Computer-Aided Design and Production of RNA Origami as Protein Scaffolds and Biosensors

Néstor Sampedro Vallina; Cody Geary; Mette Jepsen; Ebbe Sloth Andersen

doi:10.1007/978-1-0716-3028-0_3

Computer-Aided Design and Production of RNA Origami as Protein Scaffolds and Biosensors

Methods Mol Biol. 2023:2639:51-67. doi: 10.1007/978-1-0716-3028-0_3.

Authors

Néstor Sampedro Vallina¹, Cody Geary¹, Mette Jepsen¹, Ebbe Sloth Andersen²

Affiliations

¹ Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark.
² Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark. esa@inano.au.dk.

PMID: 37166710
DOI: 10.1007/978-1-0716-3028-0_3

Abstract

RNA nanotechnology is able to take advantage of the modularity of RNA to build a wide variety of structures and functional devices from a common set of structural modules. The RNA origami architecture harnesses the property of RNA to fold as it is being enzymatically synthesized by the RNA polymerase and enables the design of single-stranded devices that integrate multiple structural and functional RNA motifs. Here, we provide detailed procedures on how to design and characterize RNA origami structures. The process is illustrated by two examples: one that forms lattices and another example that acts as biosensors.

Keywords: AFM; FRET; RNA aptamers; RNA lattices; RNA nanotechnology; RNA origami; Scaffolding.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Biosensing Techniques*
Computer-Aided Design
DNA / chemistry
Nanostructures* / chemistry
Nanotechnology / methods
Nucleic Acid Conformation
Proteins
RNA / chemistry

Substances

DNA
RNA
Proteins