Compact error-resilient computational DNA tiling assemblies

  • Authors:

  • John H. Reif;Sudheer Sahu;Peng Yin

  • Affiliations:

  • Department of Computer Science, Duke University, Durham, NC;Department of Computer Science, Duke University, Durham, NC;Department of Computer Science, Duke University, Durham, NC

  • Venue:
  • DNA'04 Proceedings of the 10th international conference on DNA computing
  • Year:
  • 2004

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Abstract

The self-assembly process for bottom-up construction of nanostructures is of key importance to the emerging scientific discipline Nanoscience. However, self-assembly at the molecular scale is prone to a quite high rate of error. Such high error rate is a major barrier to large-scale experimental implementation of DNA tiling. The goals of this paper are to develop theoretical methods for compact error-resilient self-assembly and to analyze these methods by stochastic analysis and computer simulation. Prior work by Winfree provided an innovative approach to decrease tiling self-assembly errors without decreasing the intrinsic error rate ε of assembling a single tile. However, his technique resulted in a final structure that is four times the size of the original one. This paper describes various compact error-resilient tiling methods that do not increase the size of the tiling assembly. These methods apply to assembly of boolean arrays which perform input sensitive computations (among other computations). Our 2-way (3-way) overlay redundancy construction drops the error rate from ε to approximately ε2 (ε3), without increasing the size of the assembly. These results were further validated using stochastic analysis and computer simulation.