On designing DNA databases for the storage and retrieval of digital signals

In this paper we propose a procedure for the storage and retrieval of digital signals utilizing DNA. Digital signals are encoded in DNA sequences that satisfy among other constraints the Noise Tolerance Constraint (NTC) that we have previously introduced. NTC takes into account the presence of noise in digital signals by exploiting the annealing between non-perfect complementary sequences. We discuss various issues arising from the development of DNA-based database solutions (i) in vitro (in test tubes, or other materials) for short-term storage and (ii) in vivo (inside organisms) for long-term storage. We discuss the benefits and drawbacks of each scheme and its effects on the codeword design problem and performance. We also propose a new way of constructing the database elements such that a short-term database can be converted into a long term one and vice versa without the need for a re-synthesis. The latter improves efficiency and reduces the cost of a long-term database

Matrix Attachment Region-Dependent Function of the Immunoglobulin μ Enhancer Involves Histone Acetylation at a Distance without Changes in Enhancer Occupancy

Nuclear matrix attachment regions (MARs), which flank the immunoglobulin μ heavy-chain enhancer on either side, are required for the activation of the distal variable-region (V(H)) promoter in transgenic mice. Previously, we have shown that the MARs extend a local domain of chromatin accessibility at the μ enhancer to more distal sites. In this report, we examine the influence of MARs on the formation of a nucleoprotein complex at the enhancer and on the acetylation of histones, which have both been implicated in contributing to chromatin accessibility. By in vivo footprint analysis of transgenic μ gene constructs, we show that the occupancy of factor-binding sites at the μ enhancer is similar in transcriptionally active wild-type and transcriptionally inactive ΔMAR genes. Chromatin immunoprecipitation experiments indicate, however, that the acetylation of histones at enhancer-distal nucleosomes is enhanced 10-fold in the presence of MARs, whereas the levels of histone acetylation at enhancer-proximal nucleosomes are similar for wild-type and ΔMAR genes. Taken together, these data indicate that the function of MARs in mediating long-range chromatin accessibility and transcriptional activation of the V(H) promoter involves the generation of an extended domain of histone acetylation, independent of changes in the occupancy of the μ enhancer