Restriction endonucleases

[vdrover at kean.ucs.mun.ca]

	Restriction endonucleases (RE) are, as stated earlier, protein
molecules (enzymes) that cleave DNA at site specific locations. Most are
isolated from bacteria and are thus named. For instance, EcoRI was isolated 
from E.coli. If i remember correctly, they help guard a cell from invasion by 
foreign DNA, as in the case of a viral attack. Although most restriction 
enzymes recognize 6 nucleotides, some recognize 4 and 8 nucleotides, the 
former obviously having a higher probability of finding the proper sequence
. A couple of details about RE's:
	1. Restriction sites are palindromic, they are the same on both 
strands of the DNA when read 5' to 3'. eg. 5'CAGCTG3'
					   3'GTCGAC5'
	2. The actual products of a digestion can vary. Some RE cut in the 
center of a restriction site to leave 'blunt ends' while some leave 
overhangs.           |
	       ---CAGCTG---   ------>   ---CAG    CTG---
	       ---GTCGAC---             ---GTC    GAC---   (BLUNT ENDS)
                     |

                    |
               ---TATATA---   ------>   ---TA      TATA---
               ---ATATAT---             ---ATAT      AT---  (OVERHANGS)
                      |
	3. The recognition sites of some RE can be altered by methylation 
of certain bases. For instance, some RE will only cleave at a site in which 
a guanine has been methylated. This is actually the basis for some types of 
footprinting experiments where the source DNA is first methylated. Only 
nucleotides which are exposed (ie. not protected by some protein 
interaction) will be methylated and thus cleaved. 

	4. Some RE recognize imperfect palindromes, that DNA sequences that 
are palindromic only wrt the outermost nucleotides. For example, CGTCG. The 
palindrome is centered around the T.                        

	5. RE recognize double-stranded DNA only.

	If you want a list of RE and their recognition sites, check and 
biotechnology supply catalogue. Alternatively, drop me a line...I think 
I've got a small list as the information file of some program for finding 
RE sites in a DNA sequence.
					Vic Drover
					vdrover at kean.ucs.mun.ca
					St. John's, NF.