DNA replication is initiated at discrete sequences called origin (ori) of replication to which DNA polymerase and accessory proteins bind and copy both strands, as predicted by the semi-conservative replication model (Fig. 2B). In contrast to unidirectional RNA synthesis, DNAreplication in most genomes occurs bidirectionally (Fig. 2B). This results in both continuous and discontinuous synthesis of the same strand on two sides of the origin of replication. Some circular genomes, such as mitochondrial DNA, are replicated unidirectionally. In these cases, replication starting at the ori proceeds continuously in the 5´→3´ direction, followed by discontinuous synthesis of the complementary strand. Termination occurs at the same site as the ori after the circle is completely traversed. During replication of the mitochondrial genome, elongation of the continuous strand pauses at some distance from the ori, resulting in a bubble (Θ structure) structure named a D-(displacement) loop (Fig. 4A).
The single-stranded DNA genomes of certain small E. coli viruses (such as M13 and φX174) are replicated in the form of rolling circles in which unidirectional synthesis of one (virus genome) strand occurs by continuous displacement from the template (complementary strand; Fig. 4A). The initial duplex DNA (called the replicative form or RF) is the template for rolling circle synthesis and is formed first by replication of the single-stranded form. Such a single-stranded circular DNA template has been exploited in recombinant DNA techniques.
Small organisms (e.g., bacteria), as well as plasmids and many viruses, have only one ori sequence per cellular genome (4.7×106 nucleotide pairs in E. coli), which is often an uninterrupted DNA molecule (Figs. 4A and 4B). In complex organisms, with a much larger genome size (∼3×109 nucleotide pairs for mammals), which is divided into multiple discrete chromosomes, thousands of ori sequence are present (Fig. 4C), although not all of them may be active in all cells; this requires that replication be regulated and coordinated.
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