Yongxi Zhao

Synthetic control of intracellular phase separation offers exciting opportunities for engineering artificial membraneless organelles (MLOs). However, achieving precise control of DNA-based condensates in complex cellular environments remains challenging. Here, we present a phase-transforming DNA framework that enables the in situ transition of tetrahedral DNA nanostructures into functional condensates through valency-controlled subcellular sorting. With coarse-grained simulations and experiments, we demonstrate that the condensation order is governed by binding valencies of transformed building blocks. Strikingly, we revealed distinct intracellular fates of synDNA condensates, with high-order condensates escaping the endolysosomal pathway and low-order condensates trapped in the lysosome. Furthermore, we demonstrate that spatially controlled DNA condensates serve as versatile artificial MLOs, facilitating the targeted degradation of membrane proteins and prolonging the cytosolic residence of the therapeutic payloads. Our findings establish a modular design principle for constructing programmable DNA condensates in cellulo, underscoring the profound interactions between synthetic biological constructs and cellular organelles.

Microorganisms often form multimodal communities through spatial organization and coordinate collective responses via quorum sensing, which is driven by threshold accumulation of autoinducers. While artificial communities are attractive for sensing and smart materials, current systems often lack interfacial gating mechanisms with threshold‐switchable properties, making it difficult to precisely encode density‐dependent, threshold‐triggered responses associated with quorum‐like sensing. Here, we employed naturally secreted extracellular vesicles as a model community system and developed an encapsulation strategy using programmable, threshold‐gated DNA nanocages. This surface‐encapsulation strategy preserves individual integrity during community assembly by preventing membrane fusion. It also enables the programmed construction of dual‐component multimodal communities, including homogeneous clusters, core‐shell structures, and heterogeneous clusters, using sequence‐programmable DNA nanocages. By introducing pH gating and using H ⁺ generated by a GOX‐CAT positive‐feedback circuit as the autoinducer, we achieved density‐dependent signal accumulation and threshold‐triggered reversible structural switching, thereby exhibiting key operational features of quorum‐like sensing in vesicle‐based communities. This platform provides a general model for studying community organization and cooperative behaviors, with potential applications in biomimetic sensing, programmable smart materials, and stimulus‐responsive delivery systems.

A novel lucigenin@PS-COOH nanoplatform is developed for cTnT detection, featuring exceptional stability and biocompatibility. This robust immunosensing system offers a high-performance pathway for the early diagnosis of cardiac events.

DNA damage refers to chemical alterations in genomic DNA arising from endogenous or exogenous factors, and delineating the types and levels of these lesions is essential for elucidating the molecular mechanisms and regulatory networks underlying DNA repair. However, current methods are limited to one specific type of damage and often rely on DNA extraction and in vitro processing, which fails to capture the spatial distribution of diverse DNA damages within cellular context. Here we present intracellular strand break end extension-encoded amplification (ISBEA), an in situ imaging strategy that enables simultaneous visualization of multiple DNA lesion types. ISBEA uses a sequential enzymatic workflow in which glycosylases, endonucleases and exonucleases selectively recognize oxidized purines, AP sites and strand breaks, converting them stepwise into uniform 3'-hydroxyl termini. These activated termini undergo programmable extension and serve as primers to initiate DNA-encoded amplification, ultimately generating fluorescence signals present to each damage type. With spatially resolved visualization of diverse DNA damages within cells, ISBEA provides a robust platform for investigating the origins, repair pathways and biological consequences of DNA damage, offering valuable methodological support for advancing the understanding of genome stability maintenance and the development of related diseases.

