BIOG 1105-1106 | Cornell Introductory Biology, Individualized Instruction

As you have already learned, the two strands of DNA are antiparallel. This presents real difficulties during replication. The DNA polymerase III enzyme synthesizes most of the DNA. The enzyme has two subunits because both strands of parental DNA must be replicated in the same place at the same time.

Because DNA can only be synthesized in the 5' to 3' direction, one of the strands (the 3' to 5' strand) can be copied continuously and is called the leading strand, while the other, the lagging strand, is synthesized in fragments so that the 5' to 3' polymerization leads to overall growth in the 3' to 5' direction. This may be accomplished by a looping of the template for the lagging strand (see Figure below). The lagging strand would then pass through the polymerase site in the same direction as the leading-strand template in the other subunit. DNA polymerase III would then have to let go of the lagging strand template (after about 1,000 nucleotides have been added to the lagging strand). A new loop would then be formed. The gaps between fragments of the lagging strand are filled by another polymerase, DNA polymerase I, and the enzyme DNA ligase joins the fragments.

The looping of the template for the lagging strand enables the DNA polymerase III enzyme (colored yellow) at the replication fork to synthesize both daughter strands in the 5' to 3' direction. The leading strand is shown in blue, the lagging strand in green.

This figure (at left, click to enlarge) may help explain why the lagging strand must be looped during DNA synthesis. A key point is that DNA polymerase III in the replication fork is organized into a dimer - a pair of molecules linked together. Both DNA polymerases (pink structures in the diagram) are oriented in the same direction and, as you know, will move along the parent strand from the 3' end to the 5' end, synthesizing new DNA in the 5' to 3' direction. The purple ring in the diagram is DnaB helicase, an enzyme that is linked to the DNA polymerase dimer and functions in separating (unwinding) the two parent strands from each other. As helicase moves (relative to the DNA) along, it opens up the replication fork, allowing the polymerases to access the template strands. Since the polymerases are reading the templates from right to left in the diagram, the only way for the bottom template strand to pass through the polymerase in the required 3' to 5' direction is to loop the DNA strand as shown. Upon completion of one Okazaki fragment the polymerase releases that fragment and the DNA strand is pulled forward bringing the next primed region (green) into contact with the polymerase and allowing synthesis of a new fragment to begin.