Boundary components of thickened graphs

Abstract

Using linear DNA segments and branched junction molecules many different three-dimensional DNA structures (graphs) could be selfassembled. We investigate maximum and minimum numbers of circular DNA that form these structures. For a given graph G, we consider compact orientable surfaces, called thickened graphs of G, that have G as a deformation retract. The number of boundary curves of a thickened graph G corresponds to the number of circular DNA strands that assemble into the graph G. We investigate how this number changes by recombinations or edge additions and relate to some results from topological graph theory.