Question

Study the sequence of bases in a DNA molecule that is shown below and answer the question.

\( 5^{\prime} \) - GAATTC - \( 3^{\prime} \)

\( 3^{\prime} \) - CTTAAG - \( 5^{\prime} \)

How do these enzymes function ?

Hint:

The sequence is a palindrome. Think about where the enzyme cuts each strand and what kind of ends are left.

Answer 1

Step 1: Identify the sequence and the enzyme:
The given sequence GAATTC is a palindromic sequence. It reads the same on both strands in the \( 5^{\prime} \) to \( 3^{\prime} \) direction.
The enzyme that recognises it is the restriction endonuclease EcoRI.

Step 2: How the enzyme scans the DNA:
Restriction endonucleases inspect the length of a DNA molecule. They bind to the DNA at the recognition site.

Step 3: How the enzyme cuts:
The enzyme cuts both strands a little away from the centre of the palindrome. EcoRI cuts between G and A on each strand.
The two cuts are not opposite each other. So the DNA gets single stranded overhangs, called sticky ends.

Step 4: Why this is useful:
Sticky ends pair with complementary sticky ends of another DNA cut by the same enzyme. A DNA ligase then joins them.

Final Answer:
Restriction endonucleases recognise the palindromic site, bind to it and cut both strands at specific points, leaving sticky ends.