In Silico Information Processing for DNA Computing Readout Method based on DNA Engine Opticon 2 System

M.F. Mohamed Saaid, Z. Ibrahim
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Abstract

In this paper, a novel readout approach for the Hamiltonian path problem (HPP) in DNA computing based on the real-time polymerase chain reaction (PCR) is proposed. Based on this approach, real-time amplification was performed with the TaqMan probes and the TaqMan detection mechanism was exploited for the design and development of the proposed readout approach. The readout approach consists of two phases: 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 the extraction of the Hamiltonian path. In this paper, instead of using manual clustering of two different reactions in real-time PCR, a computer system is developed such that the clustering can be done automatically. This clustering process can be done quickly based on the number of nodes in the HPP problems and the TaqMan reactions and the data obtained previously is used to extract the correct Hamiltonian path.
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基于DNA Engine Opticon 2系统的DNA计算读出方法的计算机信息处理
本文提出了一种基于实时聚合酶链反应(PCR)的DNA计算中哈密顿路径问题(HPP)的读出方法。基于该方法,使用TaqMan探针进行实时扩增,并利用TaqMan检测机制设计和开发了所提出的读出方法。读出方法包括两个阶段:使用基于TaqMan的实时PCR在体外进行实时扩增,然后在计算机上进行信息处理以评估实时扩增结果,进而提取哈密顿路径。本文开发了一种计算机系统,取代了实时PCR中对两种不同反应进行人工聚类的方法。基于HPP问题的节点数和TaqMan反应,该聚类过程可以快速完成,并使用先前获得的数据提取正确的哈密顿路径。
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