Computational Generation of RNA Nanorings

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

Abstract

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 

Notes

Acknowledgment

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.

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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
  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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