Design principles for single-stranded RNA origami structures

Cody W. Geary, Ebbe Sloth Andersen*

*Corresponding author for this work

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

25 Citations (Scopus)

Abstract

We have recently introduced an experimental method for the design and production of RNA-origami nanostructures that fold up from a single strand while the RNA is being enzymatically produced, commonly referred to as cotranscriptional folding. To realize a general and scalable architecture we have developed a theoretical framework for determining RNA crossover geometries, long-distance interactions, and strand paths that are topologically compatible with cotranscriptional folding. Here, we introduce a simple parameterized model for the Aform helix and use it to determine the geometry and base-pair spacing for the five types of RNA double-crossover molecules and the curvature resulting from crossovers between multiple helices. We further define a set of paranemic loop-loop and end-to-end interactions compatible with the design of folding paths for RNA structures with arbitrary shape and programmable curvature. Finally, we take inspiration from space-filling curves in mathematics to design strand paths that have high-locality, programmed folding kinetics to avoid topological traps, and structural repeat units that might be used to create infinite RNA ribbons and squares by rolling circle transcription.

Original languageEnglish
Book seriesLecture Notes in Computer Science
Volume8727
Pages (from-to)1-19
Number of pages19
ISSN0302-9743
Publication statusPublished - 1 Jan 2014

Keywords

  • Folding
  • Kinetics
  • RNA
  • Space-filling curves
  • Structure

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