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. By organizing a number of branched junctions of DNA 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.(Brucale M. et al., 2006; Seeman N.C., 2003) 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. Furthermore, these designed nanostructures can be decorated with functional elements (such as nanoparticles or organic moieties) and be later used as elements in electronic nanocircuitry. 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. As an example of making functional devices out of the DNA nanostructures, 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) DNA 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.(Brucale M. et al., 2005) This tool is expected to expand further the possibilities of assemblying and controlling nanostructures made of DNA. Brucale, M., Zuccheri, G. and Samorì, B. (2006). "Mastering the Complexity of DNA Nanostructures." Trends in Biotechnology in press (May issue). Brucale, M., Zuccheri, G. and Samorì, B. (2005). "The dynamic properties of an intramolecular transition from DNA duplex to cytosine-thymine motif triplex." Org Biomol Chem 3(4): 575-7. Seeman, N.C. (2003). "DNA in a material world." Nature 421(6921): 427-31.

Building flexible or rigid, static or dynamic nanostructures thanks to the controlled self-assembly of oligonucleotides: one way towards nanoscale molecular assembly by design

ZUCCHERI, GIAMPAOLO;BRUCALE, MARCO;SAMORI', BRUNO
2006

Abstract

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. By organizing a number of branched junctions of DNA 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.(Brucale M. et al., 2006; Seeman N.C., 2003) 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. Furthermore, these designed nanostructures can be decorated with functional elements (such as nanoparticles or organic moieties) and be later used as elements in electronic nanocircuitry. 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. As an example of making functional devices out of the DNA nanostructures, 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) DNA 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.(Brucale M. et al., 2005) This tool is expected to expand further the possibilities of assemblying and controlling nanostructures made of DNA. Brucale, M., Zuccheri, G. and Samorì, B. (2006). "Mastering the Complexity of DNA Nanostructures." Trends in Biotechnology in press (May issue). Brucale, M., Zuccheri, G. and Samorì, B. (2005). "The dynamic properties of an intramolecular transition from DNA duplex to cytosine-thymine motif triplex." Org Biomol Chem 3(4): 575-7. Seeman, N.C. (2003). "DNA in a material world." Nature 421(6921): 427-31.
V Convegno Nazionale Materiali Molecolari Avanzati per Fotonica ed Elettronica
39
39
G. Zuccheri; M. Brucale; B. Samorì
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/11585/30559
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