scholarly journals DNA Splicing Systems with at Most Two Cutting Sites of a Non-Palindromic Restriction Enzyme

MATEMATIKA ◽  
2019 ◽  
Vol 35 (2) ◽  
pp. 129-137
Author(s):  
Nurul Izzaty Ismail ◽  
Fong Wan Heng ◽  
Nor Haniza Sarmin
Keyword(s):  
Restriction Enzyme ◽  
Restriction Enzymes ◽  
Dna Molecules ◽  
Dna Molecule ◽  
Splicing Systems ◽  
Palindromic Sequences ◽  
Dna Splicing

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.  Research on generalisations of splicing languages in DNA splicing system involving palindromic sequences for restriction enzymes has been done previously. 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 one 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.

scholarly journals Computation of Splicing Languages from DNA Splicing System Based on Sequences of Restriction Enzymes

2019 ◽  
Vol 8 (6S3) ◽  
pp. 31-42
Keyword(s):  
Restriction Enzyme ◽  
Dna Computing ◽  
Restriction Enzymes ◽  
Visual Programming ◽  
Cleavage Pattern ◽  
Dna Molecules ◽  
Splicing Systems ◽  
Dna Splicing

In DNA splicing systems, restriction enzymes and ligases cleave and recombine DNA molecules based on the cleavage pattern of the restriction enzymes. The set of molecules resulting from the splicing system depicts a splicing language. In this research, an algorithm for DNA splicing systems is developed using C++ visual programming. The splicing languages which have been characterised through some theorems based on the crossings and sequences of the restriction enzymes, are generated as the output from this computation. In order to generate the splicing languages, the algorithm detects and calculates the number of cutting sites of the restriction enzymes found in the initial molecules, determines whether the sequence of restriction enzyme is a palindrome or not, and if the restriction enzymes have the same or different crossings. The results from this research depict the splicing languages obtained from the manual computations, which contributes to the development of computational software in DNA computing.

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

2018 ◽  
Vol 14 (2) ◽  
pp. 188-192
Author(s):  
Nurul Izzaty Ismail ◽  
Wan Heng Fong ◽  
Nor Haniza Sarmin
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Restriction Enzyme ◽  
Restriction Enzymes ◽  
In Vitro Experiments ◽  
Dna Molecules ◽  
C Programming ◽  
Splicing Systems ◽  
Dna Splicing

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.   

scholarly journals Automata for DNA Splicing Languages with Palindromic and Non-Palindromic Restriction Enzymes using Grammars

MATEMATIKA ◽  
2019 ◽  
Vol 35 (4) ◽  
pp. 1-14
Author(s):  
Wan Heng Fong ◽  
Nurul Izzaty Ismail ◽  
Nor Haniza Sarmin
Keyword(s):  
Dna Sequences ◽  
Formal Language ◽  
Restriction Enzymes ◽  
Language Theory ◽  
Dna Assembly ◽  
Dna Molecules ◽  
Splicing Systems ◽  
Transition Graphs ◽  
Palindromic Sequences ◽  
Dna Splicing

In DNA splicing system, DNA molecules are cut and recombined with the presence of restriction enzymes and a ligase. The splicing system is analyzed via formal language theory where the molecules resulting from the splicing system generate a language which is called a splicing language. In nature, DNA molecules can be read in two ways; forward and backward. A sequence of string that reads the same forward and backward is known as a palindrome. Palindromic and non-palindromic sequences can also be recognized in restriction enzymes. Research on splicing languages from DNA splicing systems with palindromic and non-palindromic restriction enzymes have been done previously. This research is motivated by the problem of DNA assembly to read millions of long DNA sequences where the concepts of automata and grammars are applied in DNA splicing systems to simplify the assembly in short-read sequences. The splicing languages generated from DNA splicing systems with palindromic and nonpalindromic restriction enzymes are deduced from the grammars which are visualised as automata diagrams, and presented by transition graphs where transition labels represent the language of DNA molecules resulting from the respective DNA splicing systems.

scholarly journals Generalisations of Splicing Languages in DNA Splicing Systems Involving Two Palindromic Restriction Enzymes

2021 ◽  
Vol 17 (2) ◽  
pp. 128-138
Author(s):  
Wan Heng Fong ◽  
Nurul Izzaty Ismail ◽  
Nor Haniza Sarmin
Keyword(s):  
Restriction Enzyme ◽  
Dna Computing ◽  
Formal Language ◽  
Restriction Enzymes ◽  
Language Theory ◽  
Dna Molecules ◽  
Induction Method ◽  
Different Types ◽  
Splicing Systems ◽  
Dna Splicing

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.

scholarly journals Generalisations of DNA Splicing Systems with One Palindromic Restriction Enzyme

MATEMATIKA ◽  
2018 ◽  
Vol 34 (1) ◽  
pp. 59-71 ◽  
Author(s):  
Fong Wan Heng ◽  
Nurul Izzaty Ismail
Keyword(s):  
Restriction Enzyme ◽  
Formal Language ◽  
Restriction Enzymes ◽  
Potential Effect ◽  
Language Theory ◽  
Regular Expressions ◽  
Nitrogen Bases ◽  
Restriction Sites ◽  
Splicing Systems ◽  
Dna Splicing

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.

scholarly journals Mathematical Modelling of Some Null-Context and Uniform Splicing Systems

