Sequence Design for Stable DNA Tiles

  • Naoki Iimura
  • Masahito Yamamoto
  • Fumiaki Tanaka
  • Atsushi Kameda
  • Azuma Ohuchi
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4287)


DNA tile nanostructures have lately attracted a lot of attention as a new calculation technique and material on the nanometer scale. In forming DNA tiles, sequences need to bond in tile conformation. Conventional work can design sequences using overlapping subsequence. In this paper, we design tile sequences based on free energy. As a result of optimization, we show that we can design tile sequences as stable as conventional tiles. Moreover, we illustrate that the tile designed by the proposed method is perhaps more stable than conventional one. This method will be useful to design many tiles when forming large scale and complex DNA nanostructures.


Conventional Tile Sequence Design Evaluation Item Conventional Work Hybridization Strength 
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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Naoki Iimura
    • 1
  • Masahito Yamamoto
    • 2
  • Fumiaki Tanaka
    • 1
  • Atsushi Kameda
    • 3
  • Azuma Ohuchi
    • 2
  1. 1.Graduate School of Information Science and TechnologyHokkaido UniversityHokkaidoJapan
  2. 2.CREST, Japan Science and Technology Agency (JST) and, Graduate School of Information Science and TechnologyHokkaido UniversityHokkaidoJapan
  3. 3.Suyama Lab.Department of Life SciencesThe University of TokyoTokyoJapan

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