DNA origami

DNA origami object from viral DNA visualized by electron microscopy.Bai, X. -C.; Martin, T. G.; Scheres, S. H. W.; Dietz, H. (2012). "Cryo-EM structure of a 3D DNA-origami object". Proceedings of the National Academy of Sciences 109 (49): 20012–20017. doi:10.1073/pnas.1215713109. PMC 3523823. PMID 23169645. . The map is at the top and atomic model of the DNA colored below. Deposited in EMDB EMD-2210

DNA origami is the nanoscale folding of DNA to create non-arbitrary two- and three-dimensional shapes at the nanoscale. The specificity of the interactions between complementary base pairs make DNA a useful construction material, through design of its base sequences.[1] DNA is a well-understood material that is suitable for creating scaffolds that hold other molecules in place or to create structures all on its own.

DNA origami was the cover story of Nature on March 16, 2006.[2] Since then, DNA origami has progressed past an art form and has found a number of applications from drug delivery systems to uses as circuitry in plasmonic devices; however, most applications remain in a concept or testing phase.[3]

Overview

The idea of using DNA as a construction material was first introduced in the early 1980s by Nadrian Seeman.[4] The current method of DNA origami was developed by Paul Rothemund at the California Institute of Technology, the process involves the folding of a long single strand of viral DNA aided by multiple smaller "staple" strands.[5] These shorter strands bind the longer in various places, resulting in various shapes, including a smiley face and a coarse map of China and the Americas, along with many three-dimensional structures such as cubes.[6]

To produce a desired shape, images are drawn with a raster fill of a single long DNA molecule. This design is then fed into a computer program that calculates the placement of individual staple strands. Each staple binds to a specific region of the DNA template, and thus due to Watson-Crick base pairing, the necessary sequences of all staple strands are known and displayed. The DNA is mixed, then heated and cooled. As the DNA cools, the various staples pull the long strand into the desired shape. Designs are directly observable via several methods, including Electron Microscopy, atomic force microscopy, or fluorescence microscopy when DNA is coupled to fluorescent materials.[5]

Bottom-up self-assembly methods are considered promising alternatives that offer cheap, parallel synthesis of nanostructures under relatively mild conditions.

Since the creation of this method, software was developed to assist the process using CAD software. This allows researchers to use a computer to determine the way to create the correct staples needed to form a certain shape. One such software called caDNAno is an open source software for creating such structures from DNA. The use of software has not only increased the ease of the process but has also drastically reduced the errors made by manual calculations.[4]

Applications

Many potential applications have been suggested in literature, including enzyme immobilization, drug carry capsules, and nanotechnological self-assembly of materials. Though DNA is not the natural choice for building active structures for nanorobotic applications, due to its lack of structural and catalytic versatility, several papers have examined the possibility of molecular walkers on origami and switches for algorithmic computing.[6][7] The followings list some of the reported applications conducted in the laboratories with clinical potential.

Similar approaches

The idea of using protein design to accomplish the same goals as DNA origami has surfaced as well. Researchers at the National Institute of Chemistry in Slovenia are working on using rational design of protein folding to create structures much like those seen with DNA origami. The main focus of current research in protein folding design is in the drug delivery field, using antibodies attached to proteins as a way to create a targeted vehicle.[16][17]

See also

References

  1. Structural DNA nanotechnology: from design to applications Zadegan, R.M.; Norton, M.L (2012). "Structural DNA Nanotechnology: From Design to Applications". Int. J. Mol. Sci 13: 7149–7162. doi:10.3390/ijms13067149. PMC 3397516. PMID 22837684.
  2. Nature, Volume 440 (7082) March 16, 2006
  3. {http://www.nature.com/news/2010/100310/full/464158a.html 'Nature, Volume 464 March 10, 2010"}
  4. 1 2 "Rapid prototyping of 3D DNA-origami shapes with caDNAno", "Oxford Journal", May 11, 2009
  5. 1 2 Rothemund, Paul W. K. (2006). "Folding DNA to create nanoscale shapes and patterns". Nature 440 (7082): 297–302. doi:10.1038/nature04586. ISSN 0028-0836. PMID 16541064.
  6. 1 2 Lin, Chenxiang; Liu, Yan; Rinker, Sherri; Yan, Hao (2006). "DNA Tile Based Self-Assembly: Building Complex Nanoarchitectures". ChemPhysChem 7 (8): 1641–7. doi:10.1002/cphc.200600260. PMID 16832805.
  7. DNA 'organises itself' on silicon,BBC News, August 17, 2009
  8. Garde, Damian (May 15, 2012). "DNA origami could allow for ‘autonomous’ delivery". fiercedrugdelivery.com. Retrieved May 25, 2012.
  9. "Folded DNA becomes Trojan horse to attack cancer". NewScientist. 18 August 2012. Retrieved 22 August 2012.
  10. Jiang, Qiao; Song, Chen; Nangreave, Jeanette; Liu, Xiaowei; Lin, Lin; Qiu, Dengli; Wang, Zhen-Gang; Zou, Guozhang; Liang, Xingjie; Yan, Hao; Ding, Baoquan (2012). "DNA Origami as a Carrier for Circumvention of Drug Resistance". Journal of the American Chemical Society 134 (32): 13396–13403. doi:10.1021/ja304263n.
  11. M. Zadegan, Reza; et, al. (2012). "Construction of a 4 Zeptoliters Switchable 3D DNA Box Origami". ACS Nano 6 (11): 10050–10053. doi:10.1021/nn303767b.
  12. Spickernell, Sarah (8 April 2014). "DNA nanobots deliver drugs in living cockroaches". New Scientist. Retrieved 9 June 2014.
  13. Amir, Y; Ben-Ishay, E; Levner, D; Ittah, S; Abu-Horowitz, A; Bachelet, I (2014). "Universal computing by DNA origami robots in a living animal". Nature Nanotechnology 9 (5): 353–357. doi:10.1038/nnano.2014.58.
  14. Gibney, Michael (23 April 2014). "DNA nanocages that act like viruses bypass the immune system to deliver drugs". fiercedrugdelivery.com. Retrieved 19 June 2014.
  15. Perrault, S; Shih, W (2014). "Virus-Inspired Membrane Encapsulation of DNA Nanostructures To Achieve In Vivo Stability". ACS Nano (ACS) 8 (5): 5132–5140. doi:10.1021/nn5011914.
  16. Peplow, Mark (28 April 2013). "Protein gets in on DNA’s origami act". Nature. doi:10.1038/nature.2013.12882.
  17. Zadegan, Reza M.; Norton, Michael L. (June 2012). "Structural DNA Nanotechnology: From Design to Applications". Int. J. Mol. Sci. 13 (6): 7149–7162. doi:10.3390/ijms13067149. PMC 3397516. PMID 22837684.
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