Turning Synthetic DNA Oligonucleotides into Designed Nanostructures: Supramolecular Polymeric Chains and Dynamic Objects by Self-assembly

DNA is the molecule that encodes the hereditary information in living organisms. In the last years, the specific recognition abilities and the possibility to encode information that are intrinsic in the DNA molecule have been used to assemble nanoscale structures by design.[1] As suggested by Ned Seeman, the recognized pioneer of this field,[2] the Holliday junction is the fundamental structural element around which a great variety of structures can be designed and implemented: this is a branching point where 4 chains of double-stranded DNA meet. By organizing a number of junctions in a proper fashion, it is possible to create rigid structures that overtake the intrinsic flexibility and stochasticity of polymers to create DNA nanoscale objects with the desired size and shape. Using this type of approach, a number of monomeric or polymeric nano-objects can be assembled, with the added possibility of introducing tunable elements, that can change their geometry on an external signal, opening the way towards the construction of nanostructures with controllable dynamics. Using synthetic oligodeoxynucleotides (ODN), in our laboratory we have assembled parallelogram shaped nanostructures made of 4 blocked Holliday junctions that have “sticky ends” on their side. Programmed assembly of these ends brings to the construction of polymers that can be either flexible or rigid (100 nm of persistence length or more). Proper mixing and assembly of different monomer structures can yield different topologies: we can obtain linear, branched or circular nanostructures up to several hundred nanometers in size. The biochemical and structural characterization of these has been performed using gel eletrophoresis and atomic force microscopy. By proper functionalization of the ODNs used for the assembly, it is possible to include non-DNA objects on the structures: this seems a clever strategy to assemble (a desired number of) objects at a controlled distance on a nanostructure, with the possibility of also modulating their dynamics. As an example of this paradigm, we have assembled interacting fluorophores on a rigid parallelogram made of DNA, and we have measured a significant FRET. This does not take place if the fluorophores are, instead, free in solution, or even if they are assembled on incomplete (more flexible) parallelogram structures. Furthermore, by assemblying oligonucleotides in a pH-controlled triple helix, we have recently introduced a novel structural motif to the toolbox for DNA-based molecules constructions.[3] This tool is expected to expand further the possibilities of assemblying and controlling nanostructures made of DNA. [1] M. Brucale, G. Zuccheri, B. Samorì, Trends in Biotechnology, May 2006. [2] N. C. Seeman, Nature 2003, 421, 427. [3] M. Brucale, G. Zuccheri, B. Samorì, Org Biomol Chem 2005, 3, 575.