Yield Optimization Strategies for (DNA) Staged Tile Assembly Systems

摘要

The staged Tile Assembly Model has been introduced by De-maine et al. 2008 as an enhancement of the previous tile self-assembly model of Winfree. In this framework, the assembly is allowed to be performed in parallel in different test-tubes, and the obtained products are stored and mixed in subsequent assembly stages. Using elegant combinatorial constructions, in has been shown that staged assembly systems possess remarkable advantage in comparison to their abstract counterparts. Because of their parallel nature, one can choose from a multitude of staged assembly strategies for assembling a given target structure. In the current work we analyze these assembly variations from a kinetic perspective, in order to determine and possibly maximize, their final assembly yield. As a pre-requirement for this task, we provide a procedure for associating an analytically tractable mathematical model to a given staged assembly experiment, based on which we can predict the yield concentration of the final assembly product. As a case study, we consider various assembly strategies as well as optimized and non-optimized assembly protocols for generating a size-10 tile assembly.