A New Readout Approach in DNA Computing Based on Real-Time PCR with TaqMan Probes

  • Zuwairie Ibrahim
  • John A. Rose
  • Yusei Tsuboi
  • Osamu Ono
  • Marzuki Khalid
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4287)


A new readout approach for the Hamiltonian Path Problem (HPP) in DNA computing based on the real-time polymerase chain reaction (PCR) is investigated. Several types of fluorescent probes and detection mechanisms are currently employed in real-time PCR, including SYBR Green, molecular beacons, and hybridization probes. In this study, real-time amplification performed using the TaqMan probes is adopted, as the TaqMan detection mechanism can be exploited for the design and development of the proposed readout approach. Double-stranded DNA molecules of length 120 base-pairs are selected as the input molecules, which represent the solving path for an HPP instance. These input molecules are prepared via the self-assembly of 20-mer and 30-mer single-stranded DNAs, by parallel overlap assembly. The proposed readout approach consists of two steps: real-time amplification in vitro using TaqMan-based real-time PCR, followed by information processing in silico to assess the results of real-time amplification, which in turn, enables extraction of the Hamiltonian path. The performance of the proposed approach is compared with that of conventional graduated PCR. Experimental results establish the superior performance of the proposed approach, relative to graduated PCR, in terms of implementation time.


TaqMan Probe Hamiltonian Path Amplification Plot Hamiltonian Path Problem Input Molecule 
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  1. 1.
    Mullis, K., et al.: Specific Enzymatic Amplification of DNA in vitro: The Polymerase Chain Reaction. In: Cold Spring Harbor Symposium on Quantitative Biology, vol. 51, pp. 263–273 (1986)Google Scholar
  2. 2.
    Overbergh, L., et al.: The Use of Real-Time Reverse Transcriptase PCR for the Quantification of Cytokine Gene Expression. Journal of Biomolecular Techniques 14, 33–43 (2003)Google Scholar
  3. 3.
    Walker, N.J.: A Technique Whose Time Has Come. Science 296, 557–559 (2002)CrossRefGoogle Scholar
  4. 4.
    Bubner, B., Baldwin, I.T.: Use of Real-Time PCR for Determining Copy Number and Zygosity in Transgenic Plants. Plant Cell Reports 23, 263–271 (2004)CrossRefGoogle Scholar
  5. 5.
    Heid, C.A., et al.: Real-Time Quantitative PCR. Genome Research 6, 986–994 (1996)CrossRefGoogle Scholar
  6. 6.
    Holland, P.M., et al.: Detection of Specific Polymerase Chain Reaction Product by Utiliz-ing the 5’→3’ Exonuclease Activity of Termus Aquaticus DNA Polymerase. Proceedings of the National Academy of Sciences of the United States of America 88, 7276–7280 (1991)CrossRefGoogle Scholar
  7. 7.
    Adleman, L.: Molecular Computation of Solutions to Combinatorial Problems. Science 266, 1021–1024 (1994)CrossRefGoogle Scholar
  8. 8.
    Rose, J.A., et al.: The Effect of Uniform Melting Temperatures on the Efficiency of DNA Computing. In: DIMACS Workshop on DNA Based Computers III, pp. 35–42 (1997)Google Scholar
  9. 9.
    Wood, D.H.: A DNA Computing Algorithm for Directed Hamiltonian Paths. In: Proceedings of the Third Annual Conference on Genetic Programming, pp. 731–734 (1998)Google Scholar
  10. 10.
    Wood, D.H., et al.: Universal Biochip Readout of Directed Hamiltonian Path Problems. LNCS, vol. 2568, pp. 168–181. Springer, Heidelberg (1999)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Zuwairie Ibrahim
    • 1
  • John A. Rose
    • 2
  • Yusei Tsuboi
    • 3
  • Osamu Ono
    • 4
  • Marzuki Khalid
    • 1
  1. 1.Center for Artificial Intelligence and Robotics, Department of Mechatronics and Robotics, Faculty of Electrical EngineeringUniversiti Teknologi MalaysiaUTM Skudai, Johor Darul TakzimMalaysia
  2. 2.Institute of Information Communication TechnologyRitsumeikan Asia Pacific University, Japan Science and Technology Agency-CRESTOitaJapan
  3. 3.Bio-Mimetic Control Research Center, RIKENNagoyaJapan
  4. 4.Institute of Applied DNA ComputingMeiji UniversityJapan

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