Natural Computing

, Volume 7, Issue 2, pp 277–286

Experimental implementation and analysis of a DNA computing readout method based on real-time PCR with TaqMan probes

  • Zuwairie Ibrahim
  • John A. Rose
  • Akira Suyama
  • Marzuki Khalid

DOI: 10.1007/s11047-007-9047-7

Cite this article as:
Ibrahim, Z., Rose, J.A., Suyama, A. et al. Nat Comput (2008) 7: 277. doi:10.1007/s11047-007-9047-7


A new readout approach for the Hamiltonian Path Problem (HPP) in DNA computing based on the real-time polymerase chain reaction (PCR) is experimentally implemented and analyzed. 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 140 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.


DNA computationGraduated PCRHamiltonian path problemReadout methodReal-time PCRTaqMan probes





Double-stranded DNA


Fluorescence Resonance Energy Transfer


Hamiltonian Path Problem


Polymerase Chain Reaction


Single-stranded DNA


Traveling Salesman Problem

Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  • Zuwairie Ibrahim
    • 1
  • John A. Rose
    • 2
    • 4
  • Akira Suyama
    • 3
    • 4
  • Marzuki Khalid
    • 1
  1. 1.Department of Mechatronics and Robotics, Faculty of Electrical EngineeringCenter for Artificial Intelligence and Robotics (CAIRO), Universiti Teknologi MalaysiaJohor Darul TakzimMalaysia
  2. 2.Institute of Information Communication TechnologyRitsumeikan Asia Pacific UniversityOitaJapan
  3. 3.Department of Life Sciences and the Institute of PhysicsUniversity of TokyoTokyoJapan
  4. 4.J.S.T.-CRESTKawaguchiJapan