Synthetic DNA and RNA origami scaffolds towards in vitro and in vivo applications

Nucleic acid self-assembly is a branch of nanotechnology that uses the DNA and RNA, not only as a genetic material, but also as a structural medium. DNA origami is the evolution of the DNA assembly. Origami are nanostructures formed by a long single strand, the scaffold, held together by many shorter oligonucleotides, the staples.

Initially, the bacteriophage genomes were used as convenient source of single stranded DNA scaffold. Today the potential biotechnological applications require the scaffold to be bio-orthogonal and easily transferable from academic research to the industry.

In my recently completed PhD thesis, I focused on the synthesis, analysis and application of synthetic scaffolds designed to be bio-orthogonal. These scaffolds are based on the combinatorial De Bruijn sequence and are uniquely addressable and optimised thermodynamically. I analysed their folding efficiency (in DNA and hybrid RNA/DNA origami) and bio-orthogonality in vivo in E. coli. Finally I designed a system to study the folding dynamics, that includes functionalized origami encapsulated in giant unilamellar vesicles. This system can be used with high throughput technologies, and can simulate a simple cell-like environment which is an intermediate step towards the in vivo origami folding.