DNA computing model of graph isomorphism based on three dimensional DNA graph structures

Abstract

An DNA computing model of solving the graph isomorphism problem with 3-D DNA structures is proposed in this paper. The k-armed branched junction molecules are used to encode k-degree vertices. Double stranded molecules are used to encode edges. These molecules are to be mixed in a test tube to be ligated. The reaction product can be detected by gel electrophoresis. The time complexity of the algorithm is o(n2), where n is the number of vertices of the graph. © Springer-Verlag Berlin Heidelberg 2005.