Automation of A DNA computing readout method based on real-time PCR implemented on a lightcycler system

A DNA computer readout approach based on real-time polymerase chain reaction (PCR) for the computation of Hamiltonian Path Problem (HPP) is the main interest in this research. Based on this methodology, real-time amplification of DNA template with TaqMan probes is performed with some modifications to realize the readout. The readout approach consists of two phases: Real-time amplification in vitro followed by information processing in silico to assess the results of real-time amplification. The in silico information processing enables the extraction of the Hamiltonian path but the Taq-Man "YES" and "NO" reactions produced by real-time PCR need to be identified manually beforehand. Manual identification or classification limits the capability of automated readout. Hence, in this study, the readout approach is further improved by incorporating Fuzzy C-means clustering algorithm in the in silico information processing phase. As a result, automatic classification of the TaqMan "YES" and "NO" reactions is possible as demonstrated by the experimental results. Finally, an automated readout method can be realized as supported by the advantages of real-time PCR and Fuzzy C-means clustering algorithm.