Computational Generation of RNA Nanorings

  • Rishabh Sharan
  • Eckart Bindewald
  • Wojciech K. Kasprzak
  • Bruce A. ShapiroEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1632)


A variety of designed RNA ring structures (ranging from triangles to hexagonal rings) have been reported in the scientific literature. Designing self-assembling RNA ring structures from structural motifs is, however, a nontrivial problem as there are many combinations of motifs and linking helices. Moreover, most combinations of motifs and linker helices will not lead to ring closure. A solution to this problem was recently published using a “design-by-catalog” approach where motif combinations that lead to rings are precomputed and tabulated. Here we present a web-browser based workflow for creating RNA rings using Galaxy, a web-based platform that can be used for workflow management. An example of how these RNA rings are generated and processed to create a 3D model of the ring is discussed.

Key words

RNA Ring Closure Enumeration Scaffold 



This work has been funded in whole or in part with Federal funds from the Frederick National Laboratory for Cancer Research, National Institutes of Health, under Contract No. HHSN261200800001E. This research was supported [in part] by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does the mention of trade names, commercial products, or organizations imply endorsement by the US Government.


  1. 1.
    Guo P (2010) The emerging field of RNA nanotechnology. Nat Nanotechnol 5:833–842CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Dibrov SM, McLean J, Parsons J, Hermann T (2011) Self-assembling RNA square. Proc Natl Acad Sci 108:6405–6408CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Geary C, Rothemund PWK, Andersen ES (2014) A single-stranded architecture for cotranscriptional folding of RNA nanostructures. Science 345:799–804CrossRefPubMedGoogle Scholar
  4. 4.
    Grabow WW, Zakrevsky P, Afonin KA, Chworos A, Shapiro BA, Jaeger L (2011) Self-assembling rNA nanorings based on RNAI/II inverse kissing complexes. Nano Lett 11:878–887CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Yingling YG, Shapiro BA (2007) Computational design of an RNA hexagonal nanoring and an RNA nanotube. Nano Lett 7:2328–2334CrossRefPubMedGoogle Scholar
  6. 6.
    Jaeger L, Westhof E, Leontis NB (2001) TectoRNA: modular assembly units for the construction of RNA nano-objects. Nucleic Acids Res 29:455–463CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Nasalean L, Stombaugh J, Zirbel CL, Leontis NB (2009) RNA 3D structural motifs: definition, identification, annotation, and database searching. In: Walter NG, Woodson SA, Batey RT (eds) Non-protein coding RNAs. Springer, Berlin, pp 1–26Google Scholar
  8. 8.
    Afonin KA, Bindewald E, Yaghoubian AJ, Voss N, Jacovetty E, Shapiro BA, Jaeger L (2010) In vitro assembly of cubic RNA-based scaffolds designed in silico. Nat Nanotechnol 5:676–682CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Leontis NB, Westhof E (2014) Self-assembled RNA nanostructures. Science 345:732–733CrossRefPubMedGoogle Scholar
  10. 10.
    Afonin KA, Kireeva M, Grabow WW, Kashlev M, Jaeger L, Shapiro BA (2012) Co-transcriptional assembly of chemically modified RNA nanoparticles functionalized with siRNAs. Nano Lett 12:5192–5195CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Grabow WW, Jaeger L (2014) RNA self-assembly and RNA nanotechnology. Acc Chem Res 47:1871–1880CrossRefPubMedGoogle Scholar
  12. 12.
    Cech TR, Zaug AJ, Grabowski PJ (1981) In vitro splicing of the ribosomal RNA precursor of Tetrahymena: involvement of a guanosine nucleotide in the excision of the intervening sequence. Cell 27:487–496CrossRefPubMedGoogle Scholar
  13. 13.
    Guerrier-Takada C, Gardiner K, Marsh T, Pace N, Altman S (1983) The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35:849–857CrossRefPubMedGoogle Scholar
  14. 14.
    Kruger K, Grabowski PJ, Zaug AJ, Sands J, Gottschling DE, Cech TR (1982) Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell 31:147–157CrossRefPubMedGoogle Scholar
  15. 15.
    Ramakrishnan V (2014) The ribosome emerges from a black box. Cell 159:979–984CrossRefPubMedGoogle Scholar
  16. 16.
