6. DNA synthesis is semidiscontinuous

13.6 DNA synthesis is semidiscontinuous

Key terms defined in this section

Lagging strand of DNA must grow overall in the 3´-5´ direction and is synthesized discontinuously in the form of short fragments (5´-3´) that are later connected covalently.
Leading strand of DNA is synthesized continuously in the 5´-3´ direction.
Okazaki fragments are the short stretches of 1000-2000 bases produced during discontinuous replication; they are later joined into a covalently intact strand.
Semidiscontinuous replication is mode in which one new strand is synthesized continuously while the other is synthesized discontinuously.

The antiparallel structure of the two strands of duplex DNA poses a problem for replication. As the replication fork advances, daughter strands must be synthesized on both of the exposed parental single strands. The fork moves in the direction from 5′ V3′ on one strand, and in the direction from 3′ V5′ on the other strand. Yet nucleic acids are synthesized only from a 5′ end toward a 3′ end. The problem is solved by synthesizing the strand that grows overall from 3′ V5′ in a series of short fragments, each actually synthesized in the "backwards" direction, that is, with the customary 5′ V3′ polarity.

Figure 13.9 The leading strand is synthesized continuously while the lagging strand is synthesized discontinuously.

Consider the region immediately behind the replication fork, as illustrated in Figure 13.9. We describe events in terms of the different properties of each of the newly synthesized strands:

• On the leading strand DNA synthesis can proceed continuously in the 5′ to 3′ direction as the parental duplex is unwound.
  
• On the lagging strand a stretch of single-stranded parental DNA must be exposed, and then a segment is synthesized in the reverse direction (relative to fork movement). A series of these fragments are synthesized, each 5′ V3′; then they are joined together to create an intact lagging strand.

Discontinuous replication can be followed by the fate of a very brief label of radioactivity. The label enters newly synthesized DNA in the form of short fragments, sedimenting in the range of 7 V11S, corresponding to ~1000 V2000 bases in length. These Okazaki fragments are found in replicating DNA in both prokaryotes and eukaryotes. After longer periods of incubation, the label enters larger segments of DNA. The transition results from covalent linkages between Okazaki fragments.

(The lagging strand must be synthesized in the form of Okazaki fragments. For a long time it was unclear whether the leading strand is synthesized in the same way or is synthesized continuously. All newly synthesized DNA is found as short fragments in E. coli. Superficially, this suggests that both strands are synthesized discontinuously. However, it turns out that not all of the fragment population represents bona fide Okazaki fragments; some are pseudofragments, generated by breakage in a DNA strand that actually was synthesized as a continuous chain. The source of this breakage is the incorporation of some uracil into DNA in place of thymine. When the uracil is removed by a repair system, the leading strand has breaks until a thymine is inserted.)

So the lagging strand is synthesized discontinuously and the leading strand is synthesized continuously. This is called semidiscontinuous replication.