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Assembly of RNA Nanostructures from Double-Crossover Tiles

Part of the Methods in Molecular Biology book series (MIMB,volume 2433)

Abstract

Artificial self-assembling RNA scaffolds can be produced from many types of RNA motifs that are rationally designed. These scaffolds are of interest as nanoscale organizers, with applications in drug delivery and synthetic cells. Here we describe design strategies, production methods, and imaging of micrometer-sized RNA nanotubes and lattices that assemble from RNA tiles comprising multiple distinct strands.

Key words

  • RNA
  • RNA assembly
  • RNA nanotubes
  • RNA lattices

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  • DOI: 10.1007/978-1-0716-1998-8_18
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References

  1. Jaeger L (2001) TectoRNA: modular assembly units for the construction of RNA nano-objects. Nucleic Acids Res 29:455–463

    CrossRef  CAS  PubMed  PubMed Central  Google Scholar 

  2. Afonin KA, Viard M, Koyfman AY et al (2014) Multifunctional RNA nanoparticles. Nano Lett 14:5662–5671

    CrossRef  CAS  PubMed  PubMed Central  Google Scholar 

  3. Grabow WW, Jaeger L (2014) RNA self-assembly and RNA nanotechnology. Acc Chem Res 47:1871–1880

    CrossRef  CAS  PubMed  Google Scholar 

  4. Geary C, Rothemund PWK, Andersen ES (2014) A single-stranded architecture for cotranscriptional folding of RNA nanostructures. Science 345:799–804

    CrossRef  CAS  PubMed  Google Scholar 

  5. Han D, Qi X, Myhrvold C et al (2017) Single-stranded DNA and RNA origami. Science 358:1–10

    CrossRef  Google Scholar 

  6. Qi X, Zhang F, Su Z et al (2018) Programming molecular topologies from single-stranded nucleic acids. Nat Commun 9:4579

    CrossRef  PubMed  PubMed Central  Google Scholar 

  7. Stewart JM, Viard M, Subramanian HKK et al (2016) Programmable RNA microstructures for coordinated delivery of siRNAs. Nanoscale 8:17542–17550

    CrossRef  CAS  PubMed  PubMed Central  Google Scholar 

  8. Stewart JM, Subramanian HKK, Franco E (2017) Self-assembly of multi-stranded RNA motifs into lattices and tubular structures. Nucleic Acids Res 45:5449–5457

    CrossRef  CAS  PubMed  PubMed Central  Google Scholar 

  9. Stewart JM, Geary C, Franco E (2019) Design and characterization of RNA nanotubes. ACS Nano 13:5214–5221

    CrossRef  CAS  PubMed  Google Scholar 

  10. Delebecque CJ, Lindner AB, Silver PA, Aldaye FA (2011) Organization of intracellular reactions with rationally designed RNA assemblies. Science 333:470–474

    CrossRef  CAS  PubMed  Google Scholar 

  11. Dirks RM, Lin M, Winfree E, Pierce NA (2004) Paradigms for computational nucleic acid design. Nucleic Acids Res 32:1392–1403

    CrossRef  CAS  PubMed  PubMed Central  Google Scholar 

  12. Zadeh JN, Steenberg CD, Bois JS et al (2011) NUPACK: analysis and design of nucleic acid systems. J Comput Chem 32:170–173

    CrossRef  CAS  PubMed  Google Scholar 

  13. Tung CS, Carter ES 2nd (1994) Nucleic acid modeling tool (NAMOT): an interactive graphic tool for modeling nucleic acid structures. Comput Appl Biosci 10:427–433

    CAS  PubMed  Google Scholar 

  14. Pettersen EF, Goddard TD, Huang CC et al (2004) UCSF chimera—a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612

    CrossRef  CAS  PubMed  Google Scholar 

  15. Boniecki MJ, Lach G, Dawson WK et al (2016) SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction. Nucleic Acids Res 44:e63

    CrossRef  PubMed  Google Scholar 

  16. Ouldridge TE, Louis AA, Doye JPK (2010) DNA nanotweezers studied with a coarse-grained model of DNA. Phys Rev Lett 104:178101

    CrossRef  PubMed  Google Scholar 

  17. Suma A, Poppleton E, Matthies M et al (2019) TacoxDNA: a user-friendly web server for simulations of complex DNA structures, from single strands to origami. J Comput Chem 40:2586–2595

    CrossRef  CAS  PubMed  Google Scholar 

  18. Lisa M, Albright Barton E, Slatko (2000) Denaturing polyacrylamide gel electrophoresis. Curr Proto in Nucleic Acid Chem 00(1). https://doi.org/10.1002/0471142700.nca03bs00

  19. Rabiya S, Tuma Matthew P, Beaudet Xiaokui, Jin Laurie J, Jones Ching-Ying, Cheung Stephen, Yue Victoria L, Singer (1999) Characterization of SYBR gold nucleic acid gel stain: a dye optimized for use with 300-nm ultraviolet transilluminators. Analytic Biochem 268(2):278–288. https://doi.org/10.1006/abio.1998.3067

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Acknowledgments

Elisa Franco acknowledges support from the National Science Foundation through the CAREER award DMR 1938194. Jaimie Marie Stewart is a Merck Awardee of the Life Sciences Research Foundation.

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Correspondence to Elisa Franco .

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Stewart, J.M., Subramanian, H.K.K., Franco, E. (2022). Assembly of RNA Nanostructures from Double-Crossover Tiles. In: Karim, A.S., Jewett, M.C. (eds) Cell-Free Gene Expression. Methods in Molecular Biology, vol 2433. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1998-8_18

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  • DOI: https://doi.org/10.1007/978-1-0716-1998-8_18

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1997-1

  • Online ISBN: 978-1-0716-1998-8

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