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 computing 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 ligated molecules from the surface followed by gel electrophoresis. This surface ligation reaction is used in two new operations for DNA computing on surfaces. In a “Surface Word Append” operation, the complexity and information density of DNA word strands attached to gold surfaces are increased by appending additional words onto these word strands. The ligation reaction is also utilized as part of a “Two-Word Mark and 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...