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

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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.

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Abbreviations

bp:

Base-pairs

dsDNA:

Double-stranded DNA

FRET:

Fluorescence Resonance Energy Transfer

HPP:

Hamiltonian Path Problem

PCR:

Polymerase Chain Reaction

ssDNA:

Single-stranded DNA

TSP:

Traveling Salesman Problem

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Acknowledgments

Zuwairie Ibrahim is very grateful to Ritsumeikan Asia Pacific University (APU) for kindly granting a research subsidy to support his expenses during laboratory experimental work at APU. This work was also partially supported by a eScienceFund Research Funding (Vot No. 79033; Z. Ibrahim, N.H. Sarmin, M. Khalid), from the Ministry of Science, Technology, and Innovation (MOSTI), Malaysia, a Grant-in-Aid for Scientific Research B (18300100; J. Rose, A. Suyama), from the Japan Society for the Promotion of Science (JSPS), and JST-CREST (A. Suyama, J. Rose).

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Authors and Affiliations

  1. Department of Mechatronics and Robotics, Faculty of Electrical Engineering, Center for Artificial Intelligence and Robotics (CAIRO), Universiti Teknologi Malaysia, UTM Skudai, 81310, Johor Darul Takzim, Malaysia

    Zuwairie Ibrahim & Marzuki Khalid

  2. Institute of Information Communication Technology, Ritsumeikan Asia Pacific University, 1-1 Jumonjibaru, Beppu-shi, 874-8577, Oita, Japan

    John A. Rose

  3. Department of Life Sciences and the Institute of Physics, University of Tokyo, Tokyo, Japan

    Akira Suyama

  4. J.S.T.-CREST, Kawaguchi, Japan

    John A. Rose & Akira Suyama

Authors
  1. Zuwairie Ibrahim
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  2. John A. Rose
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  3. Akira Suyama
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  4. Marzuki Khalid
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Correspondence to Zuwairie Ibrahim.

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Ibrahim, Z., Rose, J.A., Suyama, A. et al. Experimental implementation and analysis of a DNA computing readout method based on real-time PCR with TaqMan probes. Nat Comput 7, 277–286 (2008). https://doi.org/10.1007/s11047-007-9047-7

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  • DOI: https://doi.org/10.1007/s11047-007-9047-7

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