References
-
Henninger, J. E. & Young, R. A. An RNA-centric view of transcription and genome organization. Mol. Cell 84, 3627–3643 (2024).
-
Guo, C. J., Xu, G. & Chen, L. L. Mechanisms of long noncoding RNA nuclear retention. Trends Biochem Sci. 45, 947–960 (2020).
-
Khan, M., Hou, S., Chen, M. & Lei, H. Mechanisms of RNA export and nuclear retention. Wiley Interdiscip. Rev. RNA 14, e1755 (2023).
-
Geary, C., Rothemund, P. W. K. & Andersen, E. S. A single-stranded architecture for cotranscriptional folding of RNA nanostructures. Science 345, 799–804 (2014).
-
Geary, C., Grossi, G., McRae, E. K. S., Rothemund, P. W. K. & Andersen, E. S. RNA origami design tools enable cotranscriptional folding of kilobase-sized nanoscaffolds. Nat. Chem. 13, 549–558 (2021).
-
Tran, M. P. et al. Genetic encoding and expression of RNA origami cytoskeletons in synthetic cells. Nat. Nanotech. 20, 664–671 (2025).
-
Liu, D. et al. Branched kissing loops for the construction of diverse RNA homooligomeric nanostructures. Nat. Chem. 12, 249–259 (2020).
-
Li, M. et al. In vivo production of RNA nanostructures via programmed folding of single-stranded RNAs. Nat. Commun. 9, 2196 (2018).
-
Jepsen, M. D. E. et al. Development of a genetically encodable FRET system using fluorescent RNA aptamers. Nat. Commun. 9, 18 (2018).
-
Nguyen, M. T. A., Pothoulakis, G. & Andersen, E. S. Synthetic translational regulation by protein-binding RNA origami scaffolds. ACS Synth. Biol. 11, 1710–1718 (2022).
-
Pothoulakis, G., Nguyen, M. T. A. & Andersen, E. bbeS. Utilizing RNA origami scaffolds in Saccharomyces cerevisiae for dCas9-mediated transcriptional control. Nucleic Acids Res. 50, 7176–7187 (2022).
-
Zhang, T. et al. Programmable in vitro and in vivo folding of single-stranded nucleic-acid wireframe origami. Chem 10, 2550–2563 (2024).
-
Fu, T. J. & Seeman, N. C. DNA double-crossover molecules. Biochemistry 32, 3211–3220 (1993).
-
Shen, Z. Y., Yan, H., Wang, T. & Seeman, N. C. Paranemic crossover DNA: a generalized Holliday structure with applications in nanotechnology. J. Am. Chem. Soc. 126, 1666–1674 (2004).
-
Afonin, K. A., Cieply, D. J. & Leontis, N. B. Specific RNA self-assembly with minimal paranemic motifs. J. Am. Chem. Soc. 130, 93–102 (2007).
-
Han, D. et al. Single-stranded DNA and RNA origami. Science 358, eaao2648 (2017).
-
Qi, X. et al. Programming molecular topologies from single-stranded nucleic acids. Nat. Commun. 9, 4579 (2018).
-
Sampedro Vallina, N., McRae, E. K. S., Geary, C. & Andersen, E. S. An RNA paranemic crossover triangle as A 3D module for cotranscriptional nanoassembly. Small 19, e2204651 (2022).
-
Dietz, H., Douglas, S. M. & Shih, W. M. Folding DNA into twisted and curved nanoscale shapes. Science 325, 725–730 (2009).
-
Han, D. R. et al. DNA origami with complex curvatures in three-dimensional space. Science 332, 342–346 (2011).
-
Horiya, S. et al. RNA LEGO: magnesium-dependent formation of specific RNA assemblies through kissing interactions. Chem. Biol. 10, 645–654 (2003).
-
Qi, X. D. et al. RNA origami nanostructures for potent and safe anticancer immunotherapy. Acs Nano 14, 4727–4740 (2020).
-
Filonov, G. S., Moon, J. D., Svensen, N. & Jaffrey, S. R. Broccoli: rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution. J. Am. Chem. Soc. 136, 16299–16308 (2014).
