Okazaki fragments are formed during replication of the lagging DNA strand. What determines the length of these fragments?
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$\begingroup$ possible duplicate of formation of okazaki fragments in lagging strand during replication $\endgroup$– dustinMay 9, 2015 at 17:50
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$\begingroup$ @dustin page not found $\endgroup$– aaaaa says reinstate MonicaAug 8, 2015 at 7:02
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1 Answer
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The length of Okazaki fragments is not necessarily a tight distribution. The lengths are determined by the spacing between adjacent sites where DNA primase has synthesized a short RNA primer on the lagging strand at an active DNA replication fork. In E. coli, as I recall, this occurs on an average of once per 1000 nt.
DNA polymerase holoenzyme then uses that 3'-OH on the RNA primer as a substrate and synthesizes the DNA strand complementary to the Template strand UNTIL it bumps into the next RNA primer.
It is those nicks in the newly synthesized lagging strand, that have a deoxy-3'-OH, and a ribo-5'-phosphate, (that need to be removed and ligated) that mark the boundaries of individual Okazaki fragments.
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$\begingroup$ In chromosomal DNA nucleosomes are spaced by 200 nucleotides.. so, this can be a reason of okazaki fragments limited to just 100-200 nucleotides in eukaryotes? I am confused... $\endgroup$ May 10, 2015 at 15:16
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$\begingroup$ Where did you obtain the number of 100-200 nucleotides? All eukaryotes? DNA replication in eukaryotes probably best characterized in yeast (budding yeast and fission yeast), fruit flies, rats (rat liver biochemistry?), and human cell lines, like HeLa cells. $\endgroup$– mdperryMay 10, 2015 at 15:33
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$\begingroup$ During replication, DNA is naked: no nucleosomes there. I am not sure but nucleosome formation may be later than ligation of Okazaki fragments. $\endgroup$– 243Jun 8, 2015 at 18:03