Synonyms
DNA nanostructure
Definition
DNA origami is a two- or three-dimensional nanostructure of custom shape utilizing hundreds of short “staple” single DNA strands to sew a long “scaffold” single DNA strand.
Introduction to DNA Origami
DNA, a genetic information carrier in nature, has been used as natural materials to build complex two- to three- dimensional structures at the nanometer scale. Watson-Crick base pairing rule between DNA bases where adenine (A) and guanine (G) form hydrogen bonds with thymine (T) and cytosine (C), respectively, allows to program diverse structural DNA motifs. The original idea was proposed by Seeman in 1982 [1] and was further evolved to DNA origami concept by Rothemund in 2006 [2], and now the relevant technology was termed as DNA nanotechnology. The DNA origami utilizes hundreds of short “staple” single strands with length of typically 20–50 nucleotides to sew a long “scaffold” single strand folding into two-dimensional structures of custom shape as...
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Seeman NC (1982) Nucleic acid junctions and lattices. J Theor Biol 99(2):237–247
Rothemund PW (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440(7082):297–302
Andersen ES et al (2009) Self-assembly of a nanoscale DNA box with a controllable lid. Nature 459:73–76
Ke Y et al (2009) Multilayer DNA origami packed on a square lattice. J Am Chem Soc 131(43):15903–15908
Douglas SM et al (2009) Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459(7245):414–418
Han D et al (2013) Unidirectional scaffold-strand arrangement in DNA origami. Angew Chem Int Ed 52:9031–9034
Fu TJ, Seeman NC (1993) DNA double-crossover molecules. Biochemistry 32(13):3211–3220
Castro CE et al (2011) A primer to scaffolded DNA origami. Nat Methods 8(3):221–229
Shih WM, Lin C (2010) Knitting complex weaves with DNA origami. Curr Opin Struct Biol 20(3):276–282
Zhou L et al (2013) DNA origami compliant nanostructures with tunable mechanical properties. ACS Nano 8(1):17–34
Protozanova E et al (2004) Stacked-unstacked equilibrium at the nick site of DNA. J Mol Biol 342(3):775–785
Kim DN et al (2012) Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures. Nucleic Acids Res 40(7):2862–2868
Dietz H, Douglas SM, Shih WM (2009) Folding DNA into twisted and curved nanoscale shapes. Science 325(5941):725–730
Ke Y et al (2012) Multilayer DNA origami packed on hexagonal and hybrid lattices. J Am Chem Soc 134(3):1770–1774
Han D et al (2011) DNA origami with complex curvatures in three-dimensional space. Science 332(6027):342–346
Han D et al (2013) DNA gridiron nanostructures based on four-arm junctions. Science 339(6126):1412–1415
Smith SB, Cui Y, Bustamante C (1996) Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science 271(5250):795–799
Liedl T et al (2010) Self-assembly of three-dimensional prestressed tensegrity structures from DNA. Nat Nanotechnol 5(7):520–524
Hays JB, Zimm BH (1970) Flexibility and stiffness in nicked DNA. J Mol Biol 48(2):297–317
Duckett DR, Murchie A, Lilley D (1990) The role of metal ions in the conformation of the four-way DNA junction. EMBO J 9(2):583
Martin TG, Dietz H (2012) Magnesium-free self-assembly of multi-layer DNA objects. Nat Commun 3(1103):1–6
Song J et al (2013) Isothermal hybridization kinetics of DNA assembly of two-dimensional DNA origami. Small 9(17):2954–2959
Sobczak JPJ et al (2012) Rapid folding of DNA into nanoscale shapes at constant temperature. Science 338(6113):1458–1461
Jungmann R et al (2008) Isothermal assembly of DNA origami structures using denaturing agents. J Am Chem Soc 130(31):10062–10063
Ko S (2013) RNA–DNA hybrid origami: folding of a long RNA single strand into complex nanostructures using short DNA helper strands. Chem Commun 49(48):5462–5464
Bai XC et al (2012) Cryo-EM structure of a 3D DNA-origami object. Proc Natl Acad Sci 109(49):20012–20017
Song J et al (2012) Direct visualization of transient thermal response of a DNA origami. J Am Chem Soc 134(24):9844–9847
