Jun 22, 2018 | By Thomas

Scientists at the University of California at Berkeley (UC Berkeley) have invented a new way to create DNA sequences on demand that promises to be faster and cheaper. It does not require the use of toxic chemical and is more accurate than the regular DNA synthesis technique used so far in laboratories around the world. The new method could synthesise genes 'overnight'-it could produce DNA strands ten times longer than those now manufactured artificially. Scientists said it could lead to 'DNA 3D printers' in research labs that work like the 3D printers in many modern workshops.

"If you're a mechanical engineer, it's really nice to have a 3D printer in your shop that can print out a part overnight so you can test it the next morning," said UC Berkeley graduate student Dan Arlow. "If you're a researcher or bioengineer and you have an instrument that streamlines DNA synthesis, a 'DNA printer,' you can test your ideas faster and try out more new ideas."

Synthesizing DNA is a growing business as companies order custom-made genes so they can produce biologic drugs, industrial enzymes or useful chemicals in vats of microbes. Laboratories around the world purchase synthetic genes to insert into plants or animals or try out new CRISPR-based disease therapies. Some scientists have even proposed storing information in DNA, since a gram of DNA could theoretically store the equivalent of 50 million DVDs and should be stable for centuries. However, that would mean synthesizing immensely larger quantities of DNA strands than those used in the biotech industry today.

However current DNA synthesis use a technology developed in 1981 and based on organic chemistry methodologies to produce so-called oligonucleotides about 200 bases long, because inevitable errors in the process lead to a low yield of correct sequences as the length increases. To assemble even a small gene, scientists have to synthesize it piecemeal, in segments about 200 bases long, and then stitch them together. This technique is time consuming, very costly, and not entirely precise.

Sebastian Palluk and Daniel Arlow at the Joint BioEnergy Institute, a part of Lawrence Berkeley National Laboratory. Marilyn Chung photo, Berkeley Lab.

The new “DNA 3D printer” method is based on a DNA-synthesizing enzyme and TdT (deoxynucleotidyl transferase terminal) found in cells of the immune system that naturally has the ability to add nucleotides to an existing DNA molecule in water, where DNA is most stable. Unlike the other enzymes TdT doesn't rely on an existing DNA template to copy it. Instead, it randomly adds nucleotides to genes that make antibodies for use in the immune system.

TdT works equally well adding all four DNA nucleotides, does not have side-reactions that could screw up the resulting molecule, and is very fast, extending DNA by about 200 bases per minute if you let it free-wheel, said Arlow's colleague Sebastian Palluk, a doctoral student at the Technische Universität Darmstadt in Germany and a visiting student at Berkeley Lab.

In fact, in their first trials, the Berkeley researchers showed that their faster and simpler technique is nearly as accurate in each step of the synthesis as current techniques.

"When we analyzed the products using NGS, we were able to determine that about 80 percent of the molecules had the desired 10-base sequence," Arlow said. "That means, on average, the yield of each step was around 98 percent, which is not too bad for a first go at this 50-plus-year-old problem. We want to get to 99.9 percent in order to make gene-length DNA."

Once they can reach 99.9 percent fidelity, they can synthesize a 1,000-base-long molecule in one go with a yield of more than 35 percent, which is completely impossible with current chemical synthesis techniques, Palluk said.

This new method is designed to accelerate research in multiple fields, to make it easier for bioengineers to more quickly figure out how to biomanufacture useful products. It could be a step forward in the development of synthetic biology, a branch that investigates the creation of artificial microorganisms for practical purposes.



Posted in 3D Printer



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