Under this project tools are being developed to increase the computational generality of surface-based DNA computing. It is well known that for a computing model to be general, that is, capable of efficiently simulating algorithms used in conventional electronic computing, it must be able to efficiently simulate circuits. It has been shown theoretically that the surface-based approach, when using multiple words and the MARK, DESTROY-UNMARKED, UNMARK, and APPEND operations, is a generalizable approach to computing, but this has not been implemented experimentally. The necessary tools for such an implementation is being developed. Particular tasks, which are being addressed to this end, include:
-improved designs of sets of DNA "words" that do not interfere with one another in hybridization experiments and do not contain strong secondary structure motifs.
-methods for the efficient purification of colloidal gold nanoparticles and the implementation of surface-based DNA computing using such particles as supports.
-development of a new DESTROY-UNMARKED operation, multiple-word AND operation, and multiple-word APPEND-MARKED operation.