Spectrum of a pot for DNA complexes

Abstract

Given a set of flexible branched junction DNA molecules (building blocks) with sticky ends we consider the question of determining the proper stoichiometry such that all sticky ends could end up connected. The idea is to determine the proper proportion (spectrum) of each type of molecules present, which in general is not uniform. We classify the pot in three classes: weakly satisfiable, satisfiable and strongly satisfiable according to possible components that assemble in complete complexes. This classification is characterized through the spectrum of the pot, which can be computed in PTIME using the standard Gauss-Jordan elimination method. © 2006 Springer-Verlag.