The Arrayed Primer Extension Method for DNA Microchip Analysis.
Molecular Computation of Satisfaction Problems
PirrungMichael C.
ConnorsRichard V.
OdenbaughAmy L.
Montague-SmithMichael P.
WalcottNathan G.
TollettJeff J.
2000
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.