Design of code words for DNA computers and nanostructures with consideration of hybridization kinetics

  • Authors:

  • Tetsuro Kitajima;Masahiro Takinoue;Ko-Ichiroh Shohda;Akira Suyama

  • Affiliations:

  • Department of Life Science and Institute of Physics, Graduate school of Arts and Sciences, The University of Tokyo, Tokyo, Japan;Department of Life Science and Institute of Physics, Graduate school of Arts and Sciences, The University of Tokyo, Tokyo, Japan;Department of Life Science and Institute of Physics, Graduate school of Arts and Sciences, The University of Tokyo, Tokyo, Japan;Department of Life Science and Institute of Physics, Graduate school of Arts and Sciences, The University of Tokyo, Tokyo, Japan

  • Venue:
  • DNA13'07 Proceedings of the 13th international conference on DNA computing
  • Year:
  • 2007

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Abstract

We have developed a method for designing rapidly-hybridizing orthonormal DNA sequences. Two conditions were used in the prediction method. One condition concerned the stability of the self-folded secondary structures of forward and reverse strands. The other condition concerned the nucleation capability of complementary strands at the tails of their self-folded secondary structures. These conditions were derived from the complementary strands' experimentally-determined hybridization rates' dependence on their stability and nucleation capability.These dependences were examined for 37 orthonormal DNA sequences randomly selected from our set of 300 orthonormal DNA sequences. By applying this new method to the set of 300 orthonormal DNA sequences, more than 100 rapidly-hybridizing sequences were obtained.