Universiti Teknologi Malaysia Institutional Repository

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

Ibrahim, Zuwairie and Rose, John A. and Suyama, Akira and Khalid, Marzuki (2008) Experimental implementation and analysis of a DNA computing readout method based on real-time PCR with TaqMan probes. Natural Computing , 7 (2). 277 -286. ISSN 1567-7818

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Official URL: http://www.springerlink.com/content/274762236w14u7...

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.

Item Type:Article
Uncontrolled Keywords:DNA computation, graduated PCR, hamiltonian path problem, readout method, real-time PCR, taqman probes
Subjects:T Technology > TK Electrical engineering. Electronics Nuclear engineering
Divisions:Electrical Engineering
ID Code:12563
Deposited By: Liza Porijo
Deposited On:09 Jun 2011 08:20
Last Modified:09 Jun 2011 08:20

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