DNA splicing systems with at most two cutting sites of a non-palindromic restriction enzyme

The modelling of splicing systems is simulated by the process of cleaving and recombining DNA molecules with the presence of a ligase and restriction enzymes which are biologically called as endodeoxyribonucleases. The molecules resulting from DNA splicing systems are known as splicing languages. Palindrome is a sequence of strings that reads the same forward and backward. In this research, the splicing languages resulting from DNA splicing systems with one non-palindromic restriction enzyme are determined using the notation from Head splicing system. The generalisations of splicing languages for DNA splicing systems involving a cutting site and two non-overlapping cutting sites of one non-palindromic restriction enzyme are presented in the first and second theorems, respectively, which are proved using direct and induction methods. The result from the first theorem shows a trivial string which is the initial DNA molecule; while the second theorem determines a splicing language consisting of a set of resulting DNA molecules from the respective DNA splicing system

Computation of splicing languages from DNA splicing system with one palindromic restriction enzyme

In DNA splicing system, the potential effects of sets of restriction enzymes and a ligase that allow DNA molecules to be cleaved and reassociated to produce further molecules are studied. A splicing language depicts the molecules resulting from a splicing system. In this research, a C++ programming code for DNA splicing system with one palindromic restriction enzyme for one and two (non-overlapping) cutting sites is developed. A graphical user interface, GUI is then designed to allow the user to insert the initial DNA string and restriction enzymes to generate the splicing languages which are the result of the computation of the C++ programming. This interface displays the resulting splicing languages, which depict the results from in vitro experiments of the respective splicing system. The results from this research simplify the lenghty manual computation of the resulting splicing languages of DNA splicing systems with one palindromic restriction enzyme

Circular Languages Generated by Complete Splicing Systems and Pure Unitary Languages

Circular splicing systems are a formal model of a generative mechanism of circular words, inspired by a recombinant behaviour of circular DNA. Some unanswered questions are related to the computational power of such systems, and finding a characterization of the class of circular languages generated by circular splicing systems is still an open problem. In this paper we solve this problem for complete systems, which are special finite circular splicing systems. We show that a circular language L is generated by a complete system if and only if the set Lin(L) of all words corresponding to L is a pure unitary language generated by a set closed under the conjugacy relation. The class of pure unitary languages was introduced by A. Ehrenfeucht, D. Haussler, G. Rozenberg in 1983, as a subclass of the class of context-free languages, together with a characterization of regular pure unitary languages by means of a decidable property. As a direct consequence, we characterize (regular) circular languages generated by complete systems. We can also decide whether the language generated by a complete system is regular. Finally, we point out that complete systems have the same computational power as finite simple systems, an easy type of circular splicing system defined in the literature from the very beginning, when only one rule is allowed. From our results on complete systems, it follows that finite simple systems generate a class of context-free languages containing non-regular languages, showing the incorrectness of a longstanding result on simple systems

Generalisations of DNA Splicing Systems with One Palindromic Restriction Enzyme

In DNA splicing system, the potential effect of sets of restriction enzymes and a ligase that allow DNA molecules to be cleaved and re-associated to produce further molecules is modelled mathematically. This modelling is done in the framework of formal language theory, in which the nitrogen bases, nucleotides and restriction sites are modelled as alphabets, strings and rules respectively. The molecules resulting from a splicing system is depicted as the splicing language. In this research, the splicing language resulting from DNA splicing systems with one palindromic restriction enzyme for one and two (non-overlapping) cutting sites are generalised as regular expressions

Splicing Systems from Past to Future: Old and New Challenges

A splicing system is a formal model of a recombinant behaviour of sets of double stranded DNA molecules when acted on by restriction enzymes and ligase. In this survey we will concentrate on a specific behaviour of a type of splicing systems, introduced by P\u{a}un and subsequently developed by many researchers in both linear and circular case of splicing definition. In particular, we will present recent results on this topic and how they stimulate new challenging investigations.Comment: Appeared in: Discrete Mathematics and Computer Science. Papers in Memoriam Alexandru Mateescu (1952-2005). The Publishing House of the Romanian Academy, 2014. arXiv admin note: text overlap with arXiv:1112.4897 by other author

Thermoconditional modulation of the pleiotropic sensitivity phenotype by the Saccharomyces cerevisiae PRP19 mutant allele pso4-1

The conditionally-lethal pso4-1 mutant allele of the spliceosomal-associated PRP19 gene allowed us to study this gene’s influence on pre-mRNA processing, DNA repair and sporulation. Phenotypes related to intron-containing genes were correlated to temperature. Splicing reporter systems and RT–PCR showed splicing efficiency in pso4-1 to be inversely correlated to growth temperature. A single amino acid substitution, replacing leucine with serine, was identified within the N-terminal region of the pso4-1 allele and was shown to affect the interacting properties of Pso4-1p. Amongst 24 interacting clones isolated in a two-hybrid screening, seven could be identified as parts of the RAD2, RLF2 and DBR1 genes. RAD2 encodes an endonuclease indispensable for nucleotide excision repair (NER), RLF2 encodes the major subunit of the chromatin assembly factor I, whose deletion results in sensitivity to UVC radiation, while DBR1 encodes the lariat RNA splicing debranching enzyme, which degrades intron lariat structures during splicing. Characterization of mutagen-sensitive phenotypes of rad2{Delta}, rlf2{Delta} and pso4-1 single and double mutant strains showed enhanced sensitivity for the rad2{Delta} pso4-1 and rlf2{Delta} pso4-1 double mutants, suggesting a functional interference of these proteins in DNA repair processes in Saccharomyces cerevisiae

Some properties of probabilistic semi-simple splicing systems

The concept of splicing system was first introduced by Head in 1987. This model has been introduced to investigate the recombinant behavior of DNA molecules. Over the years, various types of splicing languages have been defined and studied by different mathematicians. Splicing systems with finite sets of axioms only generate regular languages. Therefore, different restrictions have been considered to increase the computational power up to the recursively enumerable languages. In this research, a variant of splicing systems called probabilistic splicing systems has been used to define different types of splicing systems such as probabilistic simple splicing systems, probabilistic semi-simple splicing systems and probabilistic one-sided splicing systems. In probabilistic splicing systems, probabilities (real numbers in the range of 0 and 1) are associated with the axioms, and the probability p(z)of the string z generated from two strings x and y is calculated from the probability p(x)and p(y) according to the operation *(multiplication) defined on the probabilities, i.e., p(z) = p(x) * p(y)

Generalisations of splicing languages in DNA splicing systems involving two palindromic restriction enzymes

DNA splicing system is initiated by Head to mathematically model a relation between formal language theory and DNA molecules. In DNA splicing systems, DNA molecules are cut and recombined in specific ways with the existence of enzymes, which are also known as endonucleases, to produce further molecules. The resulting molecules are depicted as splicing languages by using concepts in formal languages theory. A sequence of restriction enzyme that reads the same forward and backward is called as a palindromic rule. Previously, researches on different types of splicing languages have been done. In this research, generalisations of splicing languages resulting from DNA splicing systems with non-overlapping cutting sites of two palindromic restriction enzymes are presented as theorems using the induction method. The results from this research are beneficial for researchers in the field of DNA computing since it contributes to the development of splicing languages generated from DNA splicing systems with different palindromic restriction enzymes by using these generalisations