Designer RNA nanostructures co-transcribed and self-assembled inside human cell nuclei

The use of nucleic acid-based nanostructures as synthetic biological tools to interface with and regulate cell processes remains challenging. A major obstacle lies in nuclear delivery and retention within live eukaryotic cells. Here, we present a platform of single-stranded RNAs that can co-transcriptionally fold into defined nanostructures and assemble into rings, ribbons, and nanonet-like architectures. We validate the formation of these structures in vitro using atomic force microscopy. Then, we demonstrate the functional integration of fluorescent aptamers and RNA sensing capability within the single chain by co-folding with these structures. Notably, we show that the RNA nanonets can be co-transcriptionally produced and assembled directly inside the nucleus of live human cells. We use confocal live-cell imaging and transmission electron microscopy to reveal well-defined nanostructure patterns retained in the nucleus. Together, these results establish a genetically encoded, self-assembling RNA nanostructure system with programmable geometry and localization, providing a foundation for the development of RNA-based nanodevices to examine biological properties in live cells and tissues.