Biomod/2011/Slovenia/BioNanoWizards/ideastateoftheart

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State of the art


Natural biopolymers can form the most complex and variable nanostructures, which have not been surpassed by synthetic nanomaterials. Design of biopolymers to form defined nanostructures represents a formidable challenge, even today. The first successful artificial nanostructures were built by Nadrian Seeman who used nucleic acids to form nanostructures based on nucleotide pairing (Seeman, 1982).

Debut of the DNA origami technique (Rothemund, 2006) spurred major advancement of this field. Desired DNA origami objects are built by raster filling of a long single stranded DNA molecule into the selected model with the help of synthetic short DNA oligonucleotides - so called staple strands. Since staple strands are used in excess, one can achieve high yields of various 2D or 3D DNA nanostructures.

However, DNA origami by itself is of relatively limited use. Evolving supramolecular DNA nanotechnology combines DNA's remarkable feasibility of programmable self-assembly with other chemical species, which enhance DNA with advanced chemical and physical properties. DNA origami structures already served as a template for spatial positioning of nanoparticles such as quantum dots (Bui, 2010), metal nanoparticles (Pal, 2010; Hung, 2010), carbon nanotubes (Maune, 2010) and proteins via biotin-streptavidin interactions (Sacca, 2010; Shen, 2009; Numajiri, 2010) with nanometer precision.

The main advantage of DNA origami is precise control over the position of each staple strand used in the model. Since staple strands have unique nucleotide sequences, they can serve as specific attachment sites with a resolution around 6 nm. Attachment has been usually achieved through direct chemical functionalization of nanoparticles with oligonucleotides that bind to extended parts of staple strands. These segments of staple strands do not anneal to long single stranded DNA but protrude perpendicularly from the surface of DNA origami.
Figure 1: DNA origami can be modified at selected positions using oligonucleotides, aptamers or chemical modification of staples. Advantages and drawbacks are listed for each approach.
Other popular techniques include protein-ligand interactions based on modification of staple strands with biotin, which strongly binds to streptavidin. This approach requires individual synthesis of chemically modified staple strands and selected nanoparticles. The bottleneck of this approach for accelerated advancement of the field is the limited number of available orthogonal functionalization groups, which limits the variability of molecules or particles that can be simultaneusly bound to the DNA origami. Therefore, for the successful design of complex systems involving many different chemical species, a more universal method of binding should be developed.

Proteins, although similar in their chemical composition, are by the very nature of their design endowed with capabilities of performing a broad spectrum of roles such as enzymatic, defensive (e.g. antibodies), kinetic (i.e. proteins converting energy of chemical bond into movement), structural, optical etc. Since molecules of such variety can operate under the similar chemical conditions in vivo, proteins seem a logical choice for further development of complex multicomponent nanoscale devices capable of executing complex tasks.

Therefore the use of protein domains as DNA add-ons seems to have very interesting prospects. In our project from June until November 2011 we designed a novel and universal approach for protein immobilization on the surface of DNA origami, which could provide a straightforward and affordable way of targeted spatial positioning. Check next page to see the solution proposed by the BioNanoWizards team.


  • Bui H, Onodera C, Kidwell C, Tan Y, Graugnard E, Kuang W, Lee J, Knowlton WB, Yurke B, Hughes WL (2010) Programmable periodicity of quantum dot arrays with DNA origami nanotubes. Nano Lett. 10:3367-72.
  • Hung AM, Micheel CM, Bozano LD, Osterbur LW, Wallraff GM, Cha JN (2010) Large-area spatially ordered arrays of gold nanoparticles directed by lithographically confined DNA origami. Nat. Nanotechnol. 5:121-6.
  • Maune HT, Han SP, Barish RD, Bockrath M, Goddard III WA, Rothemund PW, Winfree E (2010) Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates. Nat. Nanotechnol. 5:61-6.
  • Numajiri K, Kimura M, Kuzuya A, Komiyama M (2010)Stepwise and reversible nanopatterning of proteins on a DNA origami scaffold. Chem Commun46:5127-9.
  • Pal S, Deng Z, Ding B, Yan H, Liu Y (2010) DNA-origami-directed self-assembly of discrete silver-nanoparticle architectures. Angew. Chem. 49:2700-4.
  • Rothemund PWK (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440: 297-302.
  • Sacca B, Meyer R, Erkelenz M, Kiko K, Arndt A, Schroeder H, Rabe KS, Niemeyer CM (2010) Orthogonal protein decoration of DNA origami. Angew. Chem. 49: 9378-83.
  • Seeman NC (1982) Nucleic acid junctions and lattices. J Theor Biol 499: 237-47.
  • Shen W, Zhong H, Neff D, Norton ML (2009) NTA directed protein nanopatterning on DNA Origami nanoconstructs. J. Am. Chem. Soc. 131:6660-1.
 

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