Compact Error-Resilient Computational DNA Tiling Assemblies

Joint with Sudheer Sahu & John Reif

In Proc. Tenth International Meeting on DNA Computing, 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 thermodynamic analysis and computer simulation. Prior work by Winfree provided an innovative approach to decrease tiling self-assembly errors without decreasing the intrinsic error rate $\epsilon$ of assembling a single tile. However, his technique resulted in a final structure that is larger than the original one (four times larger for decreasing the error to $\epsilon^2$, nine times for to $\epsilon^3$). In this chapter, we describe various  compact error-resilient tiling methods that do not increase the size of the tiling assembly. These methods apply to the assembly of Boolean arrays which perform input sensitive computations (among other computations). Our 2-way (3-way) overlay redundancy construction decreases the error rate from $\epsilon$ to approximately $\epsilon^2$ ($\epsilon^3$), without increasing the size of the assembly. As in Winfree's constructions, the number of distinct tile types required is also increased in our error-resilient tiling constructions. These results were further validated using computer simulation.


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