Check out this post by our CTO Matthew Weinstock, where he comments on a resent study shining a light on the disturbing reality of plasmid DNA quality. This is a major issue for the industry! At Novel Biotechnology Inc., we address this issue and differentiate ourselves from other plasmid manufacturers in two ways: First, we have proprietary plasmid manufacturing technologies that perform significantly better than the industry standard E. coli platforms used by everyone else. This means we produce higher quality material, especially when it comes to difficult plasmids such as ITR-containing AAV vectors and large, self-amplifying RNA plasmids. Our technologies allow us to overcome the recombination events and low plasmid yield/quality issues that are common with other providers. Second, we perform extensive quality control on all plasmids that we produce. We have access to multiple sequencing platforms to enable us to sequence every base pair of a plasmid to confirm that the sequence we produce matches the desired sequence at every position. If you are frustrated or concerned when it comes to plasmid, we'd love to share how we can help streamline and accelerate your research!
Does the integrity of your plasmid DNA keep you up at night? If not, maybe it should. A recent Nature article highlights results from a large-scale study on plasmid integrity, and the results are not good. The study examined 1000s of plasmids from labs around the world and uncovered a shocking result – most plasmids have design flaws or undetected sequence errors that are likely contributing to unexpected experimental failures. The study notes several common issues with plasmids: First, poor plasmid design on the part of the experimenter compromises plasmid functionality (like failing to add a stop codon to a gene). Second, the physical sequence of the plasmid does not match the corresponding electronic sequence map. These errors are due the outdated technology that many labs use to produce their plasmids coupled with poor quality control. With a subset of plasmids subjected to sequencing in the study, the authors found that only 65% of provided plasmids matched their electronic plasmid map (meaning that 35% of plasmids either contained undesired mutations or were actually completely different plasmids than expected). Shockingly, when they examined plasmids used for gene therapy applications, they found that 36% of plasmids had mutations in one of the two ITR regions (sequences that play a critical role in the functionality of viral-based gene therapies), meaning that these plasmids will likely not function as intended. The authors concluded that “In total, we estimate that 45-50% of lab-made plasmids have undetected design and/or sequence errors that could potentially compromise the intended applications.” They further conclude that “The high error rate of lab-made plasmids suggests that many labs lack the sophisticated and nuanced expertise needed to properly design vectors and furthermore, there is insufficient quality control of the plasmids being constructed and propagated in labs.” Serving as CTO at a company developing new tech for plasmid manufacturing, I can tell you these results are not surprising, nor are they only a problem in academic labs. At Novel Biotechnology Inc., we perform extensive quality control on all the plasmids we work with, including plasmids that we receive from clients and outside vendors where undetected mutations are extremely common. In one extreme case, we analyzed a plasmid manufactured by another vendor for one of our clients and found that it was highly contaminated with multiple other plasmids which our client had never worked with – meaning the vendor had sent them a plasmid prep that was a mix of other customers’ plasmids! This not only compromised the experiments our client had planned, but given the highly proprietary nature of plasmid designs, could seriously compromise the IP position of those other companies! This wasn’t a small, unknown vendor either. This is a serious conversation that needs to be had, especially as genetic medicines rise in prominence.