- Article -
| In Silico Biology 9, 0005 (2008); ©2008, Bioinformation Systems e.V. |
In silico analysis of evolutionary patterns in restriction endonucleases
Tiratha Raj Singh1,3,* and Kamal Raj Pardasani2
1 Department of Bioinformatics, Maulana Azad National Institute of Technology (MANIT), Bhopal, India
2 Department of Mathematics, Maulana Azad National Institute of Technology (MANIT), Bhopal, India
3 Department of Zoology, Faculty of life Sciences, Tel-Aviv University, Tel-Aviv, Israel
* Corresponding author
Email: raj@eng.tau.ac.il
Edited by H. Michael; received June 07, 2008; revised December 09, 2008; accepted December 11, 2008; published December 20, 2008
Abstract
Restriction endonucleases represent one of the best studied examples of DNA binding proteins. Type II restriction endonucleases recognize short sequences of foreign DNA and cleave the target on both strands with remarkable sequence specificity. Type II restriction endonucleases are part of restriction modification systems. Restriction modification systems occur ubiquitously among bacteria and archaea. Restriction endonucleases are indispensable tools in molecular biology and biotechnology. They are important model system for specific protein-nucleic acid interactions and also serve as good example for investigating structural, functional and evolutionary relationships among various biomolecules. The interaction between restriction endonucleases and their recognition sequences plays a crucial role in biochemical activities like catalytic site/metal binding, DNA repair and recombination etc. We study various patterns in restriction endonucleases type II and analyzed their structural, functional and evolutionary role. Our studies support X-ray crystallographic studies, arguing for divergence and molecular evolution. Conservation patterns of the nuclease superfamily have also been analyzed by estimating site-specific evolutionary rates for the analyzed structures related to respective chains in this study.
Keywords: restriction-modification, endonuclease, molecular evolution, phyletic trees, evolutionary patterns, site-specific evolutionary conservation