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

Authors

    • Department of Mechatronics and Robotics, Faculty of Electrical EngineeringCenter for Artificial Intelligence and Robotics (CAIRO), Universiti Teknologi Malaysia
  • John A. Rose
    • Institute of Information Communication TechnologyRitsumeikan Asia Pacific University
    • J.S.T.-CREST
  • Akira Suyama
    • Department of Life Sciences and the Institute of PhysicsUniversity of Tokyo
    • J.S.T.-CREST
  • Marzuki Khalid
    • Department of Mechatronics and Robotics, Faculty of Electrical EngineeringCenter for Artificial Intelligence and Robotics (CAIRO), Universiti Teknologi Malaysia
Article

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

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.

Keywords

DNA computationGraduated PCRHamiltonian path problemReadout methodReal-time PCRTaqMan probes

Abbreviation

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

Copyright information

© Springer Science+Business Media B.V. 2007