A new readout approach in DNA computing based on real-time PCR with taqman probes

  • Authors:

  • Zuwairie Ibrahim;John A. Rose;Yusei Tsuboi;Osamu Ono;Marzuki Khalid

  • Affiliations:

  • Center for Artificial Intelligence and Robotics, Department of Mechatronics and Robotics, Faculty of Electrical Engineering, Universiti Teknologi Malaysia, UTM Skudai, Johor Darul Takzim, Malaysia;Institute of Information Communication Technology, Ritsumeikan Asia Pacific University, Japan Science and Technology Agency-CREST, Oita, Japan;Bio-Mimetic Control Research Center, RIKEN, Nagoya, Japan;Institute of Applied DNA Computing, Meiji University, Japan;Center for Artificial Intelligence and Robotics, Department of Mechatronics and Robotics, Faculty of Electrical Engineering, Universiti Teknologi Malaysia, UTM Skudai, Johor Darul Takzim, Malaysia

  • Venue:
  • DNA'06 Proceedings of the 12th international conference on DNA Computing
  • Year:
  • 2006

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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.