Julia Khodor and David K. Gifford
3rd Annual DIMACS Workshop on DNA-Based Computers, Philadelphia, Pennsylvania, June 1997

We report a series of experimental observations on the efficiency and fidelity of sequence-specific DNA extraction operations. We examined the solution-based annealing of bead-bound probes to target molecules followed by magnetic separation of the annealed probe-target complexes from solution. Our experiments measured how efficiently a 20-mer probe could be used to purify a 40-mer radiolabeled single-stranded target with varying target concentrations. Our result suggest that with perfectly homologous probes and targets, recovery rates of 8-24% can be expected, and when a target is not homologous to the probe less than 1% of the target is recovered. Because our conditions were designed to be ideal, the rates we obtained may represent an upper bound on the efficiency of sequence-specific separation of DNA mixtures using magnetic beads.

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