    Khaled A, Guo S, Li F, Guo P (2005) Controllable self-assembly of nanoparticles for specific delivery of multiple therapeutic molecules to cancer cells using RNA nanotechnology. Nano Lett 5:1797–1808CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Bindewald E, Grunewald C, Boyle B, O’Connor M, Shapiro BA (2008) Computational strategies for the automated design of RNA nanoscale structures from building blocks using nanoTiler. J Mol Graph Model 27:299–308CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Martinez HM, Maizel JVJ, Shapiro BA (2008) RNA2D3D: a program for generating, viewing, and comparing 3-dimensional models of RNA. J Biomol Struct Dyn 25:669–683CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Jossinet F, Ludwig TE, Westhof E (2010) Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels. Bioinformatics 26:2057–2059CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Chworos A, Severcan I, Koyfman AY, Weinkam P, Oroudjev E, Hansma HG, Jaeger L (2004) Building programmable jigsaw puzzles with RNA. Science 306:2068–2072CrossRefPubMedGoogle Scholar
  21. 21.
    Bida J, Das R (2012) Squaring theory with practice in RNA design. Curr Opin Struct Biol 22:457–466CrossRefPubMedGoogle Scholar
  22. 22.
    Afonin KA, Kasprzak W, Bindewald E, Puppala PS, Diehl AR, Hall KT, Kim TJ, Zimmermann MT, Jernigan RL, Jaeger L, Shapiro BA (2014) Computational and experimental characterization of RNA cubic nanoscaffolds. Methods 67:256–265CrossRefPubMedGoogle Scholar
  23. 23.
    Bindewald E, Hayes R, Yingling YG, Kasprzak W, Shapiro BA (2008) RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign. Nucleic Acids Res 36:D392–D397CrossRefPubMedGoogle Scholar
  24. 24.
    Schroeder KT, McPhee SA, Ouellet J, Lilley DM (2010) A structural database for k-turn motifs in RNA. RNA 16:1463–1468CrossRefPubMedPubMedCentralGoogle Scholar
  25. 25.
    Tamura M, Hendrix DK, Klosterman PS, Schimmelman NRB, Brenner SE, Holbrook SR (2004) SCOR: structural classification of RNA, version 2.0. Nucleic Acids Res 32:D182–D184CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Popenda M, Szachniuk M, Blazewicz M, Wasik S, Burke EK, Blazewicz J, Adamiak RW (2010) RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures. BMC Bioinformatics 11:1–12CrossRefGoogle Scholar
  27. 27.
    Petrov AI, Zirbel CL, Leontis NB (2013) Automated classification of RNA 3D motifs and the RNA 3D motif atlas. RNA. doi: 10.1261/rna.039438.113 PubMedPubMedCentralGoogle Scholar
  28. 28.
    Vanegas PL, Hudson GA, Davis AR, Kelly SC, Kirkpatrick CC, Znosko BM (2011) RNA CoSSMos: characterization of secondary structure motifs—a searchable database of secondary structure motifs in RNA three-dimensional structures. Nucleic Acids Res 40:D439. doi: 10.1093/nar/gkr943 CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Andronescu M, Bereg V, Hoos HH, Condon A (2008) RNA STRAND: the RNA secondary structure and statistical analysis database. BMC Bioinformatics 9:1–10CrossRefGoogle Scholar
  30. 30.
    Parlea L, Bindewald E, Sharan R, Bartlett N, Moriarty D, Oliver J, Afonin KA, Shapiro BA (2016) Ring catalog: a resource for designing self-assembling RNA nanostructures. Methods 103:128. doi: 10.1016/j.ymeth.2016.04.016 CrossRefPubMedGoogle Scholar
  31. 31.
    Lilley DM (2000) Structures of helical junctions in nucleic acids. Q Rev Biophys 33:109–159CrossRefPubMedGoogle Scholar
  32. 32.
    Afgan E, Baker D, den BM v, Blankenberg D, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Eberhard C et al (2016) The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res 44:W3CrossRefPubMedPubMedCentralGoogle Scholar
  33. 33.
    Blankenberg D, Von Kuster G, Bouvier E, Baker D, Afgan E, Stoler N, Taylor J, Nekrutenko A (2014) Dissemination of scientific software with Galaxy ToolShed. Genome Biol 15:1CrossRefGoogle Scholar
  34. 34.
    Bindewald E, Afonin K, Jaeger L, Shapiro BA (2011) Multistrand RNA secondary structure prediction and nanostructure design including pseudoknots. ACS Nano 5:9542–9551CrossRefPubMedPubMedCentralGoogle Scholar
  35. 35.
    Ponder JW, Richards FM (1987) An efficient newton-like method for molecular mechanics energy minimization of large molecules. J Comput Chem 8:1016–1024CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Rishabh Sharan
    • 1
  • Eckart Bindewald
    • 2
  • Wojciech K. Kasprzak
    • 3
  • Bruce A. Shapiro
    • 1
    Email author
  1. 1.RNA Structure and Design Section, RNA Biology LaboratoryNational Cancer Institute, National Institutes of HealthFrederickUSA
  2. 2.Frederick National Laboratory for Cancer ResearchLeidos Biomedical ResearchFrederickUSA
  3. 3.Basic Science Program, Leidos Biomedical Research, Inc.Frederick National Laboratory for Cancer ResearchFrederickUSA

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