Design tools for reporter strands and DNA origami scaffold strands

Joanna A. Ellis-Monaghan, Greta Pangborn, Nadrian C. Seeman, Sam Blakeley, Conor Disher, Mary Falcigno, Brianna Healy, Ada Morse, Bharti Singh, Melissa Westland

Research output: Contribution to journalArticle

Abstract

Self-assembly using DNA origami methods requires determining a route for the scaffolding strand through the targeted structure. Here we provide strategies and software tools for determining optimal routes for reporter or scaffolding strands through graph-like (ball-and-rod) constructs. The approach applies to complex constructs, for example arbitrary geometric embeddings of graphs rather than surface meshes, lattice subsets, and meshes on higher genus surfaces than spheres. The software notably allows the user the flexibility of specifying ranked preferences for augmenting edges and for the possible configurations of branched junctions. The greater topological complexity of arbitrary graph embeddings and meshes on higher genus surfaces can result in scaffolding strand routes that are knotted in 3 space, so we also present necessary caveats for these settings.

Original languageEnglish (US)
Pages (from-to)69-78
Number of pages10
JournalTheoretical Computer Science
Volume671
DOIs
StatePublished - Apr 6 2017

Keywords

  • Augmenting edges
  • DNA origami
  • DNA self-assembly
  • Eulerian circuits
  • Knotted DNA
  • Reporter strand
  • Scaffolding strand
  • Turning costs

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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