A method of error suppression for self-assembling DNA tiles

Abstract

Self-assembling DNA tile is an important method of molecular computation. In this method, DNA tiles self-assemble a large two-dimensional lattice by the specific hybridization between complementary strands. Hence hybridization is not a deterministic, but stochastic, process which depends on tile concentration and temperature. For that reason, it is difficult to obtain an aggregate with no error. Growth speed of the aggregate must be very low to obtain an aggregate that contains less errors. Winfree et al. proposed the Proofreading Tile Model (PTM), which achieves both a low error rate and fast growth speed by splitting tiles into pieces to enhance tile specificity. However, it remains difficult to implement because it requires a large set of completely orthogonal strands. This paper presents a novel method called Layered Tile Model (LTM) to realize the reliable self-assembly of DNA tiles. We introduce layered tiles which are covered by other tiles called protective tiles. Those protective tiles verify the correctness of connections of the former tiles. Simulation and analysis are used to evaluate LTM performance. Results demonstrate that LTM offers similar performance compared to 2 × 2 PTM. It also has unique properties that are considered to be practical for implementation. © Springer-Verlag Berlin Heidelberg 2005.