Pirrung, Michael C.
Connors, Richard V.
Odenbaugh, Amy L.
Montague-Smith, Michael P.
Walcott, Nathan G.
Tollett, Jeff J.
The Arrayed Primer Extension Method for DNA Microchip Analysis.
Molecular Computation of Satisfaction Problems
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.
polynomial time;Primer EXtension;Molecular Computation;DNA polymerase extension;APEX;DNA computer;complex;NP;method;Primer Extension Method;DNA Microchip Analysis;primer;Boolean formula;solution;Satisfaction Problems;DNA microchips;nondeterministic polynomial time;problem size;3 SAT;acid analysis
2000-02-19
https://acs.figshare.com/articles/The_Arrayed_Primer_Extension_Method_for_DNA_Microchip_Analysis_Molecular_Computation_of_Satisfaction_Problems/3676467

10.1021/ja992392j.s001