Generating DNA Code Word for DNA Computing with Real-Time PCR

M.F.M. Saaid, Z. Ibrahim, and N.H. Sarmin (Malaysia)


DNA Computing, Real-Time PCR, TaqMan probes.


A number of DNA computing models to solve mathematical graph problem such as the Hamiltonian Path Problem (HPP), Traveling Salesman Problem (TSP), and the Shortest Path Problem (SPP) have been proposed and demonstrated. Normally, the DNA sequences used for the computation should be critically designed in order to reduce error that could occur during computation. In 2007, we proposed a DNA computing readout method tailored specifically to HPP in DNA computing using real-time Polymerase Chain Reaction (PCR). We also proposed a procedure for DNA sequence design for DNA computation with output visualization on real-time PCR machine. The procedure includes DNASequenceGenerator which generate all the required sequences implemented in the experiment. In this paper, we propose different procedures by using generate-and test algorithm with several design constraints to get all the DNA sequences. The generated DNA sequences represent nodes, edges, primers, and probes that are used in DNA computation of HPP with output visualization based on real-time PCR.

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