DNA Computing Model of the Integer Linear Programming Problem Based on Molecular Beacon

  • Zhi-xiang Yin
  • Jian-zhong Cui
  • Jin Yang
  • Jin Xu
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4115)


Biological chip technology and DNA computing are new research areas in biology science and information science separately. The essential characteristic of both is the massive parallel of obtaining and managing information. The integer linear programming problem is an important problem in opsearch and it is an NP-complete problem. But up to now, there does not exist any good algorithm yet. A new DNA computing model is provided to solve a integer linear programming problem based on Molecular Beacon chip. In the method, the integer linear programming problem is solved with molecular beacon by fluorescing upon hybridization to their complementary DNA targets. The method has some significant advantages such as simple encoding, excellent sensitivity, high selectivity, low cost, low error, short operating time, reusable surface and simple experimental steps. The result suggest s the potential of Molecular Beacon used as a DNA computer chip.


Maximal Clique Complementary Strand Molecular Beacon Satisfiability Problem Integer Linear Programming Problem 
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.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Feynmam, R.P.: In: Gilbart, D.H. (ed.) Minaturization, Reinhold, New York, pp. 282–296 (1961)Google Scholar
  2. 2.
    Ouyang, Q.P., Kaplan, D.S., Liu, M., libchaber, A.: DNA Solution of the Maximal Clique Problem. Science 278, 446–449 (1997)CrossRefGoogle Scholar
  3. 3.
    Christos, H., Papadimitriou: Papadimitriou. In: Combinatorial Optimization: Algorithms and Complexity, Prentice-Hall, Inc., Englewood Cliffs, New Jersey (1989)Google Scholar
  4. 4.
    Cox, J.C.: The Complexities of DNA Computation. Tibtech 17, 151–154 (1996)Google Scholar
  5. 5.
    Adleman, L.M.: Molecular Computation of Solutions to Combinatorial Problems. Science 266, 1021–1023 (1994)CrossRefGoogle Scholar
  6. 6.
    Lipton, R.J.: DNA Solution of Hard Computational Problems. Science 268, 542–545 (1995)CrossRefGoogle Scholar
  7. 7.
    Liu, Q.: DNA Computing on Surfaces. Nature 403, 175–179 (2000)CrossRefGoogle Scholar
  8. 8.
    Wu, H.Y.: An Improved Surface-based Method for DNA Computation. Biosystem 59, 1–5 (2001)CrossRefGoogle Scholar
  9. 9.
    Yin, Z.X., Zhang, F.Y.A., Xu, J.: A Chinese Postman Problem Based on DNA Computing. Journal of Chemical Information and Computing Science 42, 222–224 (2002)Google Scholar
  10. 10.
    Head, T.: Formal Language Theory and DNA: an Analysis of the Generative Capacity of Specific Recombinant Behaviors. Bull. Math. Biol. 49, 737–759 (1997)MathSciNetGoogle Scholar
  11. 11.
    Liu, Q.: Progress Toward Demonstration of a Surface Based DNA Computation: a One Word Approach to Solve a Model Satisfiability Problem. Biosystems 52, 25–33 (1999)CrossRefGoogle Scholar
  12. 12.
    Sakamoto, K.G.A.: Hidetaka, et al.: Molecular Computation by DNA Hairpin Formation. Science 288, 1223–1226 (2000)CrossRefGoogle Scholar
  13. 13.
    Braich, R.S.: Solution of a 20-Variable 3-SAT Problem on a DNA Computer. Science 296, 499–502 (2002)CrossRefGoogle Scholar
  14. 14.
    Yin, Z.X., Zhang, F.Y.A., Xu, J.: The General Form of 0-1 Programming Problem Based on DNA Computing. Biosystems 70, 73–78 (2003)CrossRefGoogle Scholar
  15. 15.
    Wang, S.Y.A., Yang, A.M.: DNA Solution of Integer Linear Programming. Applied Mathematics and Computation 17, 626–632 (2005)CrossRefGoogle Scholar
  16. 16.
    Bondy, J.A., Murty, U.S.R.: Graph Theory with Applications. The Macmillan Press LTD, New York (1976)Google Scholar
  17. 17.
    Gass, S.L.: Linear Programming Methods and Applications, 5th edn. Mc Graw Hill Book company (1988)Google Scholar
  18. 18.
    Wang, Y.J., Wang, H., Lie, L.B., et al.: The Molecular Beacon Technology. Hua xue tong bao 67(12), 912–918 (2004)Google Scholar
  19. 19.
    Fang, X.H., Liu, X.J., Schuster, S., et al.: Designing a Novel Molecular Beacon for Surface Immobilized DNA Hybridization Studies. J. Am. Chem. Soc. 121, 2921–2922 (1999)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Zhi-xiang Yin
    • 1
    • 2
  • Jian-zhong Cui
    • 1
  • Jin Yang
    • 1
  • Jin Xu
    • 1
  1. 1.Department of Mathematics and PhysicsAnhui University of Science and TechnologyAnhui HuainanChina
  2. 2.Department of Control Science and EngineeringHuazhong University of Science and TechnologyHuibei WuhanChina

Personalised recommendations