title: Error tolerant DNA self-assembly using (2k - 1)x(2k - 1) snake tile sets.
abstract: DNA self-assembly has been advocated as a possible technique for bottom-up manufacturing of scaffolds for computing systems in the nanoscale region. However, self-assembly is affected by different types of errors (such as growth and facet roughening) that severely limit its applicability. Different methods for reducing the error rate of self-assembly using tiles as basic elements have been proposed. A particularly effective method relies on snake tile sets that utilize a square block of even size (i.e., 2k x 2k tiles, k = 2, 3, . . .). In this paper, an odd-sized square block [i.e., (2k - 1) x (2k - 1)] is proposed as basis for the snake tile set. Compared with other tile sets, the proposed snake tile sets achieve a considerable reduction in error rate at a very modest reduction in growth rate. Growth and facet roughening errors are considered and analytical results are presented to prove the reduction in error rate compared with an even-sized snake tile set. Simulation results are provided.
authors.affiliation: Department of Electrical and Computer Engineering, Northeastern University, Boston, MA 02115, USA. xma@ece.neu.edu
authors.forename: X
authors.initials: X
authors.lastname: Ma
authors.forename: J
authors.initials: J
authors.lastname: Huang
authors.forename: F
authors.initials: F
authors.lastname: Lombardi
mesh_terms: D001483:Base Sequence; D003198:Computer Simulation; D003460:Crystallization / Q000379:methods*; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D049329:Nanostructures / Q000737:chemistry* / Q000648:ultrastructure*; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA