Multiple Word DNA Computing on Surfaces

The enzymatic manipulation of DNA molecules immobilized on a surface that each contain linked, multiple "DNA words" is demonstrated, with applications to DNA computing. A new DESTROY operation to selectively remove unmarked DNA strands from surfaces, consisting of polymerase extension followed by restriction enzyme cleavage, has been developed for multiple-word DNA computing. DNA polymerase is used to extend DNA primers hybridized to DNA strands that are covalently attached to a chemically modified gold thin film. The efficiency of this surface polymerase extension reaction is >90%, as determined by removal of the extended DNA molecules from the surface followed by gel electrophoretic analysis. Complete extension of the DNA strands creates a Dpn II restriction enzyme site in the duplex DNA; these molecules may then be cleaved from the surface by addition of Dpn II, with an efficiency exceeding 90%. DNA molecules may be protected from such destruction by hybridization of a peptide nucleic acid (PNA) oligomer to one of the words. The hybridized PNA blocks polymerase extension, thereby preventing formation of the restriction site and consequent strand cleavage. The utility of these operations for DNA computing is demonstrated by solving a small (2-bit) Satisfiability problem in which information was encoded in two tandem words.