Restriction enzyme

Restriction Endonucleases recognise and cut DNA at a specific palindromic base sequences, normally 4, 6 or 8 bases long, and are used selectively to cut DNA into defined fragments at sites known as 'restriction sites'. Different restriction endonucleases are obtained and purified from different species of bacteria. These enzymes are made in bacteria to degrade viral DNA. Cutting DNA with restriction enzymes can produce fragments with either blunt or sticky ends. Different restriction enzymes recognise different DNA sequences. The product of a restriction enzyme can have either sticky ends or blunt ends as shown below. 

Examples of restriction endonucleases are:

• EcoRI - recognises the sequence 5'GAATTC'3 - sticky ends 
• BamHI - recognises the sequence 5'GGATCC'3 - sticky ends 
  
• HhaI - recognises the sequence 5'GCGC'3 - sticky ends
• XhoI - recognises the sequence 5'CTCGAG'3 - sticky ends 
• HindIII - recognises the sequence 5'AAGCTT'3 - sticky ends 
• PstI - recognises the sequence 5'CTGCAG'3 - sticky ends 
• Sau3A - recognises the sequence 5'GATC'3 (produces the same sticky ends as BamHI upon cutting)
• HaeIII - recognises the sequence 5'GGCC'3 - blunt ends 
  

Entire genomes can be digested into defined fragments by Restriction enzymes, this is called a Restriction Digest. The number of fragments formed in a digest is dependent on 2 factors:

1. The restriction enzyme used; A 4bp recogniser will statistically cut a genome in to more fragments than a 6 or 8 bp recogniser because it is more likely for there to be a repeated sequence of less bp. 
2. The size of the genome; Smaller genomes (10-100 bp, found in viruses) give fewer fragments than larger genomes (>10⁶, found in e.g. humans). 
   

Also see Restriction endonucleases