The Arrayed Primer Extension Method for DNA Microchip Analysis. Molecular Computation of Satisfaction Problems
journal contributionposted on 19.02.2000 by Michael C. Pirrung, Richard V. Connors, Amy L. Odenbaugh, Michael P. Montague-Smith, Nathan G. Walcott, Jeff J. Tollett
Any type of content formally published in an academic journal, usually following a peer-review process.
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.