SFB1551 Group leader, Andreas Walther and Postdoctoral reseracher Weixiang Chen & collaborators have developed a synthetic DNA protonucleus (PN) platform that enables localized transcription of RNA kissing loops, which subsequently condense into diverse and controllable nuclear-like architectures. Their work, just published in Nature Communications, deepens the understanding of RNA condensation and phase separation in nuclear environments while providing new strategies for designing functional nucleus-mimetic systems in synthetic biology.

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 strategies for designing functional nucleus-mimetic systems with precise architectural control.