Advertisement

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)

Abstract

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.

Keywords

Base Pair Minimum Free Energy Sequence Design Stochastic Local Search Frequency Distribution Curve 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Faulhammer, D., Cukras, A.R., Lipton, R.J., Landweber, L.F.: Molecular computation: RNA solutions to chess problems. Proc. Natl. Acad. Sci. U S A 97(4), 1385–1389 (2000)CrossRefGoogle Scholar
  2. 2.
    Braich, R.S., Chelyapov, N., Johnson, C., Rothemund, P.K., Adleman, L.: Solution of a 20-variable 3-SAT problem on a DNA computer. Science 296(5567), 499–502 (2002)CrossRefGoogle Scholar
  3. 3.
    Yan, H., Zhang, X., Shen, Z., Seeman, N.C.: A robust DNA mechanical device controlled by hybridization topology. Nature 415(6867), 62–65 (2002)CrossRefGoogle Scholar
  4. 4.
    Shih, W.M., Quispe, J.D., Joyce, G.F.: A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron. Nature 427(6975), 618–621 (2004)CrossRefGoogle Scholar
  5. 5.
    Arita, M., Kobayashi, S.: DNA sequence design using templates. New Generation Computing 20, 263–277 (2002)CrossRefMATHGoogle Scholar
  6. 6.
    Tulpan, D., Hoos, H., Condon, A.: Stochastic local search algorithms for DNA word design. In: Hagiya, M., Ohuchi, A. (eds.) DNA 2002. LNCS, vol. 2568, pp. 229–241. Springer, Heidelberg (2003)CrossRefGoogle Scholar
  7. 7.
    Kashiwamura, S., Kameda, A., Yamamoto, M., Ohuchi, A.: Two-step search for DNA sequence design. In: IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences Special Section on Papers Slected from 2003 International Technical Conference on Circuts/Systems, Computer and Communications (ITC-CSCC 2003), vol. E87-A(6), pp. 1446–1453 (2004)Google Scholar
  8. 8.
    Tanaka, F., Kameda, A., Yamamoto, M., Ohuchi, A.: Design of nucleic acid sequences for DNA computing based on a thermodynamic approach. Nucleic Acids Res. 33(3), 903–911 (2005)CrossRefGoogle Scholar
  9. 9.
    Sen, D., Gilbert, W.: Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis. Nature 334(6180), 364–366 (1988)CrossRefGoogle Scholar
  10. 10.
    Garzon, M., Deaton, R., Neather, P., Franceschetti, D.R., Murphy, R.C.: A new metric for DNA computing. In: Poceedings of 2nd Annual Genetic Programming Conference, vol. GP-97, pp. 472–478 (1997)Google Scholar
  11. 11.
    Zuker, M., Stiegler, P.: Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 9(1), 133–148 (1981)CrossRefGoogle Scholar
  12. 12.
    Gray, D.M., Hung, S.H., Johnson, K.H.: Absorption and circular dichroism spectroscopy of nucleic acid duplexes and triplexes. Methods Enzymol. 246, 19–34 (1995)CrossRefGoogle Scholar
  13. 13.
    Tanaka, F., Kameda, A., Yamamoto, M., Ohuchi, A.: Thermodynamic parameters based on a nearest-neighbor model for DNA sequences with a single-bulge loop. Biochemistry 43(22), 7143–7150 (2004)CrossRefMATHGoogle Scholar

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

Personalised recommendations