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Synthetic Genome Has Potential Value for Energy and Environment
  
By Kate Ruder

Genome Atlas of phi-X174.
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Using DNA off the shelf, scientists have—with perfect accuracy—created the genome of a harmless synthetic virus in days rather than months or years as in the past.

The advance brings science a step closer to practical applications such as developing potentially useful synthetic microbes that could someday produce hydrogen for energy or consume pollutants at coal-fired heating plants.

Scientists at the Institute for Biological Energy Alternatives (IBEA) in Rockville, Maryland , announced their findings, along with the Secretary of the Department of Energy (DOE), Spencer Abraham, at a press conference Thursday in Washington, D.C. DOE funded the research.

J. Craig Venter, president of IBEA, led the research, working with longtime collaborators Nobel Laureate Hamilton O. Smith of IBEA and Clyde A. Hutchinson of the University of North Carolina, Chapel Hill. Venter and Smith were principal collaborators on sequencing the human genome. Smith, in his 70s, and Hutchinson, in his 60s, pulled all-nighters “just like post-docs” to create the genome in record time, said Venter.

Venter and his colleagues created the genome of a virus that infects bacteria but is harmless to humans. The genome of this particular virus, called phi X, was already a bit of a celebrity in the world of genomics. In 1978, it was the first virus ever sequenced. It has been extensively studied in the laboratory since the 1950s.

In 14 days, the researchers created the artificial phi X by piecing together synthetic DNA ordered from a biotechnology company. They used a technique called polymerase cycle assembly (PCA) to link the strands of DNA together.

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The sequence and assembly of the synthetic genome matches up nearly perfectly with the sequenced genome of the natural virus. Each strand of DNA neatly overlaps its neighboring strands by 20 letters of genetic code. The new virus also infects bacterial cells just like the natural virus does.

Ultimately, the goal is to create a synthetic genome that would be 100 to 1,000 times larger than the phi X virus. Someday, researchers hope to engineer fleets of self-replicating microbes that do everything from scrubbing down emissions at coal plants to producing enough hydrogen to power cars and trucks run by hydrogen-fuel cells rather than gasoline.

Last year, a separate group of researchers synthesized a polio virus using chemicals ordered over the Internet and from mail order catalogs. The poliovirus is slightly larger than phi X. It took the researchers months to a year to complete the poliovirus project. Synthesis of a harmful virus raised ethical concerns among the public as well as the scientific community.

Although phi X is not harmful, the researchers are aware that genome synthesis needs to be handled with caution. Throughout the press conference yesterday, Venter and Abraham stressed that although the technology behind phi X raises the possibility of potential misuse, officials at the DOE and other agencies have and will continue to monitor federally funded research for security concerns.

In addition, Secretary Abraham announced the creation of a new committee at the DOE to review the phi X work for "new research opportunities." There may be several ways to use synthetic genomes in energy, the environment and medicine. The Secretary expects that the new DOE committee will foster support of novel research within several federal agencies.

Complete details of the techniques and findings will be published online in the journal The Proceedings of the National Academy of Sciences, in three weeks. The technique will not be patented.

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