Towards a Solution for the Shortest Common Superstring Problem

This paper proposes a DNA algorithm for solving an NP-complete problem (The Shortest Common Superstring Problem) by manipulation of biomolecules, and presents partial results of the experiment that implements our algorithm. The solution to this and other problems that use hybridization requires strict attention to the practical problems of hybridization. The most important aspects are the decreasing speciicity of hybridization with increasing oligonucleotide length and the impact of base sequence on the stability of DNA molecules. These limitations were taken into account in our coding of the DNA strands for the input patterns. A second problem is the requirement for a controlled experimental system, in which spurious results can be ruled out. We discuss our experimental assay and show experiments indicating that the nal results can be trusted both if the answer is yes and if it is no.