Error tolerant DNA self-assembly by link-fracturing

This paper proposes and evaluates link fracturing as an approach for error tolerance in self-assembly by utilizing a DNA chain as a link between two blocks of molecules. Through the use of restriction enzymes, link fracturing breaks the connecting DNA chain between two blocks if an incorrect assembly has occurred due to the erroneous growth of tiles. Two error tolerant techniques are proposed by fracturing of the DNA chain links, namely 1-link and 2-link. Using the tool Xgrow, simulations under the Kinetic Tile Assembly Model (KTAM) are performed. Results show that 2-link fracturing achieves an improvement in error rate as compared to a normal assembly; moreover this is accomplished with little overhead in assembly size and execution complexity. The 1-link method shows 100% error free growth with moderate overhead as compared to normal growth and other existing error tolerant methods.