10.1021/ja992392j.s001
Michael C. Pirrung
Richard V. Connors
Amy L. Odenbaugh
Michael P. Montague-Smith
Nathan G. Walcott
Jeff J. Tollett
The Arrayed Primer Extension Method for DNA Microchip Analysis.
Molecular Computation of Satisfaction Problems
2000
American Chemical Society
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 00:00:00
article
https://acs.figshare.com/articles/journal_contribution/The_Arrayed_Primer_Extension_Method_for_DNA_Microchip_Analysis_Molecular_Computation_of_Satisfaction_Problems/3676467
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.