Experimental Construction of Very Large Scale DNA Databases with Associative Search Capability

  • Authors:

  • John H. Reif;Thomas H. LaBean;Michael Pirrung;Vipul S. Rana;Bo Guo;Carl Kingsford;Gene S. Wickham

  • Affiliations:

  • -;-;-;-;-;-;-

  • Venue:
  • DNA 7 Revised Papers from the 7th International Workshop on DNA-Based Computers: DNA Computing
  • Year:
  • 2001

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Abstract

We describe on-going experiments for executing associative search queries within synthesized DNA databases. Queries are executed by hybridization of a target database strand with a complementary query strand probe. In our initial annealing experiments for processing associative search queries, we employed fluorescently labeled query strands and performed separation of fluorescent versus non-fluorescent beads using Fluorescence Activated Cell Sorting (FACS or flow cytometry). We also tested polymerase chain reaction (PCR) as an output method, and developed a PCR technique for search in the pair-wise constructed library that exploits the particular properties of words in that library. We have also implemented computer software that provides a simulation (viewable on the internet) of the experimental search procedures, as well as a simulation of input/output from conventional 2D images.