Design and simulation of self-repairing DNA lattices

Authors:
Urmi Majumder;Sudheer Sahu;Thomas H. LaBean;John H. Reif
Affiliations:
Department of Computer Science, Duke University, Durham, NC;Department of Computer Science, Duke University, Durham, NC;Department of Computer Science, Duke University, Durham, NC;Department of Computer Science, Duke University, Durham, NC
Venue:
DNA'06 Proceedings of the 12th international conference on DNA Computing
Year:
2006

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Abstract

Self-repair is essential to all living systems, providing the ability to remain functional in spite of gradual damage. In the context of self-assembly of self-repairing synthetic biomolecular systems, recently Winfree developed a method for transforming a set of DNA tiles into its self-healing counterpart at the cost of increasing the lattice area by a factor of 25. The overall focus of this paper, however, is to develop compact designs for self-repairing tiling assemblies with reasonable constraints on crystal growth. Specifically, we use a special class of DNA tiling designs called reversible tiling which when carefully designed can provide inherent self-repairing capabilities to patterned DNA lattices. We further note that we can transform any irreversible computational DNA tile set to its reversible counterpart and hence improve the self-repairability of the computational lattice. But doing the transform with an optimal number of tiles, is still an open question.