DNA Chip Readout and Evolutionary Computation

David Harlan Wood
Junghuei Chen

University of Delaware

In our laboratory, we have constructed a preliminary prototype of a universal DNA chip that can read out arbitrary graphs. Graphs include ordered schedules of tasks such as Traveling Salesman tours. When multiple answers are simultaneously present, a divide and conquer algorithm using the universal chip can isolate individual answers.

DNA computing techniques are desirable for Evolutionary Computation because they process, in parallel, populations billions of times larger than is usual for conventional computers. However, it is challenging to physically separate DNA strands according to a programmed "fitness criterion." We have designed and carried out preliminary laboratory demonstrations of "separation by fitness" using 2-dimensional Denaturing Gradient Gel Electrophoresis.