The Hydrolysis of DNA

There are many ways to hydrolyze DNA, either chemically or enzymatically.

Chemical Hydrolysis

 At very low pH (1 or less) phosphodiester bond hydrolysis occurs accompanied by breakage of the N glycosylic bond between the base and the deoxyribose.

 At very high pH, DNA is resistant to hydrolysis.

Nucleases - enzymes which hydrolyze nucleic acids

 If Nuclease hydrolyzes DNA they are termed DNAases

DNAases are classified by the nature and location of their action (Fig. 1):

Single strand break
Double strand break
Cut only 3' or 5' end nucleotide from DNA (exonuclease)
Cut only in middle of DNA (endonuclease)

Some endonucleases recognize specific base sequences between 4 and 8 base pairs in length.

This class of endonuclease is very critical to the technique of genetic engineering.
Type II Restriction Endonucleases recognize a palindromic sequence (reads the same forward as backwards) and make staggered cuts.

 For example, the EcoRI endonuclease recognizes the palindromic sequence:

     5'------G-A-A-T-T-C-----3'
     3'------C-T-T-A-A-G-----5'

Note that reading this sequence on either the top or bottom strands from the 5' to 3' ends it reads in the same order (palindromic).

The enzyme will cut the phosphodiester bond between G-A on both strands, resulting in a staggered double-stranded cut of the DNA.
 

     5'------G                     A-A-T-T-C-----3'
     3'------C-T-T-A-A                     G-----5'
 

This is useful in genetic engineering because the overhangs can be hybridized to like cut DNA from another source and a fragment inserted at the original restriction enzyme site:
 

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5'--G A-A-T-T-C---insert-G A-A-T-T-C--3'
3'--C-T-T-A-A G---insert-C-T-T-A-A G--5'

Enzymes called ligases can reform the phosphodiester bonds -:

Quiz