laboratory -made plasmide, a work horse in modern biology, have problems. Researchers carried out a systematic evaluation of the circular DNA structures by analyzing more than 2,500 plasmides that were produced in laboratories and sent to a company that offers services such as packaging the structures within viruses so that they can be used as gene therapies. The team found that almost half of the plasmide design errors had, including errors in sequences that are crucial for the expression of a therapeutic gene. The researchers published their results last month on the Preprint server biorxiv 1 .

The study reveals "a lack of knowledge" about the implementation of plasmids in the laboratory, says Hiroyuki Nakai, a geneticist at Health & Science University in Oregon, who was not involved in work. He had already noticed problems with plasmids made in the laboratory, but was surprised by the frequency of the mistakes listed by the study. There are probably a lot of scientific works that have been published for which the results are not reproducible due to errors in plasmid design, he adds.

wasted time

Plasmide are popular tools in biology laboratories, since bacteria, including the widespread model organism Escherichia coli , use structures for storing and replacing genes. This means that biologists can produce designer plasmide that contain various interesting genes, and then e. Coli can persuade them to record them and make many copies of it.

Bruce Lahn, chief scientist at Vectorbuilder, a company based in Chicago, Illinois, provides the gene delivery tools, says that he and other biologists have noticed problems with plasmid quality for years. When Lahn was a professor at the University of Chicago, a doctoral student spent six months in his laboratory to reproduce two plasmide that had been reported in scientific literature. "We didn't think about the quality of the plasmide, but then the experiment did not work" because the plasmide errors contained, he says.

Now at Vectorbuilder Lahn says that he is constantly confronted with the problem - so he decided to systematically evaluate it. When customers submit faulty plasmide, "they waste a lot of time", and the additional steps in quality control increase the costs for the production of the plasmide and their packaging in viruses, he says.

The analysis of the vectorbuilder team resulted in a smorgasbord of errors in the more than 2,500 rated plasmids. Some contained genes that coded proteins, which for e. Coli were poisonous, which means that they could slow down or stop the growth of the organisms, to the biologists to replicate their plasmides. Others that were intended for the packaging in viruses coded proteins that were poisonous for these viruses. And some contained repetitive DNA sequences that can accumulate in plasmid mutations.

review of errors

The most common mistakes found Lahn and his colleagues were connected to a key tool for gene therapy. Therapies are often packed in adeno-associated viruses (AAVS), which are largely harmless and can transport treatments into cells. When producing the plasmide for these AAVS sandwichen researchers, a therapeutic gene between sequences that are referred to as ITRs and play a crucial role in ensuring that the gene is packed in the virus for delivery. These sequences essentially send a biological signal of cells, which says "I belong to this virus". However, the team found that about 40% of the AAV plasmides in the study had mutations in the ITR regions that could falsify this important message. If researchers used this incorrectly designed plasmide, their gene therapy could not work-and it could take a long time for the scientists to find out why.

Mark Kay, a specialist in pediatrics and genetics at the Stanford School of Medicine in California, has also seen first -hand that plasmid faults can delay laboratory projects. However, he is confident that scientists can recognize and fix these mistakes. He says that gene therapy researchers know possible ITR problems and that mistakes in clinical environments are unlikely. This is because regulatory authorities such as the US Food and Drug Administration have strict standards, the researchers oblige to carefully analyze their plasmides before using them in the clinic.

nakai says that the review of plasmids for errors by sequencing could draw the researchers aware of the problems emphasized in the study. Some companies, including Plasmidsaurus in Eugene, Oregon, and Elim Biopharmaceuticals in Hayward, California, offer plasmid sequencing for about $ 15.00 per sample, says Nakai, who has no financial interest in both companies. He also recommends that new laboratory workers spend time learning from experienced plasmid designers; It is a tedious, manual process, he says, but if you make a mistake, he can waste an enormous amount of time and money.

Another way for laboratories to avoid problems is to make your plasmid sequences in open access repositories publicly accessible, says Melina Fan, Chief Scientific Officer of the non-profit organization Addgenene in Watertown, Massachusetts. Addgene offers such a repository, says Fan, and "sequences the stored plasmide and communicates the sequence data via the website for use by the community". It is important to check plasmids.

Lahn hopes that the analysis of his team directs the researchers' attention to the fact that these work animal laboratory tools are often taken for granted. "The health of the tool is something that people don't think about," he says, even though they should.