Generalisations of splicing languages from deoxyribonucleic acid splicing systems

Abstract

The mathematical modelling of recombinant deoxyribonucleic acid (DNA) utilises formal language theory which integrates the areas of applied discrete mathematics, theoretical computer science, and linguistics. In splicing systems, the presence of restriction enzymes allows DNA molecules to be cleaved and recombined to generate a new set of molecules, known as a splicing language, which can be analysed using formal language theory. Previous research on DNA splicing systems with different restriction enzymes has led to various splicing languages. However, these splicing languages are specific to the respective enzymes. In this research, the splicing languages are generalised based on the sequence of restriction enzymes which is either a palindromic sequence or a non-palindromic sequence. A palindromic sequence is a recognition sequence that reads the same way both forward and backward. Then, the splicing languages from the respective splicing systems are reduced to simple splicing systems via homomorphism. In addition, the models of splicing systems are verified through laboratory experiments to validate the theoretical results from these generalisations. Lastly, algorithms and also a graphical user interface (GUI) for splicing systems are developed using C++ visual programming to generate all splicing languages from the splicing systems involving palindromic or non-palindromic restriction enzymes. The results of this research include automata for the generalisations of splicing languages in simple splicing systems and the GUI for the computation of splicing languages. Moreover, the resulting molecules that depict the generalised splicing languages are documented in polyacrylamide gel electrophoresis (PAGE) gel photos as obtained from the experiments. The models presented in this research contribute to the advancement of DNA computing through the generalisations of splicing languages.