RNAprimer

An RNA primer is a short sequence of ribonucleic acid synthesized to initiate DNA synthesis. It provides a free 3'-hydroxyl group for DNA polymerases to start adding deoxynucleotides during DNA replication.

In bacteria, the RNA primer is created by primase, typically a DnaG-family enzyme. Primase lays down an RNA fragment of about 10 nucleotides on both the leading and lagging strands. DNA polymerase III then extends this primer with DNA nucleotides, while the lagging strand is synthesized discontinuously as Okazaki fragments.

In eukaryotes, the process is more complex. The primase–DNA polymerase α complex generates a short RNA primer of around 10 nucleotides, which is then extended briefly by DNA polymerase α before renewal of DNA synthesis by larger replicative polymerases (DNA polymerase δ on the lagging strand and ε on the leading strand). The RNA segments are later removed and replaced with DNA.

Removal and replacement of RNA primers differ between organisms. In bacteria, DNA polymerase I exhibits 5' to 3' exonuclease activity that displaces RNA primer and fills the gap with DNA, after which DNA ligase seals the nick. In eukaryotes, RNase H and other nucleases remove RNA primers, DNA polymerase δ fills in the resulting gaps, and DNA ligase seals the final nick.

RNA primers are essential for initiating DNA replication and for the proper processing of Okazaki fragments. They are temporary scaffolds that are subsequently erased and replaced with a continuous DNA strand, ensuring faithful genome duplication.