: residues form multivalent interactions and their remaking is localized. The sequence features of higher-order interactions (HOIs) are identified: tyrosine, arginine, glutamine and aspartic acid are essential, and their consecutive sequence position is also important. The interaction between corresponding motifs is highly sustained and dominates the cohesive energy of IDP. IDP condensate can be modeled as a HOI-crosslinked network. This model can successfully reproduce all reported experimental results of condensate viscoelasticity, interfacial tension and saturation concentration, and expand our insights into the molecular grammar of IDP interactions. Significance StatementThe biological functions of biomolecular condensates involve various physical properties of condensate. A unified model that describes all these physical properties is essential for the understanding of condensate functions. Our research reveals the prevalence of higher-order residue interactions in all IDP condensates we considered, which leads to extremely sustained interaction between corresponding residue motifs. Accordingly, we propose a physically crosslinked network based on higher-order residue interactions as a simplified model for condensate. This model can quantitively reproduce all reported experimental results of condensate physical properties, including viscoelasticity, interfacial tension and saturation concentration.

biophysics↗

bioRxiv2025

A PBD-dimer containing antibody drug conjugate targeting CCRL2 for high-risk MDS/AML

Patients with myelodysplastic syndrome (MDS)/acute myeloid leukemia (AML) with high-risk features including TP53 mutations and deletions have poor outcomes due to lack of effective therapies. The atypical chemokine surface receptor C-C motif chemokine receptor-like 2 (CCRL2) is overexpressed in MDS and secondary AML (sAML) compared to healthy hematopoietic cells and we recently found that TP53-mutated MDS/AML and AML with erythroid features express the highest levels of this receptor across MDS/AML subtypes. To illustrate the therapeutic potential of CCRL2 as a therapeutic target, we developed an anti-CCRL2 antibody-drug conjugate (ADC) by conjugating an anti-CCRL2 antibody with the cytotoxic drug pyrrolobenzodiazepine (PBD), which causes DNA double-strand breaks leading to cancer cell death. The anti-CCRL2 ADC demonstrated strong CCRL2-selective cytotoxicity against cell lines derived from MDS/AML patients with TP53 mutations and erythroid features, surpassing the cytotoxic effects observed with gemtuzumab and PBD-conjugated anti-CD33 and anti-CD123 ADCs. It also induced apoptosis and suppressed the clonogenicity of primary MDS/AML bone marrow samples without affecting the survival, differentiation and clonogenicity of healthy hematopoietic stem and progenitor cells. This agent also suppressed the leukemic growth of TP53-mutated MDS/AML cell line xenografts, improving mice survival and decreasing the leukemic burden in patient-derived TP53-mutated MDS/AML xenografts. In conclusion, our study introduces CCRL2 as a potential new therapeutic target in high-risk MDS/AML. Statement of significancePyrrolobenzodiazepine(PBD)-conjugated anti-CCRL2 ADC shows anti-leukemic effect in MDS/AML models including TP53-mutated disease without affecting healthy hematopoietic cells supporting that it is a promising candidate for single-agent or combination therapies in high-risk MDS/AML.

cancer biology↗

bioRxiv2025

Metabolomics-Guided Machine Learning Reveals Diagnostic and Mechanistic Biomarkers in CHB with MASLD

BackgroundMetabolic dysfunction-associated steatotic liver disease (MASLD) often coexists with chronic hepatitis B (CHB), yet early diagnosis remains challenging, particularly in non-obese patients or those with subclinical features. This study aimed to identify metabolic signatures of CHB-related MASLD and construct a predictive model using untargeted metabolomics integrated with machine learning. MethodsSerum metabolomics was performed on 160 subjects (80 CHB + MASLD and 80 healthy controls). Differential metabolites were identified and analyzed using KEGG enrichment and 4 machine learning algorithms (Random Forest, XGBoost, SVM, and LASSO). Metabolite-clinical correlations and diagnostic model performance were evaluated. ResultsA total of 924 differential metabolites were identified, with significant enrichment in pathways related to the TCA cycle, sphingolipid metabolism, and amino acid turnover. Machine learning prioritized six robust and biologically relevant metabolites: L-aspartic acid, succinic acid, caproic acid, sebacic acid, monomenthyl succinate, and glycolaldehyde, which consistently distinguished CHB + MASLD patients from controls (AUC > 0.75). These metabolites reflect key disruptions in mitochondrial function, lipid oxidation, and redox homeostasis. Integrated models combining metabolomics with clinical indices achieved perfect classification (AUC = 1.000). ConclusionCHB-associated MASLD is driven by systemic metabolic remodeling centered on mitochondrial overload, oxidative stress, and impaired amino acid metabolism. The identified metabolites provide mechanistic insights and hold promise for non-invasive MASLD screening in CHB patients. This study underscores the potential of multi-algorithmic metabolomics in advancing early diagnosis and personalized management of complex liver comorbidities.

