Treffer: PyFuRNAce: an integrated design engine for RNA origami.

Title:
PyFuRNAce: an integrated design engine for RNA origami.
Authors:
Monari L; Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.; Max Planck Institute for Medical Research, Heidelberg, Germany., Braun I; Max Planck Institute for Medical Research, Heidelberg, Germany.; Max Planck School Matter to Life, Heidelberg, Germany.; Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany., Verstraeten W; Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany., Poppleton E; Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.; Max Planck Institute for Medical Research, Heidelberg, Germany.; Max Planck Institute for Polymer Research, Mainz, Germany., Göpfrich K; Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany. k.goepfrich@zmbh.uni-heidelberg.de.; Max Planck Institute for Medical Research, Heidelberg, Germany. k.goepfrich@zmbh.uni-heidelberg.de.
Source:
Nature communications [Nat Commun] 2025 Dec 01; Vol. 16 (1), pp. 10815. Date of Electronic Publication: 2025 Dec 01.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE
Imprint Name(s):
Original Publication: [London] : Nature Pub. Group
MeSH Terms:
RNA*/chemistry , RNA*/genetics , RNA*/ultrastructure , Nanotechnology*/methods , Nanostructures*/chemistry , Software*, Nucleic Acid Conformation ; Microscopy, Atomic Force
References:
J Chem Phys. 2015 Jun 21;142(23):234901. (PMID: 26093573)
Angew Chem Int Ed Engl. 2016 Jul 25;55(31):8869-72. (PMID: 27304204)
Science. 2017 Dec 15;358(6369):. (PMID: 29242318)
Nature. 2020 Sep;585(7825):357-362. (PMID: 32939066)
J Mol Graph Model. 2008 Oct;27(3):299-308. (PMID: 18838281)
Nature. 2006 Mar 16;440(7082):297-302. (PMID: 16541064)
Science. 2014 Aug 15;345(6198):799-804. (PMID: 25124436)
Nat Protoc. 2022 Aug;17(8):1762-1788. (PMID: 35668321)
Angew Chem Int Ed Engl. 2000 Jul 17;39(14):2521-2524. (PMID: 10941124)
Nucleic Acids Res. 2009 Aug;37(15):5001-6. (PMID: 19531737)
Nat Nanotechnol. 2024 Jul;19(7):1055-1065. (PMID: 38491184)
Nucleic Acids Res. 2021 Oct 11;49(18):10265-10274. (PMID: 34508356)
J Chem Phys. 2014 Jun 21;140(23):235102. (PMID: 24952569)
Nucleic Acids Res. 2001 Jan 15;29(2):455-63. (PMID: 11139616)
Adv Healthc Mater. 2021 Jun;10(11):e2001826. (PMID: 33882195)
Nat Nanotechnol. 2024 Nov;19(11):1665-1673. (PMID: 39080489)
Nucleic Acids Res. 2012 Aug;40(14):e112. (PMID: 22539264)
Biotechnol J. 2019 Jan;14(1):e1700634. (PMID: 29802763)
J Chem Phys. 2011 Feb 28;134(8):085101. (PMID: 21361556)
Nat Commun. 2023 Jan 24;14(1):382. (PMID: 36693871)
Bioinformatics. 2009 Jun 1;25(11):1422-3. (PMID: 19304878)
Nat Nanotechnol. 2023 Jul;18(7):808-817. (PMID: 36849548)
Bioinformatics. 2010 Aug 15;26(16):2057-9. (PMID: 20562414)
Algorithms Mol Biol. 2011 Nov 24;6:26. (PMID: 22115189)
J Comput Chem. 2015 Jan 5;36(1):1-8. (PMID: 25355527)
RNA Biol. 2023 Jan;20(1):510-524. (PMID: 37498217)
Nature. 1990 Mar 29;344(6265):467-8. (PMID: 1690861)
Nat Commun. 2025 Dec 1;16(1):10815. (PMID: 41326357)
Adv Mater. 2019 May;31(21):e1808262. (PMID: 30972819)
ACS Nano. 2020 Apr 28;14(4):4727-4740. (PMID: 32275389)
Sci Adv. 2021 Sep 24;7(39):eabf4459. (PMID: 34550747)
Nature. 2015 Jul 23;523(7561):441-4. (PMID: 26201596)
ACS Nano. 2008 Jun;2(6):1213-8. (PMID: 19206339)
Mol Ther. 2024 Jul 3;32(7):2286-2298. (PMID: 38720458)
Nat Nanotechnol. 2025 May;20(5):664-671. (PMID: 40097648)
Nat Comput Sci. 2024 Nov;4(11):829-839. (PMID: 39506080)
