What is the Difference Between DNA Polymerase and Klenow Fragment

The main difference between DNA polymerase and Klenow fragment is that DNA polymerase is the enzyme that catalyzes the synthesis of DNA molecules, whereas the Klenow fragment is the largest segment of DNA polymerase I obtained by the enzymatic cleavage of protease subtilisin.

DNA polymerase and Klenow fragment are two types of protein components that involve in the synthesis of DNA molecules.

Key Areas Covered

1. What is DNA Polymerase
     – Definition, Structure, Function
2. What is Klenow Fragment
     – Definition, Structure, Function
3. Similarities Between DNA Polymerase and Klenow Fragment
     – Outline of Common Features
4. Difference Between DNA Polymerase and Klenow Fragment
     – Comparison of Key Differences

Key Terms                                                                                                                  

DNA Polymerase, Klenow Fragment

What is DNA Polymerase

DNA polymerase is the enzyme responsible for the synthesis of DNA inside the cell. Some of the significant features of DNA polymerase include the addition of nucleotides in the 5′ to 3′ direction on the growing strand and the requirement of an RNA primer – in other words, a pre-existing 3′-OH group for the initiation of synthesis. Generally, in eukaryotes, six types of DNA polymerases occur; they are DNA polymerases α, β, γ, δ, ε, and ζ. However, only α, δ, and ε polymerases take part in DNA replication. Other DNA polymerases take part in DNA repair.

Figure 1: DNA Polymerase

Moreover, the main types of DNA polymerases that occur in prokaryotes include DNA polymerase I, II, III, IV, and V. Here, DNA polymerase I has both 3′ to 5′ and 5′ to 3′ exonuclease activity. Additionally, DNA polymerase II only has 3′ to 5′ exonuclease activity. Meanwhile, DNA polymerase III holoenzyme is the main enzyme responsible for DNA replication in prokaryotes. On the contrary, DNA polymerase IV takes part in non-targeted mutagenesis. DNA polymerase V takes part in DNA repair.

What is Klenow Fragment

The Klenow fragment is the result of the proteolytic digestion of E. coli DNA polymerase I by the action of the enzyme protease subtilisin. Usually, this digestion produces two fragments, a large fragment and a small fragment. Here, the largest fragment is the Klenow fragment that contains 5′ to 3′ polymerase and 3′ to 5′ exonuclease (proofreading) activity domains. The main function of the Klenow fragment is to undergo DNA synthesis by the 5′ to 3′ polymerase activity. In addition, its 3′ to 5′ exonuclease activity is responsible for the elimination of improperly inserted bases while polymerization proceeds. This process is called the proofreading activity.

Figure 2: Klenow Fragment and DNA Polymerase I

Since the Klenow fragment contains the entire E. coli, DNA polymerase Ⅰ5′ to 3′ polymerase activity is important when the polymerization activity is required. In addition to that, it is important to fill 5′ overhangs, sequence DNA, and synthesize dsDNA, probes, and proteins. Moreover, it removes 3′ overhangs to form blunt ends. However, the Klenow fragment is unable to degrade 5’ ends. The Klenow fragment is important to generate probes using random primers. It is also important for the second strand cDNA synthesis.   

Similarities Between DNA Polymerase and Klenow Fragment

• DNA polymerase and Klenow fragment are two types of protein components.
• Both take part in the synthesis of DNA molecules.
• Both contain 5’→3′ polymerase, 3’→5′ exonuclease activities.

Difference Between DNA Polymerase and Klenow Fragment

Definition

DNA polymerase refers to a type of enzyme that is responsible for forming new copies of DNA in the form of nucleic acid molecules, while Klenow fragment refers to a large protein fragment produced when DNA polymerase I from E. coli is enzymatically cleaved by the protease subtilisin.

Significance

DNA polymerase is the enzyme that catalyzes the synthesis of DNA molecules, while the Klenow fragment is the largest segment of DNA polymerase I obtained by the enzymatic cleavage of protease subtilisin.

Activity

DNA polymerase contains 5’→3′ polymerase, 3’→5′ exonuclease, and 5’→3′ exonuclease activities, while the Klenow fragment contains only 5’→3′ polymerase and 3’→5′ exonuclease activities.

Function

The main function of DNA polymerase is to synthesize DNA molecules, while the main function of the Klenow fragment is to remove 3’ overhangs or fill in 5’ overhangs to form blunt ends.

Conclusion                                                      

In brief, DNA polymerase and Klenow fragment are two types of protein components of the enzyme for the synthesis of DNA. Generally, DNA polymerase is the enzyme responsible for the synthesis of new DNA molecules. It contains 5’→3′ polymerase, 3’→5′ exonuclease, and 5’→3′ exonuclease activities. In comparison, the Klenow fragment is the result of the enzymatic digestion of DNA polymerase I by the enzyme protease subtilisin. It contains only 5’→3′ polymerase and 3’→5′ exonuclease activities. In addition, the main function of the Klenow fragment is to remove 3’ overhangs or fill in 5’ overhangs to form blunt ends. Therefore, the main difference between DNA polymerase and Klenow fragment is the type of activities of each protein.                  

References:                

1. Biolabs, N. E. (n.d.). DNA polymerase I, large (klenow) fragment. NEB. Retrieved March 20, 2023

Image Courtesy:

1. “DNA polymerase” By Yikrazuul – Own work (CC BY SA-3.0) via Commons Wikimedia
2. “PolymeraseDomains” By Unknown – Own Work (Public Domain) via Commons Wikimedia