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#RNA primer

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Replication in Prokaryotes

RNA primer removal in prokaryotes is done by

Lagging strand synthesis leaves behind RNA primers that must be removed to create contiguous DNA strand before ligation. In prokaryotes DNA polymerase I performs this task using intrinsic 5' to 3' exonuclease that degrades RNA while simultaneously polymerizing DNA forward process called nick translation efficiently replacing RNA with DNA. RNase H also can clip RNA primers but main removal during replication is Pol I specifically. Pol III lacks this forward exonuclease, Pol II has none. After Pol I fills gap, remaining nick sealed by NAD-dependent DNA ligase.

Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 11: Pol I 5' to 3' exonuclease removes RNA primers in Okazaki processing

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Replication Basics

Primer used in DNA replication is usually

DNA polymerases are unable to initiate strand synthesis de novo, requiring pre-existing hydroxyl to elongate. Primase, specialized RNA polymerase subunit of Pol α-primase complex in eukaryotes and DnaG in bacteria, synthesizes short 8-12 nucleotide RNA primer complementary to ssDNA template, providing 3' OH substrate. RNA primer is later removed by RNase H and FEN1 and replaced by DNA via Pol δ during lagging strand maturation. Use of RNA allows marking of nascent fragments and distinction from bulk DNA for removal, prevents errors from ab initio DNA synthesis and ensures strand identity. Lead

Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 5: Primer Used in DNA Replication is Usually RNA

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