New technology developed for the large-scale editing of DNA

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While scientists have long had the ability to edit individual genes, it is a slow, expensive and hard to use process. Now researchers at Harvard and MIT have developed technologies, which they liken to the genetic equivalent of the find-and-replace function of a word processing program, that allow them to make large-scale edits to a cell's genome. The researchers say such technology could be used to design cells that build proteins not found in nature, or engineer bacteria that are resistant to any type of viral infection.

DNA consists of long strings of "letters" (A, C, G and T) - or nucleotides - that code for specific amino acids. The genetic code consists of three-letter 'words' called codons, which are formed from a sequence of three nucleotides, such as ACT, CAG. The new technology is possible because all living organisms use the same genetic code to translate those letters into amino acids, which are then strung together into proteins. While most codons specify an amino acid, there are a few that tell the cell when to stop adding amino acids to a protein chain. It was one of these "stop" condons that the researchers targeted in their research.

To make edits to the genome of E. coli, they combined a technique previously unveiled in 2009, called multiplex automated genome engineering (MAGE), with a new technology dubbed conjugative assembly genome engineering (CAGE).

Dubbed an "evolution machine" for its ability to accelerate targeted change in living cells, MAGE locates specific DNA sequences and replaces them with a new sequence as the cell copies its DNA. This allows scientists to precisely control the types of genetic changes that occur in cells as the targets are replaced, while the rest of the genome remains untouched.

The researchers used MAGE to replace the TAG codon with another stop codon, TAA, in living E. coli cells. They chose the TAG codon because, with just 314 occurrences, it is the rarest in the E. coli genome. To make the process more manageable, they first used MAGE to engineer 32 strains of E. coli, each of which has 10 TAG condons replaced.

To combine those strains and eventually end up with one that has all 314 edits, they then developed CAGE, which allows them to precisely control a naturally occurring process called conjugation that bacteria use to exchange genetic material. The CAGE method resembles a playoff bracket, with the researchers inducing the cells to transfer genes containing TAA condons at increasingly larger scales.

After the first round of CAGE, the researchers had 16 strains, each of which had double the number of TAG edits that it started with. Those 16 strains then went into a second round producing eight strains that once again possessed more TAA codons and fewer TAG. And so on, so at the four strains stage, each had about one quester of the possible TAG substitutions.

Eager to share their findings, the researchers published their results at the semi-final round, but say they believe they are now on track to produce a single combined strain with all 314 of the substitutions.

Because the alterations were done in living cells, the researchers have been able to monitor any potential harmful effects as they appear and current results suggested that the final four strains were healthy, and can survive and reproduce.

The researchers are confident that they will create a single strain in which all TAG codons are eliminated, after which they plan to delete the cell machinery that reads the TAG condon to free it up for a completely new purpose, such as encoding a novel amino acid.

In addition to adding functionality to a cell by encoding for useful new amino acids, George Church, professor of genetics at Harvard Medical School, says the technology could also be used to introduce safeguards that prevent cross-contamination between modified organisms and the wild. Additionally, it could be used to establish multi-viral resistance by rewriting code hijacked by viruses. This would be of particular interest to industries that cultivate bacteria, such as the pharmaceuticals and energy industries, where such viruses affect up to 20 percent of cultures resulting in losses in the billions of dollars.

"We're trying to challenge people to think about the genome as something that's highly malleable, highly editable," said Harris Wang, a research fellow at Harvard's Wyss Institute for Biologically Inspired Engineering

The technology, which is described in the July 15 issue of Science, is the result of a seven-year collaboration between researchers in the lab of Joseph Jacobson, associate professor in the MIT Media Lab, and George Church, professor of genetics at Harvard Medical School. Along with Wang, lead authors of the paper are Peter Carr, a research scientist at the MIT Media Lab, and Farren Isaacs, an assistant professor of molecular, cellular and developmental biology at Yale University.

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