Progress toward demonstration of a surface based DNA computation: a one word approach to solve a model satisfiability problem

A multi-base encoding strategy is used in a one word approach to surface-ba sed DNA computation. In this designed DNA model system, a set of 16 oligonu cleotides, each a 16mer, is used with the format 5'-FFFFvvvvvvvvFFFF-3' in which 4-8 bits of data are stored in eight central variable ('v') base loca tions, and the remaining fixed ('F') base locations are used as a word labe l. The detailed implementations are reported here. In order to achieve perf ect discrimination between each oligonucleotide, the efficiency and specifi city of hybridization discrimination of the set of 16 oligonucleotides were examined by carrying out the hybridization of each individual fluorescentl y tagged complement to an array of 16 addressed immobilized oligonucleotide s. A series of preliminary hybridization experiments are presented and furt her studies about hybridization, enzymatic destruction, read out and demons trations of a SAT problem are forthcoming. (C) 1999 Elsevier Science Irelan d Ltd. All rights reserved.