ENZYMATIC LIGATION REACTIONS OF DNA WORDS ON SURFACES FOR DNA COMPUTING

The enzymatic manipulation of sets of short, 16-base oligonucleotides, or DNA ''words'', is demonstrated with applications toward DNA comput ing on surfaces. The enzyme T4 DNA ligase is used to ligate (join) DNA words on a chemically modified gold thin film. The efficiency of this surface ligation reaction is 80%, as determined by removal of the lig ated molecules from the surface followed by gel electrophoresis, This surface ligation reaction is used in two new operations for DNA comput ing on surfaces. In a ''Surface Word Append'' operation, the complexit y and information density of DNA word strands attached to gold surface s are increased by appending additional words onto these word strands. The ligation reaction is also utilized as part of a ''Two-Word Mark a nd Destroy'' operation in which singly marked two-word DNA strands are selectively removed from the surface in the presence of doubly marked two-word strands. These new operations are essential for manipulation of the large combinatorial sets of linked DNA word strands required f or DNA computing.