2014 ◽  
Vol 7 (2) ◽  
Author(s):  
S. J. Lim ◽  
W. H. Fong ◽  
N. H. Sarmin ◽  
F. Karimi
Keyword(s):  
Mathematical Modelling ◽  
Restriction Enzymes ◽  
Automata Theory ◽  
Dna Molecules ◽  
Specific Chemical ◽  
Language L ◽  
Different Types ◽  
Chemical Conditions ◽  
Splicing Systems

The mathematical modelling of splicing system which involves recombination of DNA molecules was first introduced by Head in 1987. Splicing of DNA involves cutting of DNA molecules using the restriction enzymes and re-associating different fragments of DNA molecules using the ligase under some specific chemical conditions. A splicing language, L is generated if there exists a splicing system S for which L = L(S). There are different types of splicing systems which have been discussed by various researchers. Among them are the persistent splicing system, null-context and uniform splicing system. In this paper, some molecular examples on null-context splicing system and uniform splicing systems with different initial strings and combination of restriction enzymes will be discussed. Applications of automata theory on some molecular examples of null-context and uniform splicing languages will also be presented in this paper.

MODELLING OF TWO STAGES DNA SPLICING LANGUAGES ON DE BRUIJN GRAPH

2015 ◽  
Vol 78 (1) ◽  
Author(s):  
Mohammad Hassan Mudaber ◽  
Yuhani Yusof ◽  
Mohd Sham Mohamad ◽  
Aizi Nor Mazila Ramli ◽  
Wen Li Lim
Keyword(s):  
Dna Sequence ◽  
Restriction Enzymes ◽  
De Bruijn Graph ◽  
Dna Molecule ◽  
Interesting Topic ◽  
De Bruijn ◽  
Two Stages ◽  
Mathematical Graph ◽  
Dna Splicing

Finding the sequence of the genome from its compositions as well as a mathematical graph is the most interesting topic in a field of DNA molecular.  Since lack of technology is the big obstacle that biologists are facing to read a long sequence of the genome from beginning up to the end, therefore finding the compositions of the genome having very long sequence and also its description via de Bruijn graph is challenging or even impossible.  In this paper, Yusof-Goode (Y-G) approach is used to generate the DNA splicing languages based on cutting sites of initial strings (one or two cutting sites) and crossing and contexts factors of restriction enzymes. The two short sequences of DNA (8bp) and two restriction enzymes are considered to create a connection between mathematics and DNA molecular.   This relation will be presented as de Bruijn graph so that every edge of the de Bruijn graph gives a k-mer composition of DNA molecule and also each path of the de Bruijn graph gives a DNA sequence and vice-versa. Besides, the persistency and permanency of two stages DNA splicing languages can be predicted using this model.

scholarly journals Recognition of Simple Splicing Systems using SHAutomaton

2014 ◽  
Vol 4 (2) ◽  
Author(s):  
Fong Wan Heng ◽  
Nor Haniza Sarmin ◽  
Zuwairie Ibrahim
Keyword(s):  
Mathematical Model ◽  
Regular Expression ◽  
Restriction Enzymes ◽  
Automata Theory ◽  
Dna Molecules ◽  
Deterministic Automaton ◽  
Splicing Systems ◽  
The Mathematical Model ◽  
The Given ◽  
Special Case

Splicing language is the language which results from a splicing system. Splicing system was first introduced by Tom Head in 1987 as the mathematical model of systems of restriction enzymes acting on initial DNA molecules. Splicing languages are closely related to automata theory. Simple splicing systems can be recognized by SH-automata diagrams due to the regularity of splicing languages. SH-automaton defines exactly one language which is the language generated by the simple splicing system. In this paper, the concept of firm and maximal firm subwords are introduced. Some examples are then given to illustrate the maximal firm subwords of a word in a simple splicing system. Taking the SH-automata concept, which is a short compact way of encoding normal non-deterministicautomata in the special case of SH systems, the maximal firm subwords of the initial words of an SH systems serve as the labels for the associated  SH-automaton. Some examples which will show the maximal firm subwords of the words in the initial set I, the regular expression for the language generated by the given splicing system and the simplest non-deterministic automaton that recognizes the corresponding splicing system are also given

scholarly journals Out-Lab Therapy Approach Based on Elected A Restriction Enzyme to Transfer Target Gene

2018 ◽  
Vol 2 (2) ◽  
pp. 196-208
Author(s):  
Ayad Ismaeel
Keyword(s):  
Restriction Enzyme ◽  
Target Gene ◽  
Restriction Enzymes ◽  
Tp53 Gene ◽  
Restriction Enzyme Digestion ◽  
Therapy Approach ◽  
Software Packages ◽  
Important Approach ◽  
Effective Cost ◽  
Target Gene Sequence

An important approach of therapy the target gene sequence causes diseases via repair/recombine the mutated gene (gene transfer) using a restriction enzymes in the laboratory. This approach will cause multiple problems happening accompany to biological laboratory if ruled out problems outside of it like the digested DNA ran as a smear on an agarose gel, incomplete restriction enzyme digestion, extra bands in the gel, etc. The paper suggested new approach of therapy via repair/replacement mutated gene caused disease by detecting primers and finding restriction enzymes using bioinformatics tools, software, packages etc. then achieving the repair/ recombine of mutations before going to the biologic lab (out-lab) to avoid the problems associated these laboratories. Implement and apply this a proposed therapy approach on TP53 gene (which caused more than 50% of human cancers) and after confirming there is mutations on P53 tumor protein shows an effective cost, friendly therapy methodology and comprehensive.

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