Out-of-Plane Aptamer Functionalization of RNA Three-Helix Tiles

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DOI

  • Aradhana Chopra, Physik-Department E14, Technische Universität München, 85748 Garching, Germany. aradhanachopra@gmail.com.
  • ,
  • Sandra Sagredo, Physik-Department E14, Technische Universität München, 85748 Garching, Germany. sandra.sagredo@tum.de.
  • ,
  • Guido Grossi
  • Ebbe S Andersen
  • Friedrich C Simmel, Physik-Department E14, Technische Universität München, 85748 Garching, Germany. simmel@tum.de.

Co-transcriptionally folding RNA nanostructures have great potential as biomolecular scaffolds, which can be used to organize small molecules or proteins into spatially ordered assemblies. Here, we develop an RNA tile composed of three parallel RNA double helices, which can associate into small hexagonal assemblies via kissing loop interactions between its two outer helices. The inner RNA helix is modified with an RNA motif found in the internal ribosome entry site (IRES) of the hepatitis C virus (HCV), which provides a 90° bend. This modification is used to functionalize the RNA structures with aptamers pointing perpendicularly away from the tile plane. We demonstrate modifications with the fluorogenic malachite green and Spinach aptamers as well with the protein-binding PP7 and streptavidin aptamers. The modified structures retain the ability to associate into larger assemblies, representing a step towards RNA hybrid nanostructures extending in three dimensions.

Original languageEnglish
Article number507
JournalNanomaterials (Basel, Switzerland)
Volume9
Issue4
ISSN2079-4991
DOIs
Publication statusPublished - Apr 2019

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