Understanding RNA Primer Removal in DNA Replication

During DNA replication, both the leading and lagging strands are synthesized. The leading strand is synthesized continuously, while the lagging strand is synthesized discontinuously in short segments called Okazaki fragments. Both types of synthesis require a starting point, which is provided by short sequences of RNA called RNA primers.

These RNA primers are synthesized by an enzyme called primase. Once the DNA polymerase extends the new DNA strand from the 3' end of the primer, the RNA primers must be removed and replaced with DNA nucleotides. This process is particularly crucial on the lagging strand because each Okazaki fragment starts with an RNA primer.

Enzymes Involved in Lagging Strand Processing

Several enzymes play roles in completing the synthesis of the lagging strand, including the removal of RNA primers and joining the DNA fragments:

• DNA Polymerase III: This is the primary enzyme responsible for synthesizing the bulk of the new DNA strand. It extends the DNA chain from the 3' end of a primer (RNA or DNA). It has 5'→ 3' polymerase activity and 3'→ 5' exonuclease activity for proofreading.
• DNA Polymerase I: In E. coli, this enzyme has multiple functions. It has 5'→ 3' polymerase activity (to synthesize DNA), 3'→ 5' exonuclease activity (proofreading), and importantly, 5'→ 3' exonuclease activity. This 5'→ 3' exonuclease activity allows it to degrade RNA or DNA from the 5' end of a nucleotide chain, which is essential for removing RNA primers. After removing the primer, its 5'→ 3' polymerase activity then fills the gap with DNA nucleotides.
• DNA Ligase: This enzyme seals the nicks (breaks in the phosphodiester backbone) that remain after DNA polymerase I has replaced the RNA primer with DNA. It joins the 3' end of one Okazaki fragment to the 5' end of the next.
• Exonucleases (e.g., 3'→ 5' exonuclease): These enzymes remove nucleotides from the ends of DNA or RNA molecules. While DNA polymerase I and III have 3'→ 5' exonuclease activity for proofreading (removing mismatched nucleotides from the 3' end during synthesis), the specific activity needed to remove the RNA primer from its 5' end is the 5'→ 3' exonuclease activity, which is characteristic of DNA polymerase I in E. coli.

The Role of DNA Polymerase I in Primer Removal

The question asks which enzyme removes the RNA primers from the lagging strand. Based on the functions described above, DNA polymerase I is the enzyme in E. coli primarily responsible for this task. It uses its 5'→ 3' exonuclease activity to remove the RNA nucleotides one by one, moving in the direction of DNA synthesis (5' to 3'). As it removes the RNA, its 5'→ 3' polymerase activity simultaneously adds DNA nucleotides to fill the gap behind it, using the newly synthesized DNA of the previous Okazaki fragment as a template.

Therefore, the enzyme that removes the RNA primers from the lagging strand is DNA polymerase I, utilizing its unique 5'→ 3' exonuclease activity.