Automation of DNA computing readout method based on real-time PCR implemented on DNA engine opticon 2 system

Muhammad Faiz Mohamed Saaid, Ismail Ibrahim, Shahdan Sudin, Mohd Saberi Mohamad, Zulkifli Md Yusof, Jameel Abdulla Ahmed Mukred, Kamal Khalil, Zuwairie Ibrahim, Junzo Watada

    Research output: Contribution to journalArticle

    1 Citation (Scopus)

    Abstract

    Previously, an automation of a DNA computing readout method for the Hamiltonian Path Problem (HPP) has been implemented based on LightCycler System. In this study, a similar readout approach is implemented based on DNA Engine Opticon 2 System. The readout approach consists of two steps: real-time amplification in vitro using TaqMan-based real-time PCR, followed by an in silico phase. The in silico phase consists of a data clustering algorithm and an information processing to extract the Hamiltonian path after the TaqMan \YES and \NO reactions have been identified. The result indicates that the automation of DNA computing readout method can be efficiently implemented on DNA Engine Opticon 2 System.

    Original languageEnglish
    Pages (from-to)1907-1916
    Number of pages10
    JournalInternational Journal of Innovative Computing, Information and Control
    Volume8
    Issue number3 A
    Publication statusPublished - 2012 Mar

    Fingerprint

    DNA Computing
    Automation
    Hamiltonian path
    Engine
    DNA
    Engines
    Real-time
    Hamiltonians
    Data Clustering
    Information Processing
    Amplification
    Clustering Algorithm
    Clustering algorithms

    Keywords

    • Dna computing
    • Hamiltonian path problem
    • Real-time PCR

    ASJC Scopus subject areas

    • Computational Theory and Mathematics
    • Information Systems
    • Software
    • Theoretical Computer Science

    Cite this

    Saaid, M. F. M., Ibrahim, I., Sudin, S., Mohamad, M. S., Yusof, Z. M., Mukred, J. A. A., ... Watada, J. (2012). Automation of DNA computing readout method based on real-time PCR implemented on DNA engine opticon 2 system. International Journal of Innovative Computing, Information and Control, 8(3 A), 1907-1916.

    Automation of DNA computing readout method based on real-time PCR implemented on DNA engine opticon 2 system. / Saaid, Muhammad Faiz Mohamed; Ibrahim, Ismail; Sudin, Shahdan; Mohamad, Mohd Saberi; Yusof, Zulkifli Md; Mukred, Jameel Abdulla Ahmed; Khalil, Kamal; Ibrahim, Zuwairie; Watada, Junzo.

    In: International Journal of Innovative Computing, Information and Control, Vol. 8, No. 3 A, 03.2012, p. 1907-1916.

    Research output: Contribution to journalArticle

    Saaid, MFM, Ibrahim, I, Sudin, S, Mohamad, MS, Yusof, ZM, Mukred, JAA, Khalil, K, Ibrahim, Z & Watada, J 2012, 'Automation of DNA computing readout method based on real-time PCR implemented on DNA engine opticon 2 system', International Journal of Innovative Computing, Information and Control, vol. 8, no. 3 A, pp. 1907-1916.
    Saaid, Muhammad Faiz Mohamed ; Ibrahim, Ismail ; Sudin, Shahdan ; Mohamad, Mohd Saberi ; Yusof, Zulkifli Md ; Mukred, Jameel Abdulla Ahmed ; Khalil, Kamal ; Ibrahim, Zuwairie ; Watada, Junzo. / Automation of DNA computing readout method based on real-time PCR implemented on DNA engine opticon 2 system. In: International Journal of Innovative Computing, Information and Control. 2012 ; Vol. 8, No. 3 A. pp. 1907-1916.
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