Prokaryotic DNA Replication: RNA primer 

DNA pols cannot initiate synthesis of a complementary strand of DNA on a totally single-stranded template. Rather, they require an RNA primer, which is a short piece of RNA base-paired to the DNA template, thereby forming a double-stranded DNA–RNA hybrid. The free hydroxyl group on the 3′-end of the RNA primer serves as the first acceptor of a deoxynucleotide by action of a DNA pol (Fig. 1). [Note: Recall that glycogen synthase also requires a primer .]

Figure 1: Use of an RNA primer to initiate DNA synthesis. and = phosphate; dCTP = deoxycytidine triphosphate.
1. Primase: A specific RNA polymerase, called primase (DnaG), synthesizes the short stretches of RNA (~10 nucleotides long) that are complementary and antiparallel to the DNA template. In the resulting hybrid duplex, the U (uracil) in RNA pairs with A in DNA. As shown in Figure 2, these short RNA sequences are constantly being synthesized at the replication fork on the lagging strand, but only one RNA sequence at the origin of replication is required on the leading strand. The substrates for this process are 5′-ribonucleoside triphosphates, and pyrophosphate is released as each ribonucleoside monophosphate is added through formation of a 3′→5′-phosphodiester bond. [Note: The RNA primer is later removed, as described in F. below.]

Figure 2:  Elongation of the leading and lagging strands. [Note: The DNA sliding clamp is not shown for the lagging strand.]
2. Primosome: The addition of primase converts the prepriming complex of proteins required for DNA strand separation to a primosome. The primosome makes the RNA primer required for leading-strand synthesis and initiates Okazaki fragment formation in discontinuous lagging-strand synthesis. As with DNA synthesis, the direction of synthesis of the primer is 5′→3′.

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