Ligase catalyzes a reaction between the 5′ phosphate and the 3′ hydroxyl groups at the ends of DNA molecules. The enzyme calf intestinal phosphatase catalyzes the removal of the 5′5′ phosphate from DNA molecules. What would be the consequence of treating a cloning vector, before ligation, with calf intestinal phosphatase?

Verified step by step guidance

1. Understand the role of DNA ligase: DNA ligase catalyzes the formation of a phosphodiester bond between the 5′ phosphate group of one DNA strand and the 3′ hydroxyl group of another, effectively joining DNA fragments together.
2. Recognize the function of calf intestinal phosphatase (CIP): CIP removes the 5′ phosphate groups from DNA ends, leaving 5′ hydroxyl groups instead.
3. Consider the consequence of removing the 5′ phosphate groups on the cloning vector: Since ligase requires a 5′ phosphate to form the phosphodiester bond, the absence of this group on the vector DNA ends will prevent ligation from occurring.
4. Analyze the practical implication: Treating the cloning vector with CIP before ligation will prevent the vector from self-ligating (re-circularizing without an insert), which is often used to reduce background colonies in cloning experiments.
5. Summarize the overall effect: The vector DNA will be unable to ligate to itself or to any insert DNA lacking a 5′ phosphate, thus promoting the insertion of DNA fragments that have intact 5′ phosphates during the cloning process.

Key Concepts

DNA Ligase Function

DNA ligase is an enzyme that joins DNA strands by catalyzing the formation of a phosphodiester bond between the 3′ hydroxyl group of one nucleotide and the 5′ phosphate group of another. This activity is essential for sealing nicks in the DNA backbone during replication and cloning.

Role of 5′ Phosphate in Ligation

The 5′ phosphate group on DNA ends is critical for ligation because DNA ligase requires it to form the phosphodiester bond. Without the 5′ phosphate, ligase cannot join DNA fragments, preventing the formation of continuous DNA strands.

Effect of Calf Intestinal Phosphatase (CIP) Treatment

Calf intestinal phosphatase removes 5′ phosphate groups from DNA ends, thereby preventing self-ligation of cloning vectors. This treatment reduces background colonies by ensuring that only DNA fragments with 5′ phosphates (e.g., inserts) can be ligated into the vector.