primase and the RNA primer
/ PRY-mace /
DNA polymerase, the enzyme that builds new DNA, has a strange limitation: it can only add to an existing chain, never start one from scratch. It is like a printer that can keep adding pages to a stack but cannot lay down the very first page. So something else has to write the first few letters to get things going. That starter piece is the primer, and the enzyme that makes it is primase.
Primase is a special RNA polymerase. Unlike DNA polymerase, it can start a brand-new strand on a bare template, so it lays down a short stretch of RNA — typically only about ten nucleotides — complementary to the DNA template. This little RNA primer gives DNA polymerase the free 3' end it needs to begin extending with DNA. On the continuous leading strand, just one primer is needed at the start; on the discontinuous lagging strand, primase must lay down a fresh primer for every single Okazaki fragment, over and over.
Why RNA and not DNA? Starting a strand from nothing is error-prone, and using RNA flags these starter sequences as temporary and 'to be replaced.' Later, the RNA primers are removed (in bacteria by DNA polymerase I, in eukaryotes by other nucleases), the gaps are filled in with DNA, and DNA ligase seals the joins. So no RNA remains in the finished DNA — the primer is scaffolding that is taken down once the building stands.
Primase reads a DNA template ...3'-T A C G...5' and lays down the short RNA 5'-A U G C...-3' (note U, the RNA base, not T). DNA polymerase then grabs that primer's free 3' end and continues the strand in DNA. Later the AUGC RNA is excised and replaced by DNA.
The primer is a short RNA starter, later removed.
The replication primer is made of RNA, not DNA — a common confusion. The lab technique PCR uses short DNA primers instead, because there the primers are meant to stay in the product.