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Making a Genome Quickly from Scratch

A startup hopes to use the new approach to make vaccines.

A rapid DNA-synthesis technique has been used to synthesize a complete mitochondrial genome from scratch. The new method will be used to make vaccines rapidly by a startup company called Synthetic Genomics Vaccines.

Genome maker: Daniel Gibson, a professor at the J. Craig Venter Institute, is developing new ways to stitch together DNA.

The new technique allows biologists to assemble large pieces of DNA from designs edited on a computer more quickly than before. Researchers at the J. Craig Venter Institute in Rockville, Maryland, used the method to make the entire genome of a cellular organelle called the mitochondria, a step that could lead to therapies for metabolic diseases. Synthetic Genomics is partnering with pharmaceutical giant Novartis to speed the development of influenza vaccines using the approach.

“By being able to quickly synthesize DNA, we can make a new seed vaccine for influenza in 24 hours or less,” says J. Craig Venter, founder and president of the institute. It now takes several months to produce a new influenza vaccine.

Before each flu season, epidemiologists monitor the rapidly evolving flu virus over a period of months, and the World Health Organization (WHO) makes a guess about which three strains are mostly likely to spread. The WHO then develops weakened versions of these viruses, and these seed stocks are distributed to vaccine manufacturers, who incubate the weakened-virus vaccine in chicken eggs, a process that takes 35 days.

Researchers at the J. Craig Venter Institute, led by institute professor Daniel Gibson, have come up with a technique for synthesizing stretches of DNA in the size range of the viral genomes. With the right starting material, the process can be done in a few hours.

Working with a DNA sequence stored in a computer file, the researchers first divide it up into overlapping pieces that are small enough to make economically and rapidly from bottled chemicals. This is done using a standard machine called a DNA synthesizer. Several stretches of DNA are then pooled with a mix of enzymes that stitches them together in about 15 minutes. Longer pieces are again pooled with one another and the same mix of enzymes stitches them together into an even longer ordered sequence. The key, Gibson says, was finding the right combination of three enzymes to put all the DNA fragments together.

This spring, Gibson’s group used a more labor-intensive technique to make the first “synthetic cell.” They edited a bacterial genome on the computer, synthesized it with the help of yeast and then transplanted it into of another species of bacteria. Using yeast to put the genome together takes a while because the yeast has to grow overnight to stitch DNA fragments together. Yeast is still needed to make something as large as an entire bacterial genome because it can work with much more DNA than the chemicals used in the new method.

To make smaller genomes, including those of vaccines, the Venter Institute researchers don’t need yeast. If they’ve already made the shorter starting pieces of DNA, says Gibson, they can put together an entire vaccine seed stock, or the genome of a cellular organelle like the mitochondria, in a single day. That’s just what they did in work described in a paper published this week in the journal Nature Methods.

The mitochondrion is a vital part of all animal cells, playing a major role in metabolism, and it has its own genome. Mitochondrial diseases can lead to deafness, diabetes, muscle weakness, learning disabilities, and many other problems. By using the rapid DNA synthesis method to study the mitochondria, “we hope to see what causes these problems at the genetic level, and see if we can fix them,” says Gibson.

Over the next three years, Synthetic Genomics Vaccines will partner with Novartis to use these methods to make influenza vaccine stocks. Novartis is working on a cell-based vaccine growth method to replace the chicken eggs that are used to grow vaccines today. This would eliminate the need to adapt the viruses for birds, which adds time, and should be generally faster. The approach is not yet approved by the U.S. Food and Drug Administration, but trials are ongoing.

Venter says the speedier DNA synthesis technique could also make it possible to keep up with even more rapidly evolving pathogens that change too fast for conventional vaccine development to keep up. This includes HIV, malaria, and rhinovirus–one of the causes of the common cold.

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