Healing DNA Self-Assemblies Using Punctures

In self-assembly, individual components (commonly referred to as tiles) have sufficient infor mation to build templates for structures such as lat tices for two-dimensional scaffolds. Tile sets that can heal (fully or partially) an erroneous DNA assembly have been proposed. Healing requires growth to be restarted such that erroneous tiles can be removed and the correct tiles can bind to the aggregate. Punctures have been proposed for this purpose; in this paper, a puncture is intentionally induced in the self-assembly to restart the growth process. The goal of this paper is to characterize an intentionally induced puncture (and its relevant properties) on an erroneous tile site in the grown crystal as part of a healing process. This allows to propagate any newly generated error away from the source of growth (i.e. the seed tile), such that self-assembly can continue along specific directions. Different types of puncture are considered with respect to healing and related features, such as growth direction, error and aggregate types. Punctures are analyzed using a new characterization and metric; different tile sets are investigated in detail for healing of a DNA self-assembly.

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