Recording biophysical processes is crucial to understanding the cellular history and stimuli-responsive behaviors. The construction of memory machines for continuous membrane fluidity, however, remain challenging. Here, we report a biophysical-to-DNA catalytic cumulative birecorder (BioDIMER) for making individual recordings of continuous membrane fluidity events into both fluorescent signals and DNA unique molecular identifiers (UMIs) sequencing. We do this through engineered DNAzyme probe sets that accumulate bimodal signals responsive to each transient encounter on cell membrane. This in situ imaging captures spatiotemporal information, and the UMIs sequencing counts the number of transient encounters over time by digital quantification. The DNA catalytic bimodal signals enable continuous records of new events without corrupting the records of older events and achieve multidimensional interpretation of membrane fluidity timing. Using this proof-of-concept method, we recorded and deciphered differential cell membrane dynamics across diverse cell types and states, including cell cycle phases, cardiac hypertrophy, myotube differentiation, and cellular senescence. We found the first decreased and then increased change of membrane fluidity during the cell circle phases. In cardiac hypertrophy, we visualized an enhanced membrane fluidity. Oppositely, cellular senescence caused a significant reduction in membrane fluidity. They implied a highly dynamic organization of cell membrane components.

Diffusion-reaction coupling at solid-liquid interfaces has long constrained the performance of interfacial molecular assays, particularly surface-based DNA assays. Herein, we report an ice-confinement strategy that reprograms the mass transport at the solid-liquid interface. Through in situ electrochemistry and finite-element modeling, we reveal that directional freezing concentrates DNA oligonucleotides within a thin interfacial liquid layer, effectively shifting the reaction from diffusion-controlled to surface-confined regime. Moreover, with rationally designed probes, we demonstrate that ice confinement lowers interfacial energy barriers and can kinetically trap overequilibrium binding states, improving access to sterically hindered sites and structured targets. Furthermore, integrating PEGylated passivation expands the effective electrical double layer and, together with freezing, affords ultrasensitive miRNA detection to 100 aM within 30 min while suppressing amplification leakage and preserving labile RNA. Importantly, our strategy applies to different substrates (gold and glass) and multimodal signal outputs (fluorescence, Raman spectroscopy, and electrochemistry). Overall, our work establishes a kinetic modulation strategy via phase-transition-enabled physical confinement, with significant implications for biosensing, surface engineering, and molecular diagnostics.

Recent years have witnessed profound advances in spatial transcriptomics (ST). However, current ST strategies are limited to tissue sections, unable to directly profile spatiotemporal transcriptome landscapes of individual living animals. To overcome this limitation, we present acupuncture-extracted in vivo spatiotemporal transcriptomics (aivST). It is mainly based on engineering clinical-grade acupuncture gold microneedles as a spatial-barcoding array patch with high-performance DNA recognition interfaces. These interfaces first utilize nanoparticles surface deposition to increase the density of DNA probes. A freeze-thawing method is further developed to regulate interfaced DNA probes with laterally uniform distribution and vertically upright conformation, mainly by loose stretching and local concentration of these DNA probes. It increased mRNA capture with 250% and speeded up reaction (from 60 min to 15 min), compared to that without freeze-thawing surface engineering. Using this method, we explored in vivo spatiotemporal transcriptome dynamics during skin wound healing of individual mice. We found four distinct expression changes of transcripts, including continuous upregulation, continuous downregulation, initial upregulation then downregulation, and initial downregulation then upregulation. Our aivST method advances the field from sparse tissue section sampling toward in vivo measurements of biological stereotypy and variability in individual living animals.

Mechanical perturbations profoundly influence nucleobase interactions in cells, serving as key modulators of fundamental cellular processes such as transcriptional regulation. However, their precise roles remain elusive due to methodological limitations. Here, we have developed a DNA origami‐based nanobender system that probes base–base interactions under mechanical constraints. This system imposes tunable geometric and mechanical constraints on single‐stranded DNA/RNA by pulling its two ends together while adjusting its contour length, and enables the assessment of weak interactions between bases through the detection of DNA origami dimerization. Combining experiments and molecular dynamics simulations, we speculate that mechanical constraints promote stacking‐driven noncanonical base‐pairing via entropy compensation and favorable nucleobase orientation (hydrophobic exposure), advancing our understanding of base recognition diversity. Customizable nanobender parameters allow investigation of the effects of geometric and mechanical constraints on hybridization thermodynamics across DNA‐DNA, RNA‐RNA, DNA‐RNA, and epigenetically modified nucleotides. Notably, we suggest that entropy modulation mediated by mechanical constraints enables fine‐tuning of binding free energy, thereby expanding material assembly applications while conferring environmental sensitivity.