DNA origami

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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. PMID 23169645.  edit. 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 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. 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.[1] Since then, DNA origami has progressed past an art form and has found an number of applications from drug delivery systems to uses as circuitry in plasmonic devices, however most remain still a concept or testing phase.[2]

Overview[edit]

The idea of using DNA as a construction material was first introduced in the early 1980s by Nadrian Seeman.[3] 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.[4] 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.[5]

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.[4]

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.[3]

Applications[edit]

Many potential applications have been suggested in the 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.[5][6] The followings list some of the reported applications conducted in the laboratories with clinical potential.

  • Researchers at the Harvard University Wyss Institute reported the self-assembling and self-destructing drug delivery vessels using the DNA origami in the lab tests. The DNA nanorobot they created is an open DNA tube with a hinge on one side which can be clasped shut. The drug filled DNA tube is held shut by DNA aptamer, configured to identify and seek certain diseased related protein. Once the origami nanobots get to the infected cells, the aptamers break apart and release the drug. The first disease model the researchers used was leukemia and lymphoma.[7]
  • Researchers in the National Center for Nanoscience and Technology in Beijing and Arizona State University reported a DNA origami delivery vehicle for Doxorubicin, a well-known anti-cancer drug. The drug was non-covalently attached to DNA origami nanostructures through intercalation and a high drug load was achieved. The DNA-Doxorubicin complex was taken up by human breast adenocarcinoma cancer cells (MCF-7) via cellular internalization with much higher efficiency than doxorubicin in free form. The enhancement of cell killing activity was observed not only in regular MCF-7, more importantly, also in doxorubicin-resistant cells. The scientists theorized that the doxorubicin-loaded DNA origami inhibits lysosomal acidification, resulting in cellular redistribution of the drug to action sites, thus increasing the cytotoxicity against the tumor cells.[8][9]
  • In another study conducted by a group of scientists from iNANO center and CDNA Center in Aarhus university (Aarhus), researchers were able to construct a small multi-switchable 3D DNA Box Origami. The proposed nanoparticle was characterized by AFM, TEM and FRET. The constructed box was shown to have a unique reclosing mechanism, which enabled it to repeatedly open and close in response to a unique set of DNA or RNA keys. The authors proposed that this "DNA device can potentially be used for a broad range of applications such as controlling the function of single molecules, controlled drug delivery, and molecular computing.".[10]

Similar approaches[edit]

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.[11][12]

See also[edit]

References[edit]

  1. ^ Nature, Volume 440 (7082) March 16, 2006
  2. ^ {http://www.nature.com/news/2010/100310/full/464158a.html 'Nature, Volume 464 March 10, 2010"}
  3. ^ a b "Rapid prototyping of 3D DNA-origami shapes with caDNAno", "Oxford Journal", May 11, 2009
  4. ^ a b 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. 
  5. ^ a b 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. 
  6. ^ DNA 'organises itself' on silicon,BBC News, August 17, 2009
  7. ^ Garde, Damian (May 15, 2012). "DNA origami could allow for ‘autonomous’ delivery". fiercedrugdelivery.com. Retrieved May 25, 2012. 
  8. ^ "Folded DNA becomes Trojan horse to attack cancer". NewScientist. 18 August 2012. Retrieved 22 August 2012. 
  9. ^ 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. 
  10. ^ 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. 
  11. ^ {http://www.nature.com/news/protein-gets-in-on-dna-s-origami-act-1.12882 "Nature, April 28, 2013"}
  12. ^ 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.