Compact Error-Resilient Computational DNA Tiling Assemblies

  • John H. Reif
  • Sudheer Sahu
  • Peng Yin
Conference paper

DOI: 10.1007/11493785_26

Part of the Lecture Notes in Computer Science book series (LNCS, volume 3384)
Cite this paper as:
Reif J.H., Sahu S., Yin P. (2005) Compact Error-Resilient Computational DNA Tiling Assemblies. In: Ferretti C., Mauri G., Zandron C. (eds) DNA Computing. DNA 2004. Lecture Notes in Computer Science, vol 3384. Springer, Berlin, Heidelberg

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.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • John H. Reif
    • 1
  • Sudheer Sahu
    • 1
  • Peng Yin
    • 1
  1. 1.Department of Computer ScienceDuke UniversityDurhamUSA

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