International Workshop on DNA-Based Computers

DNA 2013: DNA Computing and Molecular Programming pp 61-75

DNA Sticky End Design and Assignment for Robust Algorithmic Self-assembly

  • Constantine G. Evans
  • Erik Winfree
Conference paper

DOI: 10.1007/978-3-319-01928-4_5

Volume 8141 of the book series Lecture Notes in Computer Science (LNCS)
Cite this paper as:
Evans C.G., Winfree E. (2013) DNA Sticky End Design and Assignment for Robust Algorithmic Self-assembly. In: Soloveichik D., Yurke B. (eds) DNA Computing and Molecular Programming. DNA 2013. Lecture Notes in Computer Science, vol 8141. Springer, Cham

Abstract

A major challenge in practical DNA tile self-assembly is the minimization of errors. Using the kinetic Tile Assembly Model, a theoretical model of self-assembly, it has been shown that errors can be reduced through abstract tile set design. In this paper, we instead investigate the effects of “sticky end” sequence choices in systems using the kinetic model along with the nearest-neighbor model of DNA interactions. We show that both the sticky end sequences present in a system and their positions in the system can significantly affect error rates, and propose algorithms for sequence design and assignment.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Constantine G. Evans
    • 1
  • Erik Winfree
    • 2
  1. 1.PhysicsCalifornia Institute of TechnologyUSA
  2. 2.Computer ScienceCalifornia Institute of TechnologyUSA