%0 Journal Article %A Pirrung, Michael C. %A Connors, Richard V. %A Odenbaugh, Amy L. %A Montague-Smith, Michael P. %A Walcott, Nathan G. %A Tollett, Jeff J. %D 2000 %T The Arrayed Primer Extension Method for DNA Microchip Analysis. Molecular Computation of Satisfaction Problems %U https://acs.figshare.com/articles/journal_contribution/The_Arrayed_Primer_Extension_Method_for_DNA_Microchip_Analysis_Molecular_Computation_of_Satisfaction_Problems/3676467 %R 10.1021/ja992392j.s001 %2 https://ndownloader.figshare.com/files/5766228 %K polynomial time %K Primer EXtension %K Molecular Computation %K DNA polymerase extension %K APEX %K DNA computer %K complex %K NP %K method %K Primer Extension Method %K DNA Microchip Analysis %K primer %K Boolean formula %K solution %K Satisfaction Problems %K DNA microchips %K nondeterministic polynomial time %K problem size %K 3 SAT %K acid analysis %X A high fidelity, surface-based method of nucleic acid analysis has been developed based on DNA polymerase extension of primer−template complexes on DNA microchips. The ability of the method to discriminate against mismatches and provide an almost “digital” signal recommended it for molecular computation. A DNA computer with the capability of solving nondeterministic polynomial time (NP)-complete problems (those whose time−complexity function rises exponentially with the problem size) in polynomial time using this Arrayed Primer EXtension (APEX) method was experimentally demonstrated. An algorithm involving extension of surface-bound primer−template complexes, representing solutions and clauses of a Boolean formula, is described for the solution of two-, three-, and four-variable satisfiability (SAT) problems, including a 3SAT, exploiting the theoretical concepts of Lipton. A discussion of the principles of nondeterministic computing with APEX is also provided. %I ACS Publications