Self-assembling DNA-nanoarrays containing mechanical units
Final Report Abstract
The funded project contributes to the scientific advancement of the field mainly in two aspects: i) development of an alternative conjugation strategy for functionalization of DNA nanostructures (covPA) and ii) observation of a DNA-based nanoscaffolding effect on the spectroscopic properties of G4 devices. The former issue, i.e. the covalently-linked protruding arm method, allows for the decoration of DNA-structures with basically any kind of DNA-tagged molecule. The method is highly efficient, does not affect the structural stability of the DNA motifs and does not require demanding sequence-design efforts. The method has recently proven its validity for the functionalization of 4x4 DNA superstructures with streptavidin molecules. The second aspect of the project, i.e. the DNA-nanoscaffold effect on the macroscopic properties of materials, is a rather new characteristic of DNA-nanostructures, which is only recently emerging. This work clearly demonstrates that the spectroscopic properties of a switchable material are affected by the nanometer spacing between the single devices. Due to the accessibility of a number of DNA templates of diverse shapes and dimensions, more complex and multi-responsive materials can be in principle realized and other interesting applications in the field of material science are expected to emerge in the near future. Originally, the idea was to hybridize the G4 units to a 4x4 tile bearing a canonical three-way junction protruding arm. However, I soon realized that such motifs are structurally very unstable. After attempting various alternative designs, I eventually came to the successful development of the covPA strategy. This resulted in a recent publication in Small and was fundamental for the development of the present project. Finally, during FRET-spectroscopy characterization of the various G4-constructs, I observed a clear effect of the nanoscaffold on the signal response of the systems. This prompted me to analyze other designs to investigate whether and how the nanometer distance between the G4-units may affect their performance. I therefore decided to extend the study of G4-nanoarrays to the DX design and, taking advantage of my recent experience on the DNA origami technique, attempted to realize switchable G4-modified origami. Although preliminary data on the DNA-origami system suggest the necessity to change the design of the switchable motif and/or the conditions of cycling operation, the results obtained for the DX-design confirmed the generality of the phenomenon. A final set of experiments is currently in progress to better understand the bases of such an interesting effect. I would like to stress that the unexpected results that I encountered during the development of this project were actually very fruitful. Indeed, they encouraged me to search alternative conjugation strategies for functionalization of DNA structures (i.e. the covPA design) and to deepen my knowledge of the DNA origami method.
Publications
- Analysis of the self-assembly of 4x4 DNA tiles by temperature-dependent FRET spectroscopy. ChemPhysChem 2009, 10, 3239-3248
B. Saccà, R. Meyer and C.M. Niemeyer
- Temperature-dependent FRET spectroscopy for the high-throughput analysis of self-assembled DNA nanostructures in real time. Nat. Protoc. 2009, 4, 271-285
B. Saccà, R. Meyer and C.M. Niemeyer
- Orthogonal protein decoration of DNA origami. Angew. Chem. Int. Ed. Engl. 2010, 49, 9378-9383
B. Saccà, R. Meyer, M. Erkelenz, K.S. Rabe, K. Kiko, A. Arndt and C.M. Niemeyer
- Covalent tethering of protruding arms for addressable DNA nanostructures. Small 2011, 7, 2887-2898
B. Saccà and C.M. Niemeyer
