Engineering Concepts Associated With Okazaki Fragments
Due to the importance and purpose of Okazaki fragments in DNA replication, bioengineers are using these pieces of DNA in their research. One study, published in Science on March 17, 2000, stated that the specific start and stop locations of bidirectional DNA synthesis at a human gene called Lamin B2 were discovered using DNA base exploration and information about Okazaki fragment synthesis. Based on the relative position of Okazaki fragments to the replication fork during lagging stand synthesis as well as the average length of Okazaki fragments during replication, the scientists were able to pinpoint nucleotide 3933 as the start of bidirectional synthesis. The information was, “deriving from the linking to the initiated ori of four subsequent Okazaki fragments having lengths of 143, 144, 65, and 80 nucleotides from the first to the fourth, respectively”.
Another study investigated the formation of Okazaki fragments in wild-type bacteria cells. In strains of Escherichia coli, a mutation in the sof locus, a specific location of a gene on a chromosome, resulted in hyper recombination and short DNA strands. Scientists say that the mutated gene is defective, affecting an enzyme called deoxyuridinetriphosphate diphosphohydrolase (or dUTPase), which can no longer catalyze the hydrolysis of dUTP. This mutation also decreases the amount of dUTPase in the organism, somehow increasing the amount of uracil that is being incorporated into the DNA. Because uracil is not one of the four nucleotides associated with DNA (replaced by Thymine), it must be removed as an error by the excision-repair process and replaced. Rapid removal of uracil because of increased incorporation into DNA can lead to the accumulation of short DNA fragments, which may also lead to the creation of Okazaki fragments. Learning how Okazaki fragments originate in bacteria such as E. coli allows scientists and engineers to better understand the process of DNA replication and the effects of pinpoint mutations.
Although many mutations associated with Okazaki fragments can result in cancer, studies have shown that the alteration of Okazaki fragments in nucleoside analogues such as cytarabine can lead to anti-cancer activities. For instance, cytarabine is an anti-leukemic agent that inhibits the replication of lagging stand DNA. When this agent was substituted for deoxycytidine during the replication of the SV-40 viral genome, the bending of the DNA duplex region (DDR), and the RNA-DNA hybrid duplex region (HDR) increased from 22 degrees to 41 degrees. This increased helical bending of Okazaki fragments may contribute to cytarabine's ability to inhibit the replication of lagging strand DNA and have anti-cancer properties.
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