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July 09, 2007

Synthetic biology and synthetic life milestones

Synthetic biology and synthetic life are about to make several major milestones

Note: the synthesis of 580,000 base pairs of DNA is significant. 3 million base pairs make up a ribosome. Being able to synthesize 580,000 base pairs in 2007 suggests that we could be 1 to 2 years from synthesizing our own ribosomes. It could also mean that there may not be serious hurdles to very long synthesizing of millions and billions of base pairs. There is the question of error rates, but synthesize sequences could be error corrected. This could be a powerful bootstrapping method to achieving molecular manufacturing. DNA nanotechnology would see rapid leaps in capability.

Synthesizing and replacing a bacteria's genome and sequencing DNA 13-15 times longer than previous record:
Scientists at the J. Craig Venter Institute in Rockville, Md., hope to take a giant stride in synthetic biology by creating a piece of DNA 580,076 units in length from simple chemicals, chiefly the material that constitutes DNA’s four-letter chemical alphabet. This molecule would be an exact copy of the genome of a small bacterium. Dr. Venter says he then plans to insert it into a bacterial cell. If this man-made genome can take over the cell’s functions, Dr. Venter should be able to claim he has made the first synthetic cell.

Though human cells effortlessly duplicate a genome of three billion units, the longest piece of DNA synthesized so far is just 35,000 [I have seen papers claiming 45,000 base pairs] units long.


Synthetic biologists have lofty goals

Adherents of the [synthetic biology] held their third annual conference last month in Zurich but their creations are still at the toy rocket stage. A dish of bacteria that generates a bull’s eye pattern in response to the chemicals in its environment. A network of genes that synthesizes the precursor chemical to artemisin, an anti-malaria drug. “The understanding of networks and pathways is really in its infancy and will be a challenge for decades,” says James J. Collins, a biomedical engineer at Boston University.

That hasn’t stopped synthetic biologists from dreaming. “Grow a house” is on the to-do list of the M.I.T. Synthetic Biology Working Group, presumably meaning that an acorn might be reprogrammed to generate walls, oak floors and a roof instead of the usual trunk and branches. “Take over Mars. And then Venus. And then Earth” —the last items on this modest agenda.

“The real killer app for this field has become bioenergy,” Dr. Collins says. Under the stimulus of high gas prices, synthetic biologists are re-engineering microbes to generate the components of natural gas and petroleum. Whether this can be done economically remains to be seen. But one company, LS9 of San Carlos, Calif., says it is close to that goal. Its re-engineered microbe “produces hydrocarbons that look, smell and function” very similarly to those in petroleum, said Stephen del Cardayre, the company’s vice president for research.


FURTHER READING

Cost of DNA synthesis. 10 to 70 cents per base pair in early 2007 (maybe one cent per BP with George Church process) and projected to be about 1/2000th of one cent per base pair in 2016

it [DNA sequencing and synthesis] is actually a very fundamental concept. There is almost no synthesis that doesn't involve sequencing, and vice versa. And that is why I have really emphasized this connection in my lab. They are very synergistic.


Synthetic biology making viruses that are over 100 times more effecive at fighting biofilms

DNA factories being made that are anticipating the DNA synthesis boom

Codon Devices website

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