NDLI: An improved readout method of molecular computation based on real-time PCR implemented on DNA Engine Opticon 2 System

Content Provider	IEEE Xplore Digital Library
Author	Ibrahim, Z. Saaid, M.F.M. Paramita, A.S. Suyama, A. Rose, J.A.
Copyright Year	2007
Description	Author affiliation: Univ. Teknologi Malaysia, Skudai (Ibrahim, Z.)
Abstract	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.
Starting Page	1829
Ending Page	1834
File Size	221415
Page Count	6
File Format	PDF
ISBN	9781424413393
DOI	10.1109/CEC.2007.4424695
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2007-09-25
Publisher Place	Singapore
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	DNA computing Optical computing Real time systems Engines Probes Optical polymers Information processing Stimulated emission Fluorescence Self-assembly TagMan probes DNA computation graduated PCR Hamiltonian path problem readout method real-time PCR
Content Type	Text
Resource Type	Article

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