Compact ErrorResilient Computational DNA Tiling Assemblies紧凑的容错计算DNA瓦片组件.ppt

Compact Error-Resilient Computational DNA Tiling Assemblies John H.Reif, Sudheer Sahu, and Peng Yin How to decrease assembling error? First approach Optimizing the physical environment, improving the design of the tile itself or using novel material? They admit that DNA is not suitable for constructing tiles Second approach Design of new tile sets that can reduce the total number of errors in the final structure even with the same intrinsic error rate Winfree’s proofreading - 1 The basic idea To exploit cooperative binding at the next higher level: to have several tiles that stabilize each other when they bind together Essentially, each rule tile in the original tile set is replaced by four tiles with related labels According to the aTAM, assembly from the seed tile proceeds according to the same logic as the original tile set, but scaled up in size by a factor of two *Kinetic trapping The essential feature of kinetic trapping within tile self-assembly is that once an error has occurred, both sites above the mismatched tile display an (x, y) pair that is perfectly matched by some monomer tile in solution, because tiles implementing all replacement rules are present. Thus, if such a tile arrives before the mismatched tile dissociates, the mismatched tile becomes locked in by multiple bonds and is now unlikely to dissociate (Winfree) Winfree’s proofreading - 2 If a mismatch occurs, the assembly process stalls, giving time for the initial mismatched tile to fall off and be replaced by a correct tile Errors in assemblies The pad mismatch rate ε Critical issue in 2D tiling assemblies It determines the size of the error-free assembly Key challenge in experimentally demonstrating large scale assemblies is to construct error-resilient tiles ?Winfree’s approach resulted in a final structure that is four times the size of the original one Assembly with no error corrections NXM array V(i,j) The value of i-th bit on the j-th row displayed at position (i.j) and communicate