THE FIDELITY OF TEMPLATE-DIRECTED OLIGONUCLEOTIDE LIGATION AND ITS RELEVANCE TO DNA COMPUTATION

Several different computational problems have been solved using DNA as a medium. However, the DNA computations that have so far been carried out have examined a relatively small number of possible sequence solu tions in order to find correct sequence solutions, We have encoded a s earch algorithm in DNA that required the evaluation of >16 000 000 pos sible sequence solutions in order to find a single, correct sequence s olution. Experimental evaluation of the search algorithm revealed boun ds for the accuracies of answers to other large, computationally compl ex problems and suggested methods for the optimization of DNA computat ions in general. Short oligonucleotide substrates performed substantia lly better than longer substrates, Large, computationally complex prob lems whose evaluation requires hybridization and ligation can likely b est be encoded and evaluated using short oligonucleotides at mesophili c temperatures.