Formal language theory and DNA: An analysis of the generative capacity of specific recombinant behaviors (Q1109707): Difference between revisions

This paper is an attempt to relate the theory of formal languages to the study of informational macromolecules as protein molecules, RNA, or double-stranded DNA molecules that are naturally represented as strings over symbols each of which represents an aminoacid, a ribonucleotide, or a hydrogen-bounded deoxyribonucleotide pair, respectively. The author gives a formal characterization of the generative capacity of the specified enzymatic activities operating on specified sets of double- stranded DNA molecules. Such a set is represented as a language over the four-alphabet of deoxyribonucleotide pairs. The recombinational power of enzyme activities is understood as a set of operations on strings. A language that is the closure of an initial set of strings under the given set of operations can then be studied by means of formal language theory. A new generative formalism, called here a splicing system, is described. It is shown that a subclass of splicing languages (i.e. languages generated by splicing systems) called here persistent splicing languages, coincides with the well-known class of regular languages. The formalism developed by the author also provides the basis for computer experimentation with recombination processes.