Difference Between Klenow Fragment and DNA Polymerase 1

The key difference between Klenow fragment and DNA polymerase 1 is that Klenow fragment is a large portion of DNA polymerase 1 which lacks 5′ to 3′ exonuclease activity while DNA polymerase is an enzyme of E. coli which has all three domains including 5′ to 3′ exonuclease activity.

DNA polymerase is one of the key enzymes involved in DNA replication in living organisms. There are different forms of DNA polymerase enzyme found in eukaryotes and prokaryotes based on the size and shape. DNA polymerase 1, 2 and 3 are found only in prokaryotic organisms, and they play different roles in DNA replication. DNA polymerase 1 has three domains with 5′ to 3′ polymerase, 3′ to 5′ exonuclease activity and 5′ to 3′ exonuclease activity. Klenow fragment is a proteolytic product of DNA polymerase 1. It possesses 5 to 3′ polymerase and 3′ to 5′ exonuclease activities of intact DNA polymerase 1, but it lacks the 5′ to 3′ exonuclease activity.

CONTENTS

1. Overview and Key Difference
2. What is Klenow Fragment 
3. What is DNA Polymerase 1
4. Similarities Between Klenow Fragment and DNA Polymerase 1
5. Side by Side Comparison – Klenow Fragment vs DNA Polymerase 1 in Tabular Form
6. Summary

What is Klenow Fragment?

Klenow fragment is a large portion of DNA polymerase 1. Unlike DNA polymerase 1, 5′ to 3′ exonuclease activity is not seen in Klenow fragment since it lacks the 5′ to 3′ forward exonuclease domain. Klenow fragments are produced by digesting DNA polymerase 1 with a protease called subtilisin, which is a protein-digesting enzyme. In some applications, the 3′ to 5′ exonuclease activity of the Klenow fragment becomes undesirable. It can be removed by introducing a mutation in the gene that encodes the Klenow fragment. The resulting enzyme which has only the 5′ to 3′ polymerase activity is known as the exo-Klenow fragment. Morphologically, Klenow fragment resembles the human right hand. It has N-terminal 3′-5′ exonuclease domain and the C-terminal polymerase domain separated by about 30 A.

Klenow fragment is an important tool in molecular biological techniques. Klenow fragments have multiple uses. They are extremely important in blunt-end cloning in order to produce blunt fragments. Klenow fragments can remove 3′ overhangs or fill 5′ overhangs to form blunt ends. Moreover, Klenow fragments are used to synthesize double-stranded DNA from single strands. Furthermore, they are used to prepare radioactively labelled probes using the 5’to 3′ DNA dependant DNA polymerase activity.

What is DNA Polymerase 1?

DNA polymerase 1 (Pol 1) is an enzyme found in prokaryotes which is needed for bacterial DNA replication. It is the first type of DNA polymerase discovered by Arthur Kornberg in 1956. Pol 1 is the most abundant polymerase in E. coli. It is encoded by the gene polA and composed of 928 amino acids. It consists of three domains. All three domains fulfil distinct functions. Two domains carry out 5′ to 3′ exonuclease activity and 3′ to 5′ exonuclease activity. Due to this activity possessed by Pol 1, it is popular as a DNA repairing enzyme rather than a DNA replicating enzyme. Third domain has the ability to catalyze multiple polymerizations (5′ to 3′) prior to the release the template DNA and connecting Okazaki fragments together by filling new DNA and removing RNA primers.

Pol 1 isolated from E Coli was extensively used in molecular applications. However, once the Taq Polymerase was discovered, it replaced the E Coli Pol 1 in PCR technology. Taq polymerase is kind of a thermostable DNA polymerase that belongs to Pol 1.

What are the Similarities Between Klenow Fragment and DNA Polymerase 1?

• Klenow fragment is a big portion of DNA polymerase 1.
• They have 5’to 3′ DNA dependent DNA polymerase activity and 3’to 5′ exonuclease activity that mediate proofreading.
• They are used for multiple purposes.

What is the Difference Between Klenow Fragment and DNA Polymerase 1?

The key difference between Klenow fragment and DNA polymerase 1 is that Klenow fragment lacks 5′ to 3′ exonuclease activity while DNA polymerase 1 has 5′ to 3′ exonuclease activity. Therefore, Klenow fragment has two domains, while DNA polymerase 1 has all three domains.

Below infographic shows more details of the difference between Klenow fragment and DNA polymerase 1.

Summary – Klenow Fragment vs DNA Polymerase 1

DNA polymerase 1 is an enzyme of E. coli which has three domains as 5′ to 3′ polymerization domain, 3′ to 5′ exonuclease domain and 5′ to 3′ exonuclease domain. Klenow fragment is a large portion of DNA polymerase. It lacks one domain of DNA polymerase 1, which is the 5′ to 3′ exonuclease domain. The key difference between Klenow fragment and DNA polymerase 1 is that Klenow fragments do not have  5′ to 3′ exonuclease domain while DNA polymerase 1 has 5′ to 3′ exonuclease domain.

Reference:

1. “DNA Polymerase I – An Overview | Sciencedirect Topics”. Sciencedirect.Com, 2020, Available here.
2. “Klenow Fragment”. En.Wikipedia.Org, 2020, Available here.

Image Courtesy:

1. “PolymeraseDomains” By (unknown) "Molecule of the Month", March 2000 – Protein Data Bank, (Public Domain) via Commons Wikimedia
2. “DNA polymerase” Von Yikrazuul – Eigenes Werk (CC BY-SA 3.0) via Commons Wikimedia