%0 DATA
%A Michael C., Pirrung
%A Richard V., Connors
%A Amy L., Odenbaugh
%A Michael P., Montague-Smith
%A Nathan G., Walcott
%A Jeff J., Tollett
%D 2000
%T The Arrayed Primer Extension Method for DNA Microchip Analysis.
Molecular Computation of Satisfaction Problems
%U https://acs.figshare.com/articles/The_Arrayed_Primer_Extension_Method_for_DNA_Microchip_Analysis_Molecular_Computation_of_Satisfaction_Problems/3676467
%R 10.1021/ja992392j.s001
%2 https://acs.figshare.com/ndownloader/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.