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Formal language theory and DNA: An analysis of the generative capacity of specific recombinant behaviors

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Abstract

A new manner of relating formal language theory to the study of informational macromolecules is initiated. A language is associated with each pair of sets where the first set consists of double-stranded DNA molecules and the second set consists of the recombinational behaviors allowed by specified classes of enzymatic activities. The associated language consists of strings of symbols that represent the primary structures of the DNA molecules that may potentially arise from the original set of DNA molecules under the given enzymatic activities.

Attention is focused on the potential effect of sets of restriction enzymes and a ligase that allow DNA molecules to be cleaved and reassociated to produce further molecules. The associated languages are analysed by means of a new generative formalism called a splicing system. A significant subclass of these languages, which we call the persistent splicing languages, is shown to coincide with a class of regular languages which have been previously studied in other contexts: the strictly locally testable languages.

This study initiates the formal analysis of the generative power of recombinational behaviors in general. The splicing system formalism allows observations to be made concerning the generative power of general recombination and also of sets of enzymatic activities that include general recombination.

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Authors and Affiliations

  1. Department of Mathematical Sciences, University of Alaska, 99775, Fairbanks, AK, USA

    Tom Head

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  1. Tom Head
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Head, T. Formal language theory and DNA: An analysis of the generative capacity of specific recombinant behaviors. Bltn Mathcal Biology 49, 737–759 (1987). https://doi.org/10.1007/BF02481771

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  • DOI: https://doi.org/10.1007/BF02481771

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