Graph-theoretic Formalization of Hybridization in DNA Sticker Complexes

Abstract

Sticker complexes are a formal graph-based data model for a restricted class of DNA complexes, motivated by potential applications to databases. This data model allows for a purely declarative definition of hybridization. We introduce the notion of terminating hybridization, and characterize this notion in purely graph-theoretic terms. Terminating hybridization can still produce results of exponential size. We indicate a class of complexes where hybridization is guaranteed to be polynomially bounded.