Abstract:The design of DNA sequences is critical for many research fields such as DNA self-assembly, DNA hybridization arrays, DNA computing, and PCR-based applications. DNA secondary structure prediction is the key part for these DNA nanotechnologies. In this paper, we present a dynamic programming algorithm to predict the secondary structure of single-stranded DNA tiles. The algorithm calculates all possible maximum matches based on the nearest-neighbour model and global energy minimization. Experimental results show that the algorithm performers significantly to predict secondary structures for single-stranded DNA tiles.
To general 0-1 Integer Programming Problem, we present a semi-roboticized DNA computing model. Firstly, all potential solutions of the given 0-1 Integer Programming Problem are generated. Secondly, we set the probes corresponding to constraint inequalities of 0-1 Integer Programming problem, and use these probes to design semiroboticized apparatus for separating all potential solutions automatically. Finally, we obtain the solutions of the 0-1 Integer Programming Problem. The most merit of the model is its automation characteristic, and the model fits to solve arbitrary 0-1 Integer Programming problem having arbitrary variables. Index Terms -DNA computing; 0-1 integer programming problem; feasible solutions; semi-roboticized apparatus.
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