Multiple word DNA computing on surfaces

The enzymatic manipulation of DNA molecules immobilized on a surface that e ach contain Linked, multiple "DNA words" is demonstrated, with applications to DNA computing. A new DESTROY operation to selectively remove unmarked D NA strands from surfaces, consisting of polymerase extension followed by re striction enzyme cleavage, has been developed for multiple-word DNA computi ng. DNA polymerase is used to extend DNA primers hybridized to DNA strands that are covalently attached to a chemically modified gold thin film. The e fficiency of this surface polymerase extension reaction is >90%, as determi ned by removal of the extended DNA molecules from the surface followed by g el electrophoretic analysis. Complete extension of the DNA strands creates a Dpn II restriction enzyme site in the duplex DNA; these molecules may the n be cleaved from the surface by addition of Dpn II, with an efficiency exc eeding 90%. DNA molecules may be protected from such destruction by hybridi zation of a peptide nucleic acid (PNA) oligomer to one of the words. The hy bridized PNA blocks polymerase extension, thereby preventing formation of t he restriction site and consequent strand cleavage, The utility of these op erations for DNA computing is demonstrated by solving a small (2-bit) Satis fiability problem in which information was encoded in two tandem words.