Automation of DNA Computing Readout Method Implemented on LightCycler 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 LightCycler system. Fuzzy C-Means (FCM) 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 SILICOLIGHT is built to implement the FCM clustering and the in silico algorithm, which return the desired Hamiltonian path.