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Serious errors plague DNA tool that's a workhorse of biology
https://www.nature.com/articles/d41586-024-02280-1NEWS
10 July 2024
Serious errors plague DNA tool that’s a workhorse of biology
Researchers analysed thousands of laboratory-made plasmids and discovered that nearly half of them had defects, raising questions of experimental reproducibility.
By Katherine Bourzac
Laboratory-made plasmids, a workhorse of modern biology, have problems. Researchers performed a systematic assessment of the circular DNA structures by analysing more than 2,500 plasmids produced in labs and sent to a company that provides services such as packaging the structures inside viruses so they can be used as gene therapies. The team found that nearly half of the plasmids had design flaws, including errors in sequences crucial to expressing a therapeutic gene. The researchers posted their findings to the preprint server bioRxiv last month ahead of peer review1.
The study shines a light on “a lack of knowledge” about how to do proper quality control on plasmids in the lab, says Hiroyuki Nakai, a geneticist at Oregon Health & Science University in Portland who was not involved in the work. He was already aware of problems with lab-made plasmids, but was surprised by the frequency of errors uncovered by the study. There are probably many scientific papers that have been published for which the results are not reproducible owing to errors in plasmid design, he adds.
Wasted time
Plasmids are popular tools in biology labs because bacteria, including the widely used model organism Escherichia coli, use the structures to store and exchange genes. This means that biologists can make designer plasmids containing various genes of interest, and then coax E. coli to take them up and make lots of copies.
Bruce Lahn, chief scientist at VectorBuilder, a company based in Chicago, Illinois, that provides gene-delivery tools, says that he and other biologists have been noticing problems with plasmid quality for years. For example, when Lahn was a professor at the University of Chicago, a graduate student in his lab spent six months trying to reproduce two plasmids that had been reported in the scientific literature. “We didn’t think twice about the quality of the plasmids, but then the experiment wouldn’t work” because the plasmids contained errors, he says.
[...]
10 July 2024
Serious errors plague DNA tool that’s a workhorse of biology
Researchers analysed thousands of laboratory-made plasmids and discovered that nearly half of them had defects, raising questions of experimental reproducibility.
By Katherine Bourzac
Laboratory-made plasmids, a workhorse of modern biology, have problems. Researchers performed a systematic assessment of the circular DNA structures by analysing more than 2,500 plasmids produced in labs and sent to a company that provides services such as packaging the structures inside viruses so they can be used as gene therapies. The team found that nearly half of the plasmids had design flaws, including errors in sequences crucial to expressing a therapeutic gene. The researchers posted their findings to the preprint server bioRxiv last month ahead of peer review1.
The study shines a light on “a lack of knowledge” about how to do proper quality control on plasmids in the lab, says Hiroyuki Nakai, a geneticist at Oregon Health & Science University in Portland who was not involved in the work. He was already aware of problems with lab-made plasmids, but was surprised by the frequency of errors uncovered by the study. There are probably many scientific papers that have been published for which the results are not reproducible owing to errors in plasmid design, he adds.
Wasted time
Plasmids are popular tools in biology labs because bacteria, including the widely used model organism Escherichia coli, use the structures to store and exchange genes. This means that biologists can make designer plasmids containing various genes of interest, and then coax E. coli to take them up and make lots of copies.
Bruce Lahn, chief scientist at VectorBuilder, a company based in Chicago, Illinois, that provides gene-delivery tools, says that he and other biologists have been noticing problems with plasmid quality for years. For example, when Lahn was a professor at the University of Chicago, a graduate student in his lab spent six months trying to reproduce two plasmids that had been reported in the scientific literature. “We didn’t think twice about the quality of the plasmids, but then the experiment wouldn’t work” because the plasmids contained errors, he says.
[...]
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