bioinformatics↗

bioRxiv2025

Mapping of genotype-by-environment interaction loci for Metabolic Syndrome-like traits using the multi-parent Drosophila Synthetic Population Resource determines that main genetic effects are distinct from environment dependent plastic loci

Metabolic Syndrome (MetS) risk, driven by genotype-environment interactions like diet, is rising globally. Due to its genetic and environmental complexity, the genetic architecture and interconnected traits underlying MetS is poorly understood. In Drosophila, genotype-by-diet interactions significantly influence MetS-like traits. This study used the Drosophila Synthetic Population Resource to dissect the genetic architecture of both genotypic and genotype-by-diet interaction effects underlying trait variation. The study hypotheses were: 1) Loci responsible for metabolic phenotypic variation should be shared across traits. 2) Genetic loci responsible for plasticity and epistatic interactions for metabolic traits should also be the loci responsible for the main effects. 3) Genes responsible for variation in metabolic traits should share common functions. Using a round-robin crossing scheme and novel analyses, we mapped additive, dominance, and epistatic loci--some diet-specific, others diet-independent. Main-effect and plastic loci were largely distinct, as were epistatic loci from main-effect loci, highlighting that main genetic effects alone will not explain how genetic variants interact with the environment or the genome to influence disease risk. gene-by-diet or gene-by-gene interactions influencing MetS risk. Further, tremendous cryptic genetic variation for metabolic traits is lurking in natural populations. We explored the function of candidate genes from our study empirically and with bioinformatics. While some of the candidate genes might have been expected, most would not have been identified a priori, thus with this study we have identified many new candidate mechanisms contributing to the genetic and genotype-by-diet interaction effects on MetS variance.

genetics↗

bioRxiv2025

NAD⁺ Replenishment Mitigates Cardiomyocyte Senescence and Corrects Heart Failure with Preserved Ejection Fraction in Aged Mice

Cardiomyocyte senescence, characterized by elevated cell cycle inhibitor expression, persistent DNA damage response, and mitochondrial dysfunction, contributes to myocardial stiffness and the progression of heart failure with preserved ejection fraction (HFpEF), the most common form of heart failure affecting individuals over 65. In this study, we investigated the role of NAD metabolism in cardiomyocyte senescence and cardiac function. Aged mice exhibited reduced cardiac NAD levels, impaired NAD biosynthesis and mobilization, and increased consumption, leading to suppressed SIRT1/6 activity and accumulation of senescent cardiomyocytes. This was accompanied by diastolic dysfunction consistent with HFpEF. In senescent AC16 cardiomyocytes, NAD depletion promoted senescence, which was reversed by the NAD precursors nicotinamide riboside (NR) and dihydronicotinamide riboside (NRH). In aged mice, two months of NR or NRH treatment improved diastolic function and reduced cardiomyocyte senescence. While NR primarily activated SIRT1 to suppress cell cycle arrest markers, NRH more robustly activated both SIRT1 and SIRT6, enhancing DNA damage repair. Acetylated H2AX, a SIRT6 substrate elevated in aged hearts and senescent cells, was selectively deacetylated by NRH. These findings identify NAD availability as a critical regulator of cardiac senescence and support NAD precursors, particularly NRH, as promising senescence-reducing therapies for treating aging-associated HFpEF.

pharmacology and toxicology↗

bioRxiv2025

Pentose Sugars Encode Sequence-Dependent DNA-RNA Segregation for Biomimetic Multiphase Condensates

The nucleus segregates DNA and RNA with high precision to safeguard genome stability and gene regulation despite their homologous structures, yet the underlying molecular principles have long evaded both understanding and synthetic translation. Here we show that a single atomic difference between the pentose sugars, a 2-OH in RNA versus a 2-H in DNA, suffices to drive their phase segregation with cationic peptides. This subtle chemical distinction makes RNA bind peptides more strongly than sequence-identical DNA, generating an asymmetry that, when modulated by sequence-encoded homotypic interactions, drives the formation of core-shell multiphase condensates. Using a supervised machine-learning approach, we distill these molecular principles into a predictive design rule and harness it to program a library of oligonucleotide pairs, termed SEGREGamers, that self-assemble into droplets with coexisting DNA- and RNA-rich domains. These synthetic condensates recapitulate nuclear compartment functions, including selective molecular partitioning and enhanced RNA catalysis. Our results establish a chemically encoded platform for engineering synthetic nuclear mimics and programmable biomolecular condensates, and suggest that sugar identity may have served as an ancient physical mechanism for organizing nucleic acids.

biophysics↗