Graph-theoretic formalization of hybridization in DNA sticker complexes. (English)
Cardelli, Luca (ed.) et al., DNA computing and molecular programming. 17th international conference, DNA 17, Pasadena, CA, USA, September 19‒23, 2011. Proceedings. Berlin: Springer (ISBN 978-3-642-23637-2/pbk). Lecture Notes in Computer Science 6937, 49-63 (2011).
Summary: 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.