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

Authors

  • Wan Heng Fong Universiti Teknologi Malaysia
  • Nurul Izzaty Ismail Universiti Teknologi Malaysia
  • Nor Haniza Sarmin Universiti Teknologi Malaysia

DOI:

https://doi.org/10.11113/mjfas.v17n2.1370

Keywords:

Splicing language, Palindromic, Restriction enzyme, Splicing system

Abstract

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.

Author Biographies

Nurul Izzaty Ismail, Universiti Teknologi Malaysia

Department of Mathematical Sciences, Faculty of Science

Nor Haniza Sarmin, Universiti Teknologi Malaysia

Department of Mathematical Sciences, Faculty of Science

References

T. Head, B. Math. Biol 49 (1987) 737-759.

T. Palmer, P.L. Bonner, Enzymes: Biochemistry, Biotechnology, Clinical Chemistry, 2nd ed, Woodhead Publishing Limited, UK, 2007.

P. Linz, An Introduction to Formal Languages and Automata, 4th ed, Jones and Bartlett Publisher, USA, 2006.

T. Head, Discrete. Appl. Math. 87 (1998) 139-147.

G. Păun, Discrete. Appl. Math. 70 (1996) 57-79.

D. Pixton, Discrete. Appl. Math. 69 (1996) 101-124.

Y. Yusof, N.H. Sarmin, W.H. Fong, T.E. Goode, M.A. Ahmad, An Analysis of Four Variants of Splicing System, Proceeding of the 20th National Symposium on Mathematical Sciences - Research in Mathematical Sciences: A Catalyst for Creativity and Innovation (SKSM 2012), December 18-20, 2012, AIP Conference Proceedings, Melville, NY, 2013, p. 888-895.

E. Goode, D. Pixton, in: Jonoska, N., Păun, G.,Rozenberg, G. (Eds.), Aspects of Molecular Computing, Lecture Notes in Computer Science, Springer-Verlag, Germany, 2004, p. 189-201.

T.E.G. Laun, Constants and Splicing Systems, Ph.D. Thesis, State University of New York, 1999.

I. Tomohiro, S. Inenaga, M. Takeda, Theor. Comput. Sci. 483 (2013) 162-170.

Y. Yusof, DNA Splicing System Inspired by Bio Molecular Operations, Ph.D. Thesis, Universiti Teknologi Malaysia, 2012.

H.M. Eun, Enzymology Primer for Recombinant DNA Technology, Academic Press, USA, 1996.

W.L. Lim, Y. Yusof, M.H. Mudaber, Modeling of DNA single stage splicing language via Yusof-Goode approach: One string with two rules, Proceeding of the 2nd ISM International Statictical Conference 2014 (ISM-II), Kuantan, Malaysia, August 12-14, 2014, AIP Conference Proceedings, Melville, NY, 2015, p. 695-699.

M.H. Mudaber, Y. Yusof, M.S. Mohamad, Some Sufficient Conditions for Persistency and Permanency of Two Stages DNA Splicing Languages via Yusof-Goode Approach, Proceeding of the 21th National Symposium on Mathematical Sciences (SKSM21), Penang, Malaysia, November 6-8, 2013, AIP Conference Proceedings, Melville, NY, 2014, p. 591-595.

M.A. Ahmad, N.H. Sarmin, Y. Yusof, W.H. Fong, Some Restrictions on the Existence of Second Order Limit Language, Proceeding of the 22th National Symposium on Mathematical Sciences (SKSM22), Selangor, Malaysia, November 24-26, 2014, AIP Conference Proceedings, Melville, NY, 2015, p. 020048.

W.H. Fong, N.I. Ismail, MATEMATIKA 34 (2018) 59-71.

R.M. Horton, S.N. Ho, J.K. Pullen, H.D. Hunt, Z. Cai, L.R. Pease, in: Wu,

R. (Eds.), Methods in enzymology, Academic Press, 1995, p. 363-372.

J.D. Watson, T.A. Baker, S.P. Bell, A. Gann, M. Levine, R. Losick, Molecular Biology of the Gene, 7th ed, Cold Spring Harbor Laboratory Press, New York, 2014.

Downloads

Published

29-04-2021