Efficiency and reliability of genomic information storage and retrieval in DNA-based memories with compaction

Associative memories based on DNA-affinity have been proposed [E. Baum, (1995), J. Chen et al. (2003)] and preliminary analysis have been made [T.K. Landauer et al. (1998), M.H. Garzon et al. (2003)]. Here, the effects of summarizing and compacting genomic data are evaluated. Two memory types, P [R. Deaton et al. (2002)] and CDW [J. Chen et al. (2003)], are used to test their summarization and compaction, respectively. The capabilities of each memory are evaluated and analyzed through simulations in silico [M.H. Garzon et al. (2003)]. The results of queries to each memory type are compared objectively with the results of the same queries to the whole genomic library. The PCR-based summarization technique (memory P) retains much of its functional meaning and remained sensitive enough to distinguish compacted genomes. The summarization (memory CDW) performs less efficiently and appears to retain less information than the summarization techniques, but further testing is required for a definitive assessment.