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One type of enzyme, called a primase, is required during DNA replication because DNA polymerases cannot start the synthesis of a new strand of DNA; they can only attach deoxynucleotides to a preexisting 3′ OH group. The 3′ OH group to which DNA polymerase adds a deoxynucleotide is called the primer (Figure 1.7). The requirement for a primer for DNA polymerase creates an apparent dilemma in DNA replication. When a new strand of DNA is synthesized, there is no DNA upstream (i.e., on the 5′ side) to act as a primer. Primase makes small stretches of RNA that are complementary to the template strand, which are in turn used to initiate, or prime, polymerization of a new strand of DNA (Figure 1.8). In some special situations, an RNA primer for DNA replication can be made by the RNA polymerase used for information processing (i.e., the RNA polymerase that makes all the other RNAs, including mRNA, tRNA, and rRNA; see chapter 2). Unlike DNA polymerase, primase and RNA polymerases do not require a primer to initiate the synthesis of new strands. During DNA replication, a special enzyme activity recognizes and removes the RNA primer (see below).

Table 1.1 Proteins involved in Escherichia coli DNA replication

Protein	Gene	Function
DnaA	dnaA	Initiator protein; primosome (priming complex) formation
DnaB	dnaB	DNA helicase
DnaC	dnaC	Delivers DnaB to replication complex
SSB	ssb	Binding to single-stranded DNA
Primase	dnaG	RNA primer synthesis
DNA ligase	lig	Sealing DNA nicks
DNA gyrase		Supercoiling
α	gyrA	Nick closing
β	gyrB	ATPase
DNA Pol I	polA	Primer removal; gap filling
DNA Pol III (holoenzyme)
α	dnaE	Polymerization
ε	dnaQ	3′-to-5′ editing
RNase H	rnhA	Can aid in RNA primer removal
θ	holE	Present in core (αεθ)
β	dnaN	Sliding clamp
τa	dnaX	Organizes complex; joins leading and lagging DNA Pol III
γb	dnaX	Binds clamp loaders and single-strand-binding protein
δ	holA	Clamp loading
δ'	holB	Clamp loading
χ	holC	Binds single-strand-binding protein
φ	holD	Holds χ to the clamp loader

^aFull-length product of the dnaX gene.

^bShorter product of the dnaX gene produced by translational frameshifting (see chapter 2).