Periodic Reporting for period 4 - RNA ORIGAMI (RNA-protein Nanostructures for Synthetic Biology)
Periodo di rendicontazione: 2020-10-01 al 2021-03-31
The RNA ORIGAMI project aimed at rationally designing RNA nanostructures that can be genetically expressed and function as scaffolds for controlling e.g. protein function in cells. This technology can potentially be used for a wide range of applications in synthetic biology such as production of cheaper drugs, sustainable fuel production, efficient diagnosis, and RNA medicine. The main objectives of the project were to develop design software, to characterize designed RNA scaffolds, to develop RNA sensor devices, and to demonstrate proof-of-concept applications in synthetic biology. The project succeeded in developing software tools to improve size, yield and functionalization of RNA nanostructures, demonstrated novel RNA sensors, and applied RNA nanostructures in metabolic engineering.
The RNA ORIGAMI project initially developed software for the rapid design of RNA origami structures and used biophysical characterization techniques to verify the folding of the designed structures. The software has been made publicly available in a code repository and as a webserver and has been used for obtain several research results: (1) RNA sensors were developed based on Förster Resonance Energy Transfer (FRET) between fluorescent aptamers, (2) RNA therapeutic particles were developed to control blood coagulation, (3) RNA scaffolds were used to stabilize functional motifs in E. coli cells, (4) RNA scaffolds were used to control enzymatic reactions in E. coli and yeast. These core results are being exploited for RNA medicine and metabolic engineering and have been or are in the process of being published in the scientific literature.
The RNA ORIGAMI project has improved our ability to construct genetically expressible RNA nanostructures. We have improving folding yield, reached construct sizes of 2000 bases in length, and demonstrated precise scaffolding of proteins and small molecules. The development of an aptamer-based FRET system has provided a new way to develop genetically expressible sensors systems and to measure conformational changes in cells. RNA origami has been demonstrated as a powerful tool in synthetic biology by stabilizing functional motifs in cells, by regulating protein expression, and by controlling enzymatic pathways.