Basic Applied Bioinformatics

CHAPTER 7Detection of Restriction Enzyme Sites

CS Mukhopadhyay and RK Choudhary

School of Animal Biotechnology, GADVASU, Ludhiana

7.1 INTRODUCTION

The restriction enzyme (RE) sites present on a nucleotide sequence can be detected using a suitable in silico tool. A nucleotide sequence is subjected to detection of RE site(s) in some wet‐lab experiments such as gene cloning, nucleotide sequencing, in vitro expression of a target protein, RFLP, AFLP, restriction mapping and restriction enzyme assays.

Several online tools for RE site detection are available. Some of the user‐friendly and accessible web‐based tools and their URLs (websites) have been tabulated below. Detailed procedures for determining RE sites using all these web tools will not be covered. This chapter will show how to use NEBCutter (New England Biolabs) as a tool for identifying RE sites.

1. NEBCutter (http://tools.neb.com/NEBcutter2/index): New England Biolabs hosts this RE site mapper software.
2. Webcutter 2.0 (http://rna.lundberg.gu.se/cutter2/): Another RE site detection software (online, free) for linear and circular DNA.
3. Mapper (http://arbl.cvmbs.colostate.edu/molkit/mapper/index.html): Java platform‐based online software for mapping the RE sites on a target sequence.
4. Web Map (https://pga.mgh.harvard.edu/web_apps/web_map/start): This tool maps the RE sites for circular or linear nucleotide sequences. The reverse complement of the given sequence can also be checked for mapping of RE sites.
5. Restriction‐Mapper ( ...