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

Content Provider	Springer Nature Link
Author	Fujibayashi, Kenichi Zhang, David Yu Winfree, Erik Murata, Satoshi
Copyright Year	2008
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.
Starting Page	589
Ending Page	612
Page Count	24
File Format	PDF
ISSN	15677818
Journal	Natural Computing
Volume Number	8
Issue Number	3
e-ISSN	15729796
Language	English
Publisher	Springer Netherlands
Publisher Date	2008-07-09
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Algorithmic self-assembly Assembly errors Branch migration DNA self-assembly Protecting molecules Statistical Physics, Dynamical Systems and Complexity Artificial Intelligence (incl. Robotics) Processor Architectures Evolutionary Biology Theory of Computation
Content Type	Text
Resource Type	Article
Subject	Computer Science Applications

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