Abstract
The DNA origami method enables the creation of complex nanoscale objects that can be used to organize molecular components and to function as reconfigurable mechanical devices. Of relevance to synthetic biology, DNA origami structures can be delivered to cells where they can perform complicated sense-and-act tasks, and can be used as scaffolds to organize enzymes for enhanced synthesis. The design of DNA origami structures is a complicated matter and is most efficiently done using dedicated software packages. This chapter describes a procedure for designing DNA origami structures using a combination of state-of-the-art software tools. First, we introduce the basic method for calculating crossover positions between DNA helices and the standard crossover patterns for flat, square, and honeycomb DNA origami lattices. Second, we provide a step-by-step tutorial for the design of a simple DNA origami biosensor device, from schematic idea to blueprint creation and to 3D modeling and animation, and explain how careful modeling can facilitate later experimentation in the laboratory.
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References
Seeman NC (1982) Nucleic acid junctions and lattices. J Theor Biol 99(2):237–247
Seeman NC (2010) Nanomaterials based on DNA. Annu Rev Biochem 79:65–87
Rothemund PWK (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440(7082):297–302
Qian L et al (2006) Analogic China map constructed by DNA. Chinese Science Bulletin
Andersen ES et al (2008) DNA origami design of dolphin-shaped structures with flexible tails. ACS Nano 2(6):1213–1218
Sharma J et al (2008) Toward reliable gold nanoparticle patterning on self-assembled DNA nanoscaffold. J Am Chem Soc 130(25):7820–7821
Ke Y et al (2008) Self-assembled water-soluble nucleic acid probe tiles for label-free RNA hybridization assays. Science 319(5860):180–183
Andersen ES et al (2009) Self-assembly of a nanoscale DNA box with a controllable lid. Nature 459(7243):73–76
Douglas SM et al (2009) Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459(7245):414–418
Dietz H, Douglas SM, Shih WM (2009) Folding DNA into twisted and curved nanoscale shapes. Science 325(5941):725–730
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
Han D et al (2013) Unidirectional scaffold-strand arrangement in DNA origami. Angew Chem Int Ed Engl 52(34):9031–9034
Wei B, Dai M, Yin P (2012) Complex shapes self-assembled from single-stranded DNA tiles. Nature 485(7400):623–626
Ke Y et al (2012) Three-dimensional structures self-assembled from DNA bricks. Science 338(6111):1177–1183
Andersen ES (2010) Prediction and design of DNA and RNA structures. N Biotechnol 27(3):184–193
Douglas SM et al (2009) Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Res 37(15):5001–5006
Williams S et al (2009) Tiamat: a three-dimensional editing tool for complex DNA structures. In: Goel A, Simmel F, SosÃk P (eds) DNA computing. Springer, Berlin, pp 90–101
Zhu J et al (2009) UNIQUIMER 3D, a software system for structural DNA nanotechnology design, analysis and evaluation. Nucleic Acids Res 37(7):2164–2175
Pettersen EF et al (2004) UCSF Chimera—a visualization system for exploratory research and analysis. J Comput Chem 25(13):1605–1612
Kim D-NN et al (2012) Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures. Nucleic Acids Res 40(7):2862–2868
Zhang DY, Seelig G (2011) Dynamic DNA nanotechnology using strand-displacement reactions. Nat Chem 3(2):103–113
Zadeh JN et al (2011) NUPACK: analysis and design of nucleic acid systems. J Comput Chem 32(1):170–173
Ouldridge TE, Louis AA, Doye JP (2011) Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model. J Chem Phys 134(8):085101
Ke Y et al (2009) Multilayer DNA origami packed on a square lattice. J Am Chem Soc 131(43):15903–15908
Andersen E, Nielsen M (2009) DNA origami design of 3D nanostructures
Castro CE et al (2011) A primer to scaffolded DNA origami. Nat Methods 8(3):221–229
Wang JC (1979) Helical repeat of DNA in solution. Proc Natl Acad Sci U S A 76(1):200–203
Fu TJ, Seeman NC (1993) DNA double-crossover molecules. Biochemistry 32(13):3211–3220
Douglas S, Bachelet I, Church G (2012) A logic-gated nanorobot for targeted transport of molecular payloads. Science 335(6070):831–834
Ke Y, Voigt NV, Fradkov E, Shih WM (2012) Two design strategies for enhancement of multilayer–DNA-origami folding: underwinding for specific intercalator rescue and staple-break positioning. Chem Sci 3
Martin T, Dietz H (2012) Magnesium-free self-assembly of multi-layer DNA objects. Nat Commun 3:1103
Dirks RM et al (2004) Paradigms for computational nucleic acid design. Nucleic Acids Res 32(4):1392–1403
Acknowledgement
This work was supported by a Sapere Aude Starting Grant from the Danish Council for Independent Research (DFF-0602-01772) and the Centre for DNA Nanotechnology (http://cdna.au.dk/) funded by the Danish National Research Foundation (DNRF81).
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Selnihhin, D., Andersen, E.S. (2015). Computer-Aided Design of DNA Origami Structures. In: Marchisio, M. (eds) Computational Methods in Synthetic Biology. Methods in Molecular Biology, vol 1244. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1878-2_2
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DOI: https://doi.org/10.1007/978-1-4939-1878-2_2
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