The DNA from a Coding Perspective

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The prospect of DNA has changed over the last decade from a solely digitally coded sequence to a digital entity with analog characteristics. These analog characteristics stem from the physical properties of the DNA polymer. The four different bases not only codein certain combination for proteins but at the same time also assign physical and information theoretic properties like entropy, thermodynamic stability, or specific 3D conformations to the polymer. These physical or information theoretic properties are fundamental for the regulation of gene expression. This dual coding of proteins and DNA structure is largely independent due to the redundancy of the protein coding and structural coding. In the previous project we were able to show that genes are strategically positioned on the bacterial chromosome to utilize DNA properties of distinct chromosomal regions to differentiate temporal gene expression patterns. Furthermore, we realized some aspects that allows for some unequal error protection that we would now make the center of investigations, of course, still investigating the links between analog and digital information, since this is essential for the considered coding anyhow, but otherwise looking into the different levels of unequal error protection, starting from the mapping between codons and amino acids, over memory along the DNA strands modeled by Markov models or context trees, up to the regulatory Networks interpreted as a code graph. To this end, we can profit from our experiences in UEP coding and our basis in the understanding of the analog and digital properties of the DNA.