Replication

Another property of DNA polymerase poses a second problem in understanding replication. DNA polymerases are unable to initiate synthesis of a new DNA strand from scratch; they can only add nucleotides to the 3′ end of an existing strand, which can be either DNA or RNA. Thus, the synthesis of each strand must be started (primed) by some other enzyme.

The priming problem is solved by a specialized RNA polymerase, called DNA primase, which synthesizes a short (3 to 10 nucleotides) RNA primer strand that DNA polymerase extends. On the leading strand, only one small primer is required at the very beginning. On the lagging strand, however, each Okazaki fragment requires a separate primer.

Before Okazaki fragments can be linked together to form a continuous lagging strand, the RNA primers must be removed and replaced with DNA. In bacteria, this processing is accomplished by the combined action of RNase H and DNA polymerase I. RNase H is a ribonuclease that degrades RNA molecules in RNA/DNA double helices. In addition to its polymerase activity, DNA polymerase I is a 5′-to-3′ nuclease, so it too can degrade RNA primers. After the RNA primer is removed and the gap is filled in with the correct DNA, DNA ligase seals the nick between the two Okazaki fragments, making a continuous lagging strand.