-
Ouellet, J. RNA fluorescence with light-up aptamers. Front. Chem. 4, 29 (2016).
-
Byron, S. A., Van Keuren-Jensen, K. R., Engelthaler, D. M., Carpten, J. D. & Craig, D. W. Translating RNA sequencing into clinical diagnostics: opportunities and challenges. Nat. Rev. Genet. 17, 257–271 (2016).
-
Zhu, Y., Zhu, L., Wang, X. & Jin, H. RNA-based therapeutics: an overview and prospectus. Cell Death Dis. 13, 644 (2022).
-
Isermann, T., Sers, C., Der, C. J. & Papke, B. KRAS inhibitors: resistance drivers and combinatorial strategies. Trends Cancer 11, 91–116 (2025).
-
Stickler, S., Rath, B. & Hamilton, G. Targeting KRAS in pancreatic cancer. Oncol. Res. 32, 799–805 (2024).
-
Yang, Q. et al. Angle-controllable RNA tiles for programable array assembly and RNA sensing. Nat. Commun. 16, 3728 (2025).
-
Rogers, T. A., Andrews, G. E., Jaeger, L. & Grabow, W. W. Fluorescent monitoring of RNA assembly and processing using the split-spinach aptamer. ACS Synth. Biol. 4, 162–166 (2014).
-
Alam, K. K., Tawiah, K. D., Lichte, M. F., Porciani, D. & Burke, D. H. A fluorescent split aptamer for visualizing RNA–RNA assembly in vivo. ACS Synth. Biol. 6, 1710–1721 (2017).
-
Schonborn, J. et al. Monoclonal antibodies to double-stranded RNA as probes of RNA structure in crude nucleic acid extracts. Nucleic Acids Res. 19, 2993–3000 (1991).
-
Weber, F., Wagner, V., Rasmussen, S. B., Hartmann, R. & Paludan, S. R. Double-stranded RNA is produced by positive-strand RNA viruses and DNA viruses but not in detectable amounts by negative-strand RNA viruses. J. Virol. 80, 5059–5064 (2006).
-
Li, X., Kim, H., Litke, J. L., Wu, J. & Jaffrey, S. R. Fluorophore-promoted RNA folding and photostability enables imaging of single broccoli-tagged mRNAs in live mammalian cells. Angew. Chem. Int. Ed. Engl. 59, 4511–4518 (2020).
-
Katahira, J. Nuclear export of messenger RNA. Genes 6, 163–184 (2015).
-
Song, Z., Lin, J., Li, Z. & Huang, C. The nuclear functions of long noncoding RNAs come into focus. Noncod. RNA Res. 6, 70–79 (2021).
-
Herman, A. B., Tsitsipatis, D. & Gorospe, M. Integrated lncRNA function upon genomic and epigenomic regulation. Mol. Cell 82, 2252–2266 (2022).
-
Shokrollahi, M. & Mekhail, K. Interphase microtubules in nuclear organization and genome maintenance. Trends Cell Biol. 31, 721–731 (2021).
-
van Steensel, B. & Belmont, A. S. Lamina-associated domains: links with chromosome architecture, heterochromatin, and gene repression. Cell 169, 780–791 (2017).
-
Williams, S. et al. in DNA Computing. (eds. A. Goel, F. C. Simmel & P. Sosík) 90-101 (Springer Berlin Heidelberg, 2009).
-
Ennifar, E., Walter, P., Ehresmann, B., Ehresmann, C. & Dumas, P. Crystal structures of coaxially stacked kissing complexes of the HIV-1 RNA dimerization initiation site. Nat. Struct. Biol. 8, 1064–1068 (2001).
-
Lee, A. J. & Crothers, D. M. The solution structure of an RNA loop–loop complex: the ColE1 inverted loop sequence. Structure 6, 993–1007 (1998).
-
Goddard, T. D. et al. UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25 (2018).
-
Zadeh, J. N. et al. NUPACK: analysis and design of nucleic acid systems. J. Comput. Chem. 32, 170–173 (2011).
-
Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406–3415 (2003).
