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<body>
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.
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<img
style="font-family: Arial; width: 890px; height: 600px;" alt=""
src="http://openwetware.org/images/3/30/Slika21nova.png"> |
| 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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