DNA replication at the ends of DNA is an important topic to understand for the MCAT exam. In eukaryotes, there is what is called the ‘end replication problem’ (Figure 1). Recall that during DNA replication, synthesis occurs at both the leading strand and the lagging strand. In the leading strand, which is synthesized in the 5′ to 3′ direction, nucleotides are added continuously by DNA polymerase. In terms of the lagging strand, which moves in the 3′ to 5′ direction, DNA is replicated in fragments since DNA polymerase can only add nucleotides in the 5′ to 3′ direction. In this way, multiple RNA primers are required so that DNA polymerase can function.

The discontinuous nature of DNA synthesis at the lagging strand results in short fragments of synthesized DNA called Okazaki fragments. Also, the RNA primers, since they are made of RNA, have to be replaced with DNA. This action is done by another DNA polymerase, which will connect each DNA strand to the one following it in a 5′ to 3′ direction. The problem, however, is that the last Okazaki fragment, at the end of the lagging strand, does not have a DNA strand before it. Therefore, the DNA polymerase cannot connect the last DNA strand to anything. In other words, there is not a 3′ hydroxyl group for DNA polymerase to use. In this way, since RNA is less stable than DNA, the RNA primer at the end of the lagging strand will simply degrade, which leaves an overhang where the lagging strand has failed to replicate the DNA fully.