Specificity of Hybridization Between DNA Sequences Based on Free Energy

  • Fumiaki Tanaka
  • Atsushi Kameda
  • Masahito Yamamoto
  • Azuma Ohuchi
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3892)


We investigated the specificity of hybridization based on a minimum free energy (ΔG min ) through gel electrophoresis analysis. The analysis, using 94 pairs of sequences with length 20, showed that sequences that hybridize each other can be separated using the constraint ΔG min ≤–14.0, but cannot be separated using the number of base pairs (BP) in the range from 9 to 18. This demonstrates that the ΔG min is superior to the BP in terms of the capability to separate specific from non-specific sequences. Furthermore, the comparison between sequence design based on ΔG min and that based on the BP, done through a computer simulation, showed that the former outperformed the latter in terms of the number of sequences designed successfully as well as the ratio of successfully designed sequences to the total number of sequences checked.


Base Pair Minimum Free Energy Sequence Design Stochastic Local Search Frequency Distribution Curve 
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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Fumiaki Tanaka
    • 1
  • Atsushi Kameda
    • 2
  • Masahito Yamamoto
    • 2
    • 3
  • Azuma Ohuchi
    • 2
    • 3
  1. 1.Graduate School of EngineeringHokkaido UniversitySapporoJapan
  2. 2.CREST, Japan Science and Technology CorporationKawaguchi, SaitamaJapan
  3. 3.Graduate School of Information Science and TechnologyHokkaido UniversitySapporoJapan

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