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

In this paper, an automation of DNA computing readout method based on real-time Polymerase Chan Reaction (PCR) is developed, which employs a hybrid in vitro-in silico approach. In the in vitro phase, TaqMan-based real-time PCR reactions are performed in parallel, to investigate the ordering of pairs of nodes in the Hamiltonian Path Problem (HPP), in terms of relative distance from the DNA sequence encoding the known start node. The real-time PCR experiment is implemented on DNA Engine Opticon II system. Alternative Fuzzy C-Means (AFCM) clustering algorithm is used to identify automatically two different reactions in real-time PCR, followed by in silico algorithm, which in turn, enables extraction of the Hamiltonian path. A software called “SILICOIN” is built to implement the AFCM clustering and the in silico algorithm, which return the desired Hamiltonian path.

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