Wei X et al (2013) Mapping the thermal behavior of DNA origami nanostructures. J Am Chem Soc 135(16):6165–6176
Kauert DJ et al (2011) Direct mechanical measurements reveal the material properties of three-dimensional DNA origami. Nano Lett 11(12):5558–5563
Yoo J, Aksimentiev A (2013) In situ structure and dynamics of DNA origami determined through molecular dynamics simulations. Proc Natl Acad Sci 110(50):20099–20104
Rothemund PW et al (2004) Design and characterization of programmable DNA nanotubes. J Am Chem Soc 126(50):16344–16352
O’Neill P et al (2006) Sturdier DNA nanotubes via ligation. Nano Lett 6(7):1379–1383
Gore J et al (2006) DNA overwinds when stretched. Nature 442(7104):836–839
Bryant Z et al (2003) Structural transitions and elasticity from torque measurements on DNA. Nature 424(6946):338–341
Bustamante C, Bryant Z, Smith SB (2003) Ten years of tension: single-molecule DNA mechanics. Nature 421(6921):423–427
Kim DN, Nguyen CT, Bathe M (2011) Conformational dynamics of supramolecular protein assemblies. J Struct Biol 173(2):261–270
Kim DN et al (2011) Conformational dynamics data bank: a database for conformational dynamics of proteins and supramolecular protein assemblies. Nucleic Acids Res 39(Suppl 1):451–455
McQuarrie DA (1976) Statistical Mechanics. Harper & Row, New York
Arbona JM, Aimé JP, Elezgaray J (2012) Folding of small origamis. J Chem Phys 136(6):065102
Arbona JM, Elezgaray J, Aimé JP (2012) Modelling the folding of DNA origami. EPL (Europhys Lett) 100(2):28006
Arbona JM, Aimé JP, Elezgaray J (2013) Cooperativity in the annealing of DNA origamis. J Chem Phys 138(1):015105
Fujibayashi K, Murata S (2009) Precise simulation model for DNA tile self-assembly. IEEE Trans Nanotechnol 8(3):361–368
Neuman KC, Nagy A (2008) Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy. Nat Methods 5(6):491
Wang T et al (2012) Design and characterization of 1D nanotubes and 2D periodic arrays self-assembled from DNA multi-helix bundles. J Am Chem Soc 134(3):1606–1616
Schiffels D, Liedl T, Fygenson DK (2013) Nanoscale structure and microscale stiffness of DNA nanotubes. ACS Nano 7(8):6700–6710
Zhao YX et al (2012) DNA origami delivery system for cancer therapy with tunable release properties. ACS Nano 6(10):8684–8691
Endo M, Yang Y, Sugiyama H (2013) DNA origami technology for biomaterials applications. Biomater Sci 1(4):347–360
Kuzyk A et al (2012) DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response. Nature 483(7389):311–314
Nickels PC, Feldmann J, Liedl T (2014) Hierarchical assembly of metal nanoparticles, quantum dots and organic dyes using DNA origami scaffolds. Nat Nanotechnol 9:74–78
Mangalum A, Rahman M, Norton ML (2013) Site-specific immobilization of single-walled carbon nanotubes onto single and one-dimensional DNA origami. J Am Chem Soc 135(7):2451–2454
Woo S, Rothemund PW (2011) Programmable molecular recognition based on the geometry of DNA nanostructures. Nat Chem 3(8):620–627
Zhao Z, Yan H, Liu Y (2010) A route to scale up DNA origami using DNA tiles as folding staples. Angew Chem 122(8):1456–1459
Kershner RJ et al (2009) Placement and orientation of individual DNA shapes on lithographically patterned surfaces. Nat Nanotechnol 4:557–561
Rajendran A et al (2010) Programmed two-dimensional self-assembly of multiple DNA origami jigsaw pieces. ACS Nano 5(1):665–671
Endo M et al (2011) Two-dimensional DNA origami assemblies using a four-way connector. Chem Commun 47(11):3213–3215
Högberg BR, Liedl T, Shih WM (2009) Folding DNA origami from a double-stranded source of scaffold. J Am Chem Soc 131(26):9154–9155
Tabata O (2010) A closer look at DNA nanotechnology. Nanotechnol Mag IEEE 4(4):13–17
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Ma, Z., Kim, YJ., Kim, DN., Tabata, O. (2015). DNA-DNA Origami. In: Kobayashi, S., Müllen, K. (eds) Encyclopedia of Polymeric Nanomaterials. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-29648-2_321
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