Natural Computing

, Volume 8, Issue 3, pp 589–612

Error suppression mechanisms for DNA tile self-assembly and their simulation

  • Kenichi Fujibayashi
  • David Yu Zhang
  • Erik Winfree
  • Satoshi Murata
Article

DOI: 10.1007/s11047-008-9093-9

Cite this article as:
Fujibayashi, K., Zhang, D.Y., Winfree, E. et al. Nat Comput (2009) 8: 589. doi:10.1007/s11047-008-9093-9

Abstract

Algorithmic self-assembly using DNA-based molecular tiles has been demonstrated to implement molecular computation. When several different types of DNA tile self-assemble, they can form large two-dimensional algorithmic patterns. Prior analysis predicted that the error rates of tile assembly can be reduced by optimizing physical parameters such as tile concentrations and temperature. However, in exchange, the growth speed is also very low. To improve the tradeoff between error rate and growth speed, we propose two novel error suppression mechanisms: the Protected Tile Mechanism (PTM) and the Layered Tile Mechanism (LTM). These utilize DNA protecting molecules to form kinetic barriers against spurious assembly. In order to analyze the performance of these two mechanisms, we introduce the hybridization state Tile Assembly Model (hsTAM), which evaluates intra-tile state changes as well as assembly state changes. Simulations using hsTAM suggest that the PTM and LTM improve the optimal tradeoff between error rate \(\epsilon\) and growth speed r, from \(r \approx \beta \epsilon^{2.0}\) (for the conventional mechanism) to \(r \approx \beta \epsilon^{1.4}\) and \(r \approx \beta \epsilon^{0.7}\), respectively.

Keywords

Algorithmic self-assembly Assembly errors Branch migration DNA self-assembly Protecting molecules 

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Kenichi Fujibayashi
    • 1
  • David Yu Zhang
    • 2
  • Erik Winfree
    • 2
    • 3
  • Satoshi Murata
    • 1
  1. 1.Department of Computational Intelligence and Systems ScienceTokyo Institute of TechnologyYokohamaJapan
  2. 2.Department of Computation and Neural SystemsCalifornia Institute of TechnologyPasadenaUSA
  3. 3.Department of Computer ScienceCalifornia Institute of TechnologyPasadenaUSA

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