Faster, cheaper way to synthesise DNA developed

Scientists have pioneered a new way to synthesise DNA sequences through a creative use of enzymes that promises to be faster, cheaper and more accurate. The discovery, by researchers at Lawrence Berkeley National Laboratory (Berkeley Lab) in the US, could address a critical bottleneck in biology research. "Nature makes biomolecules using enzymes, and those enzymes are amazingly good at handling DNA and copying DNA. Typically our organic chemistry processes are not anywhere close to the precision that natural enzymes offer," said Sebastian Palluk, graduate student at Joint BioEnergy Institute (JBEI) in the US.

The idea of using an enzyme to make DNA is not new - scientists have been trying for decades to find a way to do it, without success. The enzyme of choice is called TdT (terminal deoxynucleotidyl transferase), which is found in the immune system of vertebrates and is one of the few enzymes in nature that writes new DNA from scratch rather than copying DNA. The problem with existing approaches to using enzymes for DNA synthesis is that the catalytic site of the enzyme is not large enough to accept the nucleotide with a blocking group attached.

"People have basically tried to 'dig a hole' in the enzyme by mutating it to make room for this blocking group," said Daniel Arlow, a graduate student JBEI. This is tricky because it can interfere with the activity of the enzyme, said Arlow. "Instead of trying to dig a hole in the enzyme, what we do is tether one nucleotide to each TdT enzyme via a cleavable linker," he said. "That way, after extending a DNA molecule using its tethered nucleotide, the enzyme has no other nucleotides available to add, so it stops," Arlow said.

"A key advantage of this approach is that the backbone of the DNA - the part that actually does the chemical reaction - is just like natural DNA, so we can try to get the full speed out of the enzyme," he said.
"Our dream is to make a gene overnight. Where we're trying to produce fuels and chemicals from biomass, DNA synthesis is a key step. If you speed that up, it could drastically accelerate the whole  process of discovery," Arlow said.