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

Authors:
Zuwairie Ibrahim;John A. Rose;Akira Suyama;Marzuki Khalid
Affiliations:
Department of Mechatronics and Robotics, Faculty of Electrical Engineering, Center for Artificial Intelligence and Robotics (CAIRO), Universiti Teknologi Malaysia, Johor Darul Takzim, Malaysia 813 ...;Institute of Information Communication Technology, Ritsumeikan Asia Pacific University, Oita, Japan 874-8577 and J.S.T.-CREST, Kawaguchi, Japan;Department of Life Sciences and the Institute of Physics, University of Tokyo, Tokyo, Japan and J.S.T.-CREST, Kawaguchi, Japan;Department of Mechatronics and Robotics, Faculty of Electrical Engineering, Center for Artificial Intelligence and Robotics (CAIRO), Universiti Teknologi Malaysia, Johor Darul Takzim, Malaysia 813 ...
Venue:
Natural Computing: an international journal
Year:
2008

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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 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.