Direction of Replication

In DNA synthesis, new nucleotides are joined one at a time to the 3' end of the newly synthesized strand. DNA poly-merases, the enzymes that synthesize DNA, can add nucleotides only to the 3' end of the growing strand (not the 5' end), so new DNA strands always elongate in the same 5'-to-3' direction (5':3'). Because the two single-stranded DNA templates are antiparallel and strand elongation is always 5':3', if synthesis on one template proceeds from, say, right to left, then synthesis on the other template must proceed in the opposite direction, from left to right (iFigure 12.8). As DNA unwinds during replication, the antiparallel nature of the two DNA strands means that one template is exposed in the 5': 3' direction and the other template is exposed in the 3': 5' direction (see Figure

12.8); so how can synthesis take place simultaneously on both strands at the fork?

As the DNA unwinds, the template strand that is exposed in the 3':5' direction (the lower strand in Figures 12.8 and

12.9) allows the new strand to be synthesized continuously, in the 5': 3' direction. This new strand, which undergoes continuous replication, is called the leading strand.

The other template strand is exposed in the 5': 3' direction (the upper strand in Figures 12.8 and 12.9). After a short length of the DNA has been unwound, synthesis must proceed 5':3'; that is, in the direction opposite that of unwinding (I Figure 12.9). Because only a short length of DNA needs to be unwound before synthesis on this strand gets started, the replication machinery soon runs out of template. By that time, more DNA has unwound, providing new template at the 5' end of the new strand. DNA synthesis must start anew at the replication fork and proceed in the direction opposite that of the movement of the fork until it runs into the previously replicated segment of DNA. This process is repeated again and again, so synthesis of this strand is in short, discontinuous bursts. The newly made strand that undergoes discontinuous replication is called the lagging strand.

The short lengths of DNA produced by discontinuous replication of the lagging strand are called Okazaki fragments, after Reiji Okazaki, who discovered them. In bacterial cells, each Okazaki fragment ranges in length from about 1000 to 2000 nucleotides; in eukaryotic cells, they are about 100 to 200 nucleotides long. Okazaki fragments on the lagging strand are linked together to create a continuous new DNA molecule.

Let's relate the direction of DNA synthesis to the modes of replication examined earlier. In the theta model (I Figure 12.10a), the DNA unwinds at one particular location, the origin, and a replication bubble is formed. If the bubble has two forks, one at each end, synthesis takes place simultaneously at both forks (bidirectional replication). At each fork, synthesis on one of the template strands proceeds in the same direction as that of unwinding; the newly replicated strand is the leading strand with continuous replication. On the other template strand, synthesis is proceeding in the direction opposite that of unwinding; this newly synthesized strand is the lagging strand with discontinuous replication. Focus on just one of the template strands within the bubble. Notice that synthesis on this template

12.8 DNA synthesis takes place simultaneously but in opposite directions on the two DNA template strands. DNA replication at a single replication fork begins when a double-stranded DNA molecule unwinds to provide two single-strand templates.

strand is continuous at one fork but discontinuous at the other. This difference arises because DNA synthesis is always in the same direction (5': 3'), but the two forks are moving in opposite directions.

Replication in the rolling-circle model (I Figure 12.10b) is somewhat different, because there is no replication bubble.

^ On the lower template strand, DNA synthesis proceeds continuously in the 5'—3' direction, the same as that of unwinding.

^ On the lower template strand, DNA synthesis proceeds continuously in the 5'—3' direction, the same as that of unwinding.

Unwinding —i and replication Newly synthesized DNA

On the upper template strand, DNA synthesis begins at the fork and proceeds in the direction opposite that of unwinding; so it soon runs out of template.

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