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
Conference paper

DOI: 10.1007/11925903_27

Part of the Lecture Notes in Computer Science book series (LNCS, volume 4287)
Cite this paper as:
Ibrahim Z., Rose J.A., Tsuboi Y., Ono O., Khalid M. (2006) A New Readout Approach in DNA Computing Based on Real-Time PCR with TaqMan Probes. In: Mao C., Yokomori T. (eds) DNA Computing. DNA 2006. Lecture Notes in Computer Science, vol 4287. Springer, Berlin, Heidelberg

Abstract

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.

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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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