Researchers in Denmark optimize DNA synthesis

Breaking new ground 9. jul 2021 2 min PhD, Professor Kurt Vesterager Gothelf Written by Kristian Sjøgren

A new discovery makes storing the building blocks for making synthetic DNA easier. The method also enables specific types of DNA, including ones useful for the pharmaceutical industry, to be synthesized directly for the first time.

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COVID-19 has, if anything, made the synthesis of DNA a rapidly evolving field.

Most of the world’s synthetic DNA is used in the polymerase chain reaction (PCR), the technique used to determine whether a person tests positive for COVID-19.

Although synthetic DNA is used today for many purposes, from COVID-19 verification to drug production, synthesis is not perfect.

The ingredients used to make synthetic DNA have limited shelf life, and the types of experimental DNA that can be made with current methods are limited.

However, researchers in Denmark have swept away all these challenges by inventing a method to make these unstable building blocks immediately before they are used in DNA synthesis. The researchers can even attach new types of molecules to the building blocks so that they can do new things.

“The key problem with building blocks for DNA synthesis is that moisture in the air is enough to degrade them. This is both expensive and problematic for the machines that synthesize DNA. Developing a way to make the unstable building blocks immediately before use is therefore an important step forward,” explains a researcher behind the new study, Kurt Gothelf, Professor, Interdisciplinary Nanoscience Center (iNANO), Aarhus University.

The research has been published in Nature Communications.

Existing building blocks are unstable

DNA mostly consists of bases (A, T, G and C) attached to a backbone of sugar and phosphorus molecules.

When researchers synthesize artificial DNA, they design the DNA on a computer and then let an automated DNA synthesizer assemble the DNA by using the recipe and phosphoramidite building blocks.

The problem with phosphoramidites, however, is that they are unstable and degrade when in contact moisture in the air.

Their unstable and reactive nature also makes it hard to attach molecules to the DNA, such as dyes or similar markers that can be important for tracking.

The pharmaceutical industry may also be interested in attaching various molecules to the DNA, since the small fragments of genetic material can perform new and health-promoting functions in the body – none of which can be carried out using today’s technology.

As mentioned, synthesizing DNA is an impressive feat of technology, but there are still bumps in the road.

Stabilizing unstable building blocks

The researchers in Kurt Gothelf’s group have addressed the problem of the unstable phosphoramidites by developing a system that can make them in real time.

The researchers use stable chemical substances (nucleosides) and convert them into phosphoramidites by running the nucleosides through a column.

The nucleosides are intrinsically stable, and the conversion to phosphoramidites is rapid and precise and can be done on site just before they are used in the automated synthesizer.

When researchers make phosphoramidites, the process normally takes around 12 hours, but the technique developed here reduces the time to 20 minutes.

“We plan to directly link our technology and the automated synthesizers, so that technicians no longer have to fill the automated synthesizers with unstable phosphoramidites but can instead use nucleosides directly. This will revolutionize the synthesis of DNA and makes the building blocks we use in the automated synthesizers closer to natural building blocks,” says Kurt Gothelf.

Making new types of drugs

The researchers have already patented their invention and are investigating commercializing it in collaboration with potential partners.

Kurt Gothelf says that there is great potential in both savings in synthesizing DNA and being able to synthesize new types of DNA that cannot be made using automated synthesizers today.

Ninety percent of all synthetic DNA is used today for PCR, but in recent years more and more DNA-based drugs have been marketed, and they are also often created using automated synthesizers.

The need for DNA-based drugs will probably be even greater in the future, and they should be able to do more than the current generation of drugs.

“Our technology enables us to do things that cannot be done today. We may want to insert a molecular handle in the form of an azide in DNA-based drugs, because these handles can be used to insert substances that can combat cancer. Normally, molecular handles cannot be incorporated synthetically because they degrade before the DNA is synthesized. But our method is so fast that we can use molecules in our synthesis that cannot be used today. This is the second major perspective of our invention,” concludes Kurt Gothelf.

On-demand synthesis of phosphoramidites” has been published in Nature Communications. In 2017, the Novo Nordisk Foundation awarded Kurt Gothelf a Challenge Programme grant for the Center for Multifunctional Biomolecular Drug Design (CEMBID) project.

Kurt Gothelf’s research is founded upon organic chemistry and branches out into DNA nanotechnology, bioconjugation, nucleic acid chemistry, medicinal...

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