A multidisciplinary research team in California has uncovered new details about a key enzyme that makes DNA sequencing possible. They say the findings will have implications for everything from personalized medicine to our understanding of evolution.
“Enzymes make life possible by catalyzing chemical transformations that otherwise would just take too long for an organism,” says Greg Weiss, University of California-Irvine’s (UCI) professor of chemistry and a co-corresponding author of the new study. “One of the transformations we’re really interested in is essential for all life on the planet—it’s the process by which DNA is copied and repaired.”
The team set out to better understand Taq, an enzyme that replicates DNA. Taq is already well-known to researchers because it is the basis of polymerase chain reaction, a technique with thousands of applications, from forensics to PCR tests for detecting COVID-19. However, the team found that the enzyme, as it helps make new copies of DNA, behaves completely unlike what was previously thought. Instead of behaving like a well-oiled, efficient machine continuously churning out DNA copies, the enzyme acts like an indiscriminate shopper who cruises the aisles of a store, throwing everything they see into the shopping cart.
“Instead of carefully selecting each piece to add to the DNA chain, the enzyme grabs dozens of misfits for each piece added successfully,” says Weiss. “Like a shopper checking items off a shopping list, the enzyme tests each part against the DNA sequence it’s trying to replicate.”
It is also well-known that Taq rejects any wrong items that land into its proverbial shopping cart, and that this rejection is key to successfully duplicating a DNA sequence. But how frequently Taq rejects correct bases was surprising to the research group. “It’s the equivalent of a shopper grabbing half a dozen identical cans of tomatoes, putting them in the cart, and testing all of them when only one can is needed,” Weiss says. In other words, Taq is much less efficient at doing its job than it could be.
The find is a step toward revolutionizing medical care, according to Philip Collins, a professor in the UCI Department of Physics & Astronomy. “Every single person has a slightly different genome,” says Collins, “with different mutations in different places. Some of those are responsible for diseases, and others are responsible for absolutely nothing. To really get at whether these differences are important for healthcare—for properly prescribing medicines—you need to know the differences accurately.”
Science does not know how enzymes like Taq achieve accuracy, adds Collins, whose lab created nano-scale devices for studying Taq’s behavior. “How do you guarantee to a patient that you’ve accurately sequenced their DNA when it’s different from the accepted human genome? Does the patient really have a rare mutation or did the enzyme simply make a mistake?”
The findings could also be used to develop improved versions of Taq that waste less time making copies of DNA, Weiss adds.
The findings have implications outside of healthcare as well. Every scientific field that relies on accurate DNA sequencing stands to benefit from a better understanding of how Taq works. For example, scientists interpreting evolutionary histories using ancient DNA rely on assumptions about how DNA changes over time, and those assumptions rely on accurate genetic sequencing.
“We’ve entered the century of genomic data,” says Collins. “At the beginning of the century we unraveled the human genome for the very first time, and we’re starting to understand organisms and species and human history with this newfound information from genomics, but that genomic information is only useful if it’s accurate.”
The findings were published recently in Science Advances.