Constructing synthetic nuclear architectures via transcriptional condensates in a DNA protonucleus

Constructing synthetic nuclear architectures via transcriptional condensates in a DNA protonucleus | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Constructing synthetic nuclear architectures via transcriptional condensates in a DNA protonucleus Andreas Walther, Miao Xie, Weixiang Chen, Maria Roy This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5959823/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 10 Sep, 2025 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Abstract Nuclear biomolecular condensates are essential sub-compartments within the cell nucleus and play key roles in transcription and RNA processing. Bottom-up construction of nuclear architectures in synthetic settings is non-trivial but vital for understanding the mechanisms of condensates in real cellular systems. Here, we present a facile and versatile synthetic DNA protonucleus (PN) platform that facilitates localized transcription of branched RNA motifs with kissing loops (KLs) for subsequent condensation into complex condensate architectures. We identify salinity, monomer feeding, and KL-PN interactions as key parameters to control co-transcriptional condensation of these KLs into diverse artificial nuclear patterns, including single and multiple condensates, interface condensates, and biphasic condensates. Over time, KL transcripts co-condense with the PN matrix, with the final architecture determined by their interactions, which can be precisely modulated using a short DNA invader strand that outcompetes these interactions. Our findings deepen the understanding of RNA condensation in nuclear environments and provide new strategies for designing functional nucleus-mimetic systems with precise architectural control. Physical sciences/Chemistry/Supramolecular chemistry/Self-assembly Physical sciences/Nanoscience and technology/DNA nanotechnology/DNA nanostructures Physical sciences/Nanoscience and technology/DNA nanotechnology/Organizing materials with DNA Physical sciences/Materials science/Soft materials Full Text Additional Declarations There is NO Competing Interest. Supplementary Files SupplementaryInformation.pdf Supplementary Information MovieS1.mp4 LOCAL TRANSCRIPTION IN DNA PROTONUCLEUS MovieS2.mp4 CO-CONDENSATE OF TRANSCRAPTIONAL KL AND DNA MATRIX IN PN MovieS3.mp4 INVASION OF ‘o*-Atto647’ DISSASSEMBLES CO-CONDENSATES IN PN Cite Share Download PDF Status: Published Journal Publication published 10 Sep, 2025 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. 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