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An improved readout method of molecular computation based on real-time PCR implemented on DNA engine opticon 2 system

Ibrahim, Zuwairie and Mohamed Saaid, Muhammad Faiz and S. Paramita, Adi and Akira, Suyama and Rose, John A. (2007) An improved readout method of molecular computation based on real-time PCR implemented on DNA engine opticon 2 system. In: 2007 IEEE Congress on Evolutionary Computation, CEC 2007. Institute of Electrical and Electronics Engineers, New York, 1829 -1834. ISBN 978-142441340-9

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Official URL: http://dx.doi.org/10.1109/CEC.2007.4424695


A readout approach for the Hamiltonian Path Problem (HPP) in DNA computing based on the real-time polymerase chain reaction (PCR) is re-implemented on DNA Engine Opticon 2 System. Several types of fluorescent probes and detection mechanisms are currently employed in real-time PCR, including SYBR Green, molecular beacons, and hybridization probes. Based on the new approach, 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. In this study, 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 experimental result is compared with that of previously implementation on Roche LightCycler System. Experimental results establish an easier method to interpret the output of real-time PCR for the subsequent in silico information processing.

Item Type:Book Section
Additional Information:2007 IEEE Congress on Evolutionary Computation, CEC 2007; 25 September 2007 through 28 September 2007
Uncontrolled Keywords:DNA computation, graduated PCR, hamiltonian path problem, readout method, real-time PCR, TaqMan probes
Subjects:Q Science > QC Physics
T Technology > TK Electrical engineering. Electronics Nuclear engineering
Divisions:Electrical Engineering
ID Code:12496
Deposited By: Liza Porijo
Deposited On:03 Jun 2011 05:20
Last Modified:02 Oct 2017 07:47

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