PARALLEL OVERLAP ASSEMBLY FOR THE CONSTRUCTION OF COMPUTATIONAL DNA LIBRARIES

Algorithms for computing with DNA currently require the construction o f pools of molecules in which each distinct molecule represents a diff erent starting point for the calculation. We have begun building such pools using the technique of parallel overlap assembly that is already used for the generation of diversity in biologically useful combinato rial search techniques such as gene shuffling. Unlike these applicatio ns, a pool in a molecular computer must be complete, containing all po ssible strands, and ordered, having minimal contamination from incorre ctly assembled DNA. We present an experiment in which parallel overlap assembly is used to construct a computational pool and an experiment in which this pool is used to solve the NP-complete maximal-clique pro blem. (C) 1997 Academic Press Limited.