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DNA was personified in Jurassic Park, where the animated double helix that called himself Mr. DNA took you and a group of skeptical scientists through the oversimplified (and obviously fictional) steps to creating dino DNA — but there is some reality in this.
For all you dinosaur enthusiasts out there, synthesizing DNA can’t bring T.Rex and Brachiosaurus back from extinction. Though creating genes in a lab sounds like the original eureka moment of Jurassic Park, synthesizing human DNA has done everything from genetic sequencing and editing to detecting diseases like the current plague we are living through. There is just one step that has always been problematic.
Oligonucleotides, or sequences produced by DNA, are the stars when it comes to all the sci-fi things manufactured DNA can do. It is the process that makes them which can go sideways. This process needs phosphoramidites, which tend to be unstable, for setting off the necessary reactions that create oligonucleotides. Temperatures over -4 degrees Fahrenheit threaten their stability. Unfortunately, there is no way to cool them down with the instruments used in DNA synthesis. This can mean they degrade before they are ever put to use.
Chemists Kurt Gothelf, Troels Skrydstrup, and Alexander Sandahl, who co-led a study recently published in Nature Communications, now have an answer for that. Gothelf, who specializes in automated DNA synthesis, Skrydstrup, and both of their research teams, including Sandahl, have developed a new patented way to manufacture some really unstable building blocks for DNA. Artificial DNA is often used in research labs and hospitals, and for identifying diseases (like COVID-19). This breakthrough can make the process much faster.
“The problem is that phosphoramidites tolerate the humidity in air very poorly,” Gothelf told SYFY WIRE in an interview. “When applied on automated DNA synthesizers, they must be dissolved in a solvent, acetonitrile, and in that state they only last for a few days to a few weeks before they degrade. It would not help much to cool the solutions and furthermore anything that is cooled attracts humidity.”
While phosphoramidites can be stable in powder form, so long as they stay in the fridge, they become prone to degrading again when used in DNA synthesis. Manual synthesis can take up to 12 hours with all the precautions that scientists have to take to keep the phosphoramidites intact. What Gothelf and Skrystrup came up with instead was a method that uses resin as a defense against things falling apart. Resin has no problem being integrated into automatic DNA synthesis. They start with nucleosides, sub-structures of DNA and RNA that are behind metabolism, zapping signals to cells and more functions we can’t live without.
Nucleosides flushed through solid resin undergo phosphorylation at warp speed—for just a few minutes—compared to how long it took before. Previous methods relied on manual placement of phosphoramidites onto a specialized part of an instrument that would start the process of synthesizing DNA. Manual mishaps are cancelled out in the new method because there is no intervention needed when the the resin transfers phosphorylated nucleosides, which have now morphed into phosphoramidites, directly to the synthesizing part of the instrument. There is no more risk of phosphoramidites degrading because they are used right when they are created.
“The resin reagent that is not used remains on the resin and therefore we obtain a pure phosphoramidite product. As a result, we don’t have to purify the products, which saves us a lot of time,” Gothelf said. “In the traditional method where starting materials and reagents are mixed in a flask, the reaction is slower, and you have to separate excess reagents and purify the product, which is very time-consuming.”
Now that Gothelf and his colleagues have found out how to hit the fast-forward button on this process, this could mean advancements in disease tests, CRISPR-Cas9 gene editing tech, and drugs that target extremely specific problems. There are two pieces of synthetic oligonucleotides that can mean a COVID test coming back positive or negative. Each of these pieces has a sequence that is an exact match for one in the virus genome. To prove that there is virus DNA there, the oligonucleotides start a PCR (Polymerase Chain Reaction) that multiples the copies of virus DNA from several to millions, so its presence is more visible.
Gothelf believes there is even more on the horizon for oligonucleotides now that they can be produced with a fraction of the hassle.
“The method makes it easier to prepare synthetic DNA and other synthetic oligonucleotides, which have a lot of important applications,” he said. “Aptamers, which are also developed from synthetic oligonucleotides, can recognize and bind to other proteins and molecules, constituting an alternative to the much larger and more complex antibodies.”
He is also excited about what he called the “futuristic potential” of DNA nanotechnology, in which self-assembling DNA controls matter on a nanoscale. Just don’t expect dinosaurs anytime soon.