Reconfigurable DNA-nanochambers as dynamic compartmentalization systems
Final Report Abstract
The funded project contributed to the scientific advancement of the field with the following results: (i) The spatially coordinated action of a team of small DNA motor units tethered to an origami structure can be used to actuate global structural transformations in a predictable and reversible fashion. (ii) Tethering of switchable units to a common origami scaffold enhances their mechanical performance in respect to the same amount of motors freely diffusing in solution. (iii) Merging DNA nanotechnology and supramolecular chemistry, a spatially defined envelope of weak non-covalent interactions can be placed around the surface of a single protein to favor its encapsulation in a programmable way. (iv) DNA boundaries enhance the entropic avidity of multiple ligands towards a common target as well as the enzymatic activity of the internalized protein towards a substrate. The original idea proposed in the project was to develop a system for the selective encapsulation and release of a desired protein. The main objective, i.e. protein encapsulation, has been successfully achieved, leading to publications in high-impact journals. Concerning protein release, we encountered an unexpected, but extremely intriguing result. As described above, once the protein is trapped inside the DNA cage, its release was, in our hands, extremely difficult, even in absence of ligands. The reasons for this interesting phenomenon are still unknown. We aim at investigating further this issue on other DNA/protein systems, in order to understand the general principles governing this process and the role of the specific DNA-protein pair. During the development of this project, we have faced several other unexpected questions, related for example to issues of cooperativity, tethering and entropic avidity and how these are related to the geometry of the system under investigation. We have faced these topics carefully and systematically to establish more solid bases for future works (which are now in course). For this reason, the initial plan was slightly changed, dedicating more efforts on fundamental theoretical questions and moving applicative aspects to a later stage. We are currently performing an additional series of binding assays to quantify the avidity contribution. Molecular dynamic simulations and atomistic models are also ongoing. Our goal would be to draw the energy landscape of the reactions involved within the DNA compartment: from ligand binding, to ligand-induced allosteric effects in the active site of the protein, till the kinetics of substrate degradation. This should hopefully provide a full theoretical explanation of the experimental data observed and a unifying view of the formation and function of the DNA-protein complex.
Publications
- Reversible reconfiguration of DNA origami nanochambers monitored by single-molecule FRET. Angew. Chem. Int. Ed. Engl. 2015, 54, 3592-3597
B. Saccà, Y. Ishitsuka, R. Meyer, A. Sprengel, E.C. Schöneweiß, G.U. Nienhaus and C.M. Niemeyer
(See online at https://doi.org/10.1002/anie.201408941) - (2017) Nanotechnology and the unique role of DNA. In DNA nanotechnology for bioanalysis. From hybrid DNA nanostructures to functional devices (ed. G. Arrabito and L. Wang), World Scientific, Singapore
E.C. Schöneweiß, A. Jaekel and B. Saccà
- (2017): Enzyme-functionalized DNA nanostructures as tools for organizing and controlling enzymatic reactions. In: MRS Bull. 42 (12), S. 920–924
G. Grossi, A. Jaekel, E.S. Andersen and B. Saccà
(See online at https://doi.org/10.1557/mrs.2017.269) - Tailored protein encapsulation into a DNA host using geometrically organized supramolecular interactions. Nat. Commun. 2017, 8, 14472
A. Sprengel, P. Lill, P. Stegemann, K. Bravo-Rodriguez, E.C. Schöneweiß, M. Merdanovic, D. Gudnason, M. Aznauryan, L. Gamrad, S. Barcikowski, E. Sanchez-Garcia, V. Birkedal, C. Gatsogiannis, M. Ehrmann and B. Saccà
(See online at https://doi.org/10.1038/ncomms14472) - The collective behavior of spring-like motifs tethered to a DNA origami nanostructure. Nanoscale 2017, 9, 4486-4496
E.C. Schöneweiß and B. Saccà
(See online at https://doi.org/10.1039/C6NR08314E)
