Leading and lagging strands
DNA polymerase builds only in the 5′ to 3′ direction, and the two template strands run in opposite directions. Put those two facts together at a fork that opens in one direction, and the two new strands have to be made in very different ways.
The leading strand: one smooth run
On one template strand, building 5′ to 3′ means heading straight toward the opening fork. As helicase unzips more DNA, the polymerase just keeps going. This daughter strand, made continuously in the same direction the fork moves, is the leading strand. It needs only one RNA primer, laid down at the origin.
The lagging strand: short pieces, backward
On the other template strand, building 5′ to 3′ means heading away from the fork. The polymerase can make only a short stretch before it runs into the piece it built earlier. Meanwhile the fork has opened more DNA up ahead, so a new primer is laid down near the fork and another short piece is built, again pointing away from the fork.
This daughter strand, made as a series of short pieces in the direction opposite the fork’s movement, is the lagging strand. Its pieces are called Okazaki fragments, after Reiji and Tsuneko Okazaki, who discovered them. Every Okazaki fragment begins with its own RNA primer.
Notice that neither template is special. The strands are made differently only because the two templates are antiparallel and DNA polymerase can build only 5′ to 3′. Both daughter strands grow 5′ to 3′; what differs is whether that direction points toward the fork or away from it.
Two forks, swapped roles
An origin produces two forks moving in opposite directions. Each fork makes one leading strand and one lagging strand, but the forks use opposite templates for each. If the fork moving left uses the top template for its leading strand, then the fork moving right uses that same top template for its lagging strand, and vice versa.
Finishing the lagging strand in E. coli
In the bacterium E. coli, two DNA polymerases share the work. DNA polymerase III does most of the copying. It has a ring-shaped part called the clamp protein that keeps it from falling off the template as it slides along, so it can add many nucleotides in one go. Staying attached like this is called processivity. DNA polymerase I does cleanup.
On the leading strand, primase makes a single primer at the origin, and DNA polymerase III extends it toward the fork. The lagging strand takes more steps:
- DNA primase makes an RNA primer on the exposed template near the fork.
- DNA polymerase III extends the primer with DNA, building an Okazaki fragment until it reaches the previous fragment.
- DNA polymerase I removes the RNA primer of the previous fragment, chewing it away in the 5′ to 3′ direction.
- DNA polymerase I fills the resulting gap with DNA.
- DNA ligase forms the last missing covalent bond in the backbone, joining the two fragments into one continuous strand.
Who does what
| Protein | Job in replication |
|---|---|
| DNA helicase | Separates the two strands of the double helix |
| Single-strand binding protein | Holds the separated strands apart so they don’t re-form a helix |
| DNA topoisomerase | Removes tightened coils (supercoils) ahead of the fork |
| DNA primase | Makes short RNA primers |
| DNA polymerase | Builds the leading and lagging strands, removes RNA primers, and fills the gaps (in E. coli: III builds, I removes primers and fills in) |
| DNA ligase | Joins adjacent Okazaki fragments with a covalent bond |
Check yourselfWhich daughter strand needs more RNA primers, and why?
The lagging strand. It is built away from the fork as many separate Okazaki fragments, and each fragment needs its own primer. The leading strand is built continuously toward the fork and needs only one primer at the origin.
Practice questions
1 of 2
What are the short pieces of newly made DNA that are later joined to form the lagging strand?
2 of 2
Which daughter strand is built continuously, in the same direction the replication fork moves?