July 15, 2011

New DNA Rewriting Tools

(Ivanhoe Newswire) "“ New tools have been revealed for rewriting the code of life. Most DNA editing tools are slow, expensive, and hard to use. Now, scientists have developed fast and more efficient genome-scale editing tools.

"The payoff doesn't really come from making a copy of something that already exists, you have to change it"”functionally and radically," George Church, a professor of genetics at Harvard Medical School who led the research effort, was quoted saying.

From that change, there are three goals. The first is to add functionality to a cell by encoding for useful new amino acids. The second is to introduce safeguards that prevent cross-contamination between modified organisms and the wild. Third, is to establish multi-viral resistance by rewriting code taken over by viruses. In industries that develop bacteria, including pharmaceuticals and energy, such viruses affect up to 20 percent of cultures.

The researchers also replaced occurrences of a codon, which is a DNA "word" of three nucleotide letters, in 32 strains of E. coli, and then coaxed those partially-edited strains along an evolutionary path toward a single cell line in which all 314 instances of the codon had been replaced. "That many edits surpasses current methods by two orders of magnitude," Harris Wang, one of the lead authors, and a research fellow in Church's lab at the Wyss Institute for Biologically Inspired Engineering at Harvard University, was quoted saying.
Amino acid codons are protein building blocks in the genetic code, but few codons tell the cell when to stop adding amino acids to a protein chain. It was one of these "stop" codons that the scientists targeted in their research. Making it a main target, the TAG stop codon is the most uncommon word in the E. coli genome, with just 314 occurrences. The researchers replaced instances of the TAG codon with another stop codon, TAA, in living E. coli cells, by using a small-scale engineering process called MAGE "“ Multiplex Automated Genome Engineering.

The team constructed 32 strains taken together that included every possible TAA replacement, while MAGE yielded cells in which TAA codons replaced some but not all TAG codons. Then, using bacteria's natural ability to trade genes through a process called conjugation, the team induced the cells to transfer genes containing TAA codons at increasingly larger scales. Through basketballs' "March Madness" explanation, "The new method, called CAGE, conjugative assembly genome engineering, resembles a playoff bracket"”a hierarchy that winnows 16 pairs to eight to four to two to one"”with each round's winner possessing more TAA codons and fewer TAG," Farren Isaacs, another lead author, and assistant professor of molecular, cellular and developmental biology at Yale University, was quoted saying.

"We're testing decades-old theories on the conservation of the genetic code, and we're showing on a genome-wide scale that we're able to make these changes," Isaacs said.

As CAGE reached the semifinal round, the results indicated that the final four strains were healthy. "We encountered a great deal of skepticism early on that we could make so many changes and preserve the health of these cells," Peter Carr, another lead author, and a research scientist at the MIT Media Lab, was quoted saying.

The researchers believe they will create a single strain where TAG codons are completely eliminated. Their next step is to delete the cell's machinery that reads the TAG gene "” freeing up the codon for a completely new purpose, such as encoding a novel amino acid.

SOURCE: Science, July 14, 2011.