Nucleic Acids Res. 2024 Jul 5;52(W1):W13-W18. (PMID: 38747339)
Nucleic Acids Res. 2022 Jan 7;50(D1):D246-D252. (PMID: 34747480)
Nat Methods. 2020 Mar;17(3):261-272. (PMID: 32015543)
Nucleic Acids Res. 2020 Jul 9;48(12):e72. (PMID: 32449920)
Science. 1990 Aug 3;249(4968):505-10. (PMID: 2200121)
ACS Nano. 2022 Oct 25;16(10):16608-16616. (PMID: 36178116)
Int J Mol Sci. 2021 Mar 30;22(7):. (PMID: 33808496)
Science. 2016 Jun 24;352(6293):1534. (PMID: 27229143)
ACS Nano. 2019 May 28;13(5):5214-5221. (PMID: 31007017)
Nature. 1990 Aug 30;346(6287):818-22. (PMID: 1697402)
Nat Nanotechnol. 2011 Sep 11;6(10):658-67. (PMID: 21909084)
Nano Lett. 2004 Sep;4(9):1717-23. (PMID: 21171616)
Nat Mater. 2021 Sep;20(9):1264-1271. (PMID: 33875848)
Nature. 2025 Mar;639(8056):1106-1108. (PMID: 40128371)
Science. 2004 Dec 17;306(5704):2068-72. (PMID: 15604402)
Nat Chem. 2021 Jun;13(6):549-558. (PMID: 33972754)
Nat Nanotechnol. 2010 Sep;5(9):676-82. (PMID: 20802494)
Proteins. 2023 Dec;91(12):1790-1799. (PMID: 37615316)
J Am Chem Soc. 2023 Aug 9;145(31):17112-17124. (PMID: 37498993)
Nat Commun. 2024 Jul 30;15(1):6244. (PMID: 39080253)
J Theor Biol. 1982 Nov 21;99(2):237-47. (PMID: 6188926)
Methods. 2011 Jun;54(2):239-50. (PMID: 21163354)
Bioinformatics. 2015 Oct 15;31(20):3377-9. (PMID: 26099263)
Grant Information:
101076997 EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council); RGP003/2023 Human Frontier Science Program (HFSP); CRC 392 Deutsche Forschungsgemeinschaft (German Research Foundation); CRC 1638 Deutsche Forschungsgemeinschaft (German Research Foundation)
Substance Nomenclature:
63231-63-0 (RNA)
Entry Date(s):
Date Created: 20251201 Date Completed: 20251201 Latest Revision: 20251204
Update Code:
20251204
PubMed Central ID:
PMC12669765
DOI:
10.1038/s41467-025-66290-x
PMID:
41326357
Database:
MEDLINE

Weitere Informationen

Recent developments in medicine and biotechnology have revealed the transformative power of RNA design. To realize the full potential of RNA nanotechnology and RNA origami, user-friendly design tools are needed. Here, we present pyFuRNAce, an open-source, Python-based software package with a graphical user interface that enables the design of complex RNA nanostructures, with particular focus on co-transcriptional RNA origami. PyFuRNAce integrates the entire RNA origami workflow-from motif definition and blueprint design to sequence generation and primer selection-into a single, user-friendly platform. Built around a motif-based assembly paradigm, the software enables users to create and modify custom RNA nanostructures through an intuitive web interface with streamlined design steps and real-time 3D visualization. We use pyFuRNAce to design three distinct RNA nanostructures, including self-assembling RNA filaments, RNA droplets, and the largest co-transcriptional RNA origami to date, consisting of 2501 nucleotides. The structures and their high-yield assembly are validated experimentally with atomic force microscopy and confocal fluorescence imaging. By consolidating multiple design stages into a unified environment, pyFuRNAce broadens the scope and reduces the barrier of entry for RNA nanotechnology, accelerating the development of functional RNA origami structures for applications in medicine, biotechnology, and synthetic biology.
(© 2025. The Author(s).)

Competing interests: The authors declare no competing interests.