42, During replication, the RNA primer is degraded by the 5′ – 3′ exonuclease activity of
(1) RNAseH

(2) FEN-1 (flap endonuclease 1)

(3) Topoisomerase II B

(4) DNA polymerase

Introduction

During DNA replication, short RNA primers are synthesized to initiate DNA synthesis on both the leading and lagging strands. These RNA primers must be removed and replaced with DNA to form a continuous strand. The removal of RNA primers is carried out by enzymes with 5′→3′ exonuclease activity, which degrade RNA nucleotides starting from their 5′ ends.

Candidate Enzymes for RNA Primer Removal

1. RNase H

   • Degrades the RNA strand of RNA-DNA hybrids but does not have strong 5′→3′ exonuclease activity to remove the entire primer.

   • Acts mainly by nicking RNA in hybrids but leaves some RNA nucleotides behind.

2. FEN-1 (Flap Endonuclease 1)

   • A key enzyme in eukaryotes responsible for removing RNA primers during lagging strand synthesis.

   • Possesses 5′→3′ exonuclease and flap endonuclease activities, cleaving displaced RNA primers as flap structures during Okazaki fragment maturation.

   • Works in coordination with DNA polymerase δ or ε to remove primers and allow gap filling.

3. Topoisomerase II B

   • Involved in relieving supercoiling and DNA topology during replication, not in primer removal.

4. DNA Polymerase

   • DNA polymerase I in prokaryotes has 5′→3′ exonuclease activity that removes RNA primers while simultaneously synthesizing DNA (nick translation).

   • In eukaryotes, DNA polymerases δ and ε lack 5′→3′ exonuclease but work with FEN-1 to remove primers.

Summary by Organism

Correct Answer for the Question

Given the options and the context of 5′→3′ exonuclease activity specifically responsible for RNA primer removal:

(2) FEN-1 (flap endonuclease 1)

Explanation

• FEN-1 is the major enzyme that removes RNA primers during eukaryotic DNA replication by cleaving the RNA flap generated when DNA polymerase displaces the RNA primer.

• RNase H initiates degradation but does not completely remove primers.

• DNA polymerase (specifically DNA polymerase I in prokaryotes) also removes primers but is not the best answer if the question targets eukaryotic replication or general 5′→3′ exonuclease activity.

• Topoisomerase II B is unrelated to primer removal.

Conclusion

The RNA primer is degraded primarily by the 5′→3′ exonuclease activity of FEN-1 during DNA replication, ensuring proper maturation of Okazaki fragments and continuity of the lagging strand.