Static Watson-Crick regular grammar

Abstract

DNA computing, or more generally, molecular computing, is a recent development at the interface of computer science and molecular biology. In DNA computing, many computational models have been proposed in the framework of formal language theory and automata such as Watson-Crick grammars and sticker systems. A Watson-Crick grammar is a grammar model that generates double stranded strings, whereas a sticker system is a DNA computing model of the ligation and annealing operations over DNA strands using the Watson-Crick complementarity to form a complete double stranded DNA sequence. Most of the proposed DNA computing models make use of this concept, including the Watson-Crick grammars and sticker systems. Watson-Crick grammars and their variants can be explored using formal language theory which allows the development of new concepts of Watson-Crick grammars.  In this research, a new variant of Watson-Crick grammar called a static Watson-Crick regular grammar is introduced as an analytical counterpart of sticker systems. The computation of a sticker system starts from a given set of incomplete double stranded sequence to form a complete double stranded sequence. Here, a static Watson-Crick regular grammar differs from a dynamic Watson-Crick regular grammar in generating double stranded strings: the latter grammar produces each strand string “independently” and only check for the Watson-Crick complementarity of a generated complete double stranded string at the end, while the former grammar generates both strand strings “dependently”, i.e., checking for the Watson-Crick complementarity for each complete substring. In this paper, computational properties of static Watson-Crick regular grammars are investigated to correlate with the Chomsky hierarchy and hierarchy of the families of dynamic Watson-Crick regular languages. The relationship between families of languages generated by static Watson-Crick regular grammars with several variants of sticker systems, Watson-Crick regular grammars and Chomsky grammars are presented by showing the hierarchy.