Natural Computing

, Volume 14, Issue 3, pp 491–503

DNA origami and the complexity of Eulerian circuits with turning costs

  • Joanna A. Ellis-Monaghan
  • Andrew McDowell
  • Iain Moffatt
  • Greta Pangborn
Article

Abstract

Building a structure using self-assembly of DNA molecules by origami folding requires finding a route for the scaffolding strand through the desired structure. When the target structure is a 1-complex (or the geometric realization of a graph), an optimal route corresponds to an Eulerian circuit through the graph with minimum turning cost. By showing that it leads to a solution to the 3-SAT problem, we prove that the general problem of finding an optimal route for a scaffolding strand for such structures is NP-hard. We then show that the problem may readily be transformed into a traveling salesman problem (TSP), so that machinery that has been developed for the TSP may be applied to find optimal routes for the scaffolding strand in a DNA origami self-assembly process. We give results for a few special cases, showing for example that the problem remains intractable for graphs with maximum degree 8, but is polynomial time for 4-regular plane graphs if the circuit is restricted to following faces. We conclude with some implications of these results for related problems, such as biomolecular computing and mill routing problems.

Keywords

DNA origami DNA self-assembly Turning cost Eulerian circuit Hamiltonian cycle Threading strand Biomolecular computing Mill routing Computational complexity A-trails 

Mathematics Subject Classification

92E10 05C45 05C85 

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Joanna A. Ellis-Monaghan
    • 1
  • Andrew McDowell
    • 2
  • Iain Moffatt
    • 2
  • Greta Pangborn
    • 3
  1. 1.Department of MathematicsSaint Michael’s CollegeColchesterUSA
  2. 2.Department of MathematicsRoyal Holloway, University of LondonEghamUK
  3. 3.Department of Computer ScienceSaint Michael’s CollegeColchesterUSA

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