Okazaki Fragments

∞ generated and posted on 2016.12.06 ∞

Relatively short polymers of DNA that are synthesized in association with replication of what is known as the lagging strand during DNA replication.

An Okazaki Fragment is a fragment of DNA that is named after a person (Reiji Okazaki) and which is formed during DNA replication to deal with the fact that DNA can be replicated in only one direction, so the other direction, as associated with the other strand, must be replicated essentially backwards, except it can't be, so it is replicated in short forward bursts instead, resulting in the formation of short (Okazaki) fragments which, subsequently, are stitched together into a much larger whole.

Semiconservative DNA replication of double-stranded DNA requires more or less simultaneous polymerization of DNA off of two antiparallel DNA templates. This process is complicated by the requirement that DNA be synthesized in only the 5' to 3' direction. As a result, one strand of DNA can be newly synthesized continuously, the so-called leading strand or continuous strand, but the other strand, the lagging strand, must be synthesized episodically.

The process of DNA replication involves the separation of the two strands of the DNA double helix, which occurs at a moving location known as a replication fork. The result is a continuous separation of strands, only one of which can serve as a continuous template. The other strand, though also made available continuously, must be replicated in the direction of away from the replication fork.

This process results in a lagging-strand template that is continuously being made available but cannot be used until enough template has been made available that initiating another round of DNA replication on that strand becomes worthwhile. The resulting stretch of newly synthesized DNA that is associated with this lagging strand or discontinuous strand is called an Okazaki fragment.

Okazaki fragments, as with DNA replication in general, requires RNA priming, which serves as the beginning of an Okazaki fragment. These RNA primers are subsequently removed by DNA polymerase at the end of Okazaki fragment polymerization (i.e., primer removal from the previous Okazaki fragment in conjunction with completion of the current Okazaki fragment). The complete but still separated Okazaki fragments are then joined into a single strand of DNA via the enzyme, DNA ligase.

One way to consider the concepts of continuous versus discontinuous replication of DNA is in terms of obtaining tape from a role of tape. Sometimes you need a lot of tape and can unroll the tape as you adhere the tape. In this case, the tape essentially is applied as fast as it is unrolled and is being unrolled as fast as it is applied, though with each process occurring in slightly different locations.

By contrast, how does one typically employ smaller pieces of tape, that is, fragments of tape? Here the tendency is not to apply the tape as one unrolls it but instead to remove only as much tape as one thinks one needs and then apply those pieces of tape individually. In this case the unrolling and the application truly are not occurring at the same time. Further, if you need multiple, small pieces of tape, then the taping process literally is discontinuous, that is, broken up into a bunch of individual steps rather than occurring in one big, long step.

As you might imagine, the formation of Okazaki fragments is a lot like using many individual pieces of tape rather than being similar to using tape as one long roll. In addition, instead of the tape adhering to paper or a wall, what the DNA template strand adheres to is incoming DNA nucleotides that form the newly synthesized strand, i.e., adherence in the form of base pairing. What isn't the same is that DNA "tape" template is never actually torn off the "roll", but then, no metaphor is perfect…