Abstract. A new readout approach for the Hamiltonian Path Problem (HPP) in DNA computing based on the real-time polymerase chain reaction (PCR) is investigated. Several types of fluorescent probes and detection mechanisms are currently employed in real-time PCR, including SYBR Green, molecular beacons, and hybridization probes. In this study, real-time amplification performed using the TaqMan probes is adopted, as the TaqMan detection mechanism can be exploited for the design and development of the proposed readout approach. Doublestranded DNA molecules of length 120 base-pairs are selected as the input molecules, which represent the solving path for an HPP instance. These input molecules are prepared via the self-assembly of 20-mer and 30-mer single-stranded DNAs, by parallel overlap assembly. The proposed readout approach consists of two steps: 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 extraction of the Hamiltonian path. The performance of the proposed approach is compared with that of conventional graduated PCR. Experimental results establish the superior performance of the proposed approach, relative to graduated PCR, in terms of implementation time. 172 1

A novel approach to phylogenetic tree construction using stochastic optimization and clustering

Abstract—Molecular computing has proved its possibility to solve weighted graph problem such as Hamiltonian Path Problem (HPP), Traveling Salesman Problem (TSP)

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Abstract: Problem Statement: 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 a computation. Previously, we have proposed a DNA computing readout method tailored specifically to HPP in DNA computing using real-time Polymerase Chain Reaction (PCR). The DNA sequences were designed based on a procedure and DNASequenceGenerator was employed to generate the sequences required for the experiment. The drawback of the previous approach is that a pool of DNA sequences need to be generated by DNASequenceGenerator before the selection is done manually, based on several design constraints. Hence, an automatic and systematic approach is needed to generate the DNA sequences based on design constraints. Approach: In this study, a generate-and-test approach was proposed for the same problem subjected to several design constraints. The generateand-test algorithm consists of two main levels. The first level considered the basic constraints of DNA sequence design, which were melting temperature, GC-percentage, similarity, continuity, hairpin, and H-measure. This was followed by the second level that includes specific constraints formulated based

This is an Open Access article distributed under the terms of the Creative Commons Attribution License