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Experimental Implementation of Tile Assembly

  • Reference work entry
  • First Online:
Encyclopedia of Algorithms

  • 126 Accesses

Years and Authors of Summarized Original Work

  • 2007; Schulman, Winfree

  • 2008; Fujibayashi, Hariadi, Park, Winfree, Murata

  • 2009; Barish, Schulman, Rothemund, Winfree

  • 2012; Schulman, Yurke, Winfree

Problem Definition

From the earliest works on tile self-assembly, abstract theoretical models and experimental implementations have been linked. In 1998, in addition to developing the abstract and kinetic Tile Assembly Models (aTAM and kTAM) [14], Winfree et al. demonstrated the use of DNA tiles to construct a simple, periodic lattice [16]. Periodic lattices and “uniquely addressed” assemblies, where each tile type appears once in each assembly, have been widely studied, with systems employing up to a thousand unique tiles in three dimensions [8, 13]. While these systems provide insight into the behavior of DNA tile systems, algorithmic tile systems of more theoretical interest pose specific challenges for experimental implementation.

In the aTAM, abstract tiles attach individually to empty...

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Recommended Reading

  1. Barish RD, Rothemund PWK, Winfree E (2005) Two computational primitives for algorithmic self-assembly: copying and counting. Nano Lett 5(12):2586–2592. doi:10.1021/nl052038l

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  3. Chen HL, Goel A (2005) Error free self-assembly using error prone tiles. In: DNA 10, Milan. LNCS, vol 3384. Springer, pp 702–707

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  5. Evans CG, Winfree E (2013) DNA sticky end design and assignment for robust algorithmic self-assembly. In: DNA 19, Tempe. LNCS, vol 8141. Springer, pp 61–75. doi:10.1007/978-3-319-01928-4_5

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  6. Evans CG, Hariadi RF, Winfree E (2012) Direct atomic force microscopy observation of DNA tile crystal growth at the single-molecule level. J Am Chem Soc 134:10,485–10,492. doi:10.1021/ja301026z

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  7. Fujibayashi K, Hariadi R, Park SH, Winfree E, Murata S (2008) Toward reliable algorithmic self-assembly of DNA tiles: a fixed-width cellular automaton pattern. Nano Lett 8(7):1791–1797. doi:10.1021/nl0722830

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  10. Schulman R, Winfree E (2007) Synthesis of crystals with a programmable kinetic barrier to nucleation. PNAS 104(39):15,236–15,241. doi:10.1073/pnas.0701467104

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  12. Schulman R, Yurke B, Winfree E (2012) Robust self-replication of combinatorial information via crystal growth and scission. PNAS 109(17):6405–6410. doi:10.1073/pnas.1117813109

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Authors and Affiliations

  1. Division of Biology and Bioengineering, California Institute of Technology, 1200 E California Blvd, MC 136-93, Pasadena, CA, USA

    Constantine G. Evans

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  1. Constantine G. Evans
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Correspondence to Constantine G. Evans .

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Editors and Affiliations

  1. Department of Electrical Engineering and Computer Science, Northwestern University, Evanston, IL, USA

    Ming-Yang Kao

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Evans, C.G. (2016). Experimental Implementation of Tile Assembly. In: Kao, MY. (eds) Encyclopedia of Algorithms. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-2864-4_674

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