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

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.