RNA origami: Design of co-transcriptionally folding RNA scaffolds and devices for synthetic biology applications
Introduced over a decade ago, the DNA origami method allowed the efficient design and self-assembly of molecular pegboards to spatially organize biomolecules and nanoparticles as well as the creation of dynamic nanoscale devices. We have recently introduced a new method called "single-stranded RNA origami" that allows the rational design of co-transcriptionally folding RNA nanostructures, which have the benefit, over DNA origami structures, of being expressible in cells. Here we expand the scale and diversity of the RNA origami architecture by developing new software to automate the 3D modeling of structures and to improve thermodynamic design of sequences. Förster resonance energy transfer (FRET) between light-up aptamers or fluorescent proteins is used to demonstrate nanometer-scale positional control on RNA scaffolds and to characterize dynamic RNA devices that switch conformation in response to the binding of small-molecule ligands, RNA sequences or proteins. The FRET output is used to demonstrate scaffolding of fluorescent proteins on RNA origami scaffolds when expressed in E. coli cells. I will finally discuss different approaches we are taking to use the RNA origami method to develop biosensors, scaffolds for enzymatic pathways and transcriptional control systems for applications in synthetic biology.
Ebbe Sloth Andersen is an associate professor at the Interdisciplinary Nanoscience Center at Aarhus University and is also affiliated with the Department of Molecular Biology and Genetics. He did his PhD studies on HIV RNA structure and function in the laboratory of Professor Jørgen Kjems at Aarhus Univeristy and did his Postdoc work in the context of the Centre for DNA Nanotechnology lead by Professor Kurt Gothelf. As assistant professor he has been a visiting associate at California Institute of Technology working with Professor Paul Rothemund, inventor of the DNA origami method, to develop the RNA origami methodology. Ebbe has been running his own research group since 2012 with a focus on designing DNA and RNA nanoscale devices for applications in diagnostics, medicine and recently synthetic biology.