Question

Describe what a palindromic sequence is in DNA. How do restriction enzymes work? What would the sticky ends be for EcoR1 (which cuts GAATTC between the G and A)?

Answer 1

A palindromic sequence is a sequence on DNA which have the same sequence when read in 5' -3' direction on one strand and 5'-3' direction in the complementary strand or we can say that a palindromic sequence is read same on the same directions but on two complementary strands of DNA.

e.g. Consider a serquence 5' ------ AAGCTT---- 3'

3' ------TTCGAA----- 5'

The sequence is read as AAGCTT from 5' - 3' end in one strand and the sequence on the complementary strand is same AAGCTT when read in 5'-3' direction on the complementary strand. hence this is an example of palindrome.

Restriction enzymes are the endonucleases which cut DNA at specific sites. These sites have variable base length but the important feature of these sequences is that they are palindromic sequences. Each restriction enzyme cuts at the specific palindromic sequence.

e.g. EcoRI is the restriction enzyme which specifically cuts DNA at GAATTC palindromic site.

The restriction endonuclease digestion will be shown as:

5' --------GIAATTC---------- 3'

3' --------CTTAAIG----------- 5'

The enzyme EcoRI cuts between G and A on both strands (indicated by Red lines)

The product of the restriction digestion is:

  5' --------G AATTC---------- 3'

3' --------CTTAA G----------- 5'

The digestion generates sticky ends which are AATT on one fragment (Green) and AATT on the other fragment (Blue) when read in 5' - 3' direction on both fragments.

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