Do-It-Yourself DNA: Scientists assemble first synthetic genome

Starting from custom-made segments of DNA, scientists have succeeded in putting together an entire microbial genome in the lab. The researchers plan to transplant this genome into a microbe in the hope that the cell will “boot up” and use the synthetic DNA.

The completed genome is a single DNA molecule with about 583,000 letters of genetic code—18 times the size of the previous record for laboratory—made DNA.

Researchers at the J. Craig Venter Institute in Rockville, Md., based their homemade genome on that of Mycoplasma genitalium, a single-celled parasite that infects people’s genitals. The parasite has one of the smallest known genomes.

To distinguish the synthetic genome from a natural one, team leader Hamilton O. Smith and his colleagues added telltale “bar codes” of genetic code to their recipe. The researchers also crippled the gene that makes the parasite infectious.

Smith’s team then divided the recipe into 101 pieces and bought made-to-order copies of each piece from biotech supply companies in Washington State, California, and Germany. “Gene sequencing is now a commodity,” explains researcher John I. Glass, but the largest made-to-order DNA available commercially is only about 5,000 to 6,000 letters long.

The scientists stitched together these 101 pieces of DNA in stages. The ends of each piece overlapped those of its neighbors in the sequence by about 80 letters of code, enabling the scientists to join consecutive pieces using enzymes. By building groups of neighboring pieces into progressively larger segments, the team eventually created four long chunks, each containing about one-quarter of the genome.

At that point, the project hit a snag. The four giant DNA molecules were too big to put into Escherichia coli bacteria, which the researchers had used to make copies of the DNA segments at each earlier stage. Without lots of copies of these large segments, stitching them together in lab dishes would be difficult.

To solve that problem, Smith and colleagues inserted the segments into cells of brewer’s yeast (Saccharomyces cerevisiae). The yeast’s DNA-repair enzymes put the four pieces together, the team reports in the Jan. 24 online edition of Science.

“The exciting thing is that the yeast assembly did work. We weren’t sure that it would,” Glass says. When the scientists checked the sequence of letters in the resulting DNA, it matched their recipe exactly.

George Church, a geneticist at Harvard Medical School in Boston, says he applauds the work but wonders about the technique’s long-term usefulness. “It was a giant step for mycoplasma-kind, and a slightly more modest one for human beings,” Church comments. For biotech applications, he says, “I just ask what is it that we can’t do in E. coli that they’ll be able to do with mycoplasma.”

Smith and coworkers previously showed that they could transplant the entire genome of one species of mycoplasma into a related species (SN: 6/30/07, p. 403). The researchers are now attempting to repeat this feat using a synthetic genome instead of a natural one. If they succeed, the resulting cell will be the first living organism with a human-made genome (SN: 1/12/08, p. 27).