New Chip Produces DNA Faster, Cheaper

Device can do in two days what now takes two weeks.

Jingdong Tian, assistant professor of biomedical engineering at Duke's Pratt School of Engineering.
Jingdong Tian, assistant professor of biomedical engineering at Duke's Pratt School of Engineering.

Duke University bioengineers have designed a 1-by-3
inch chip that can produce custom-made segments of DNA in two days that
currently would require many large pieces of equipment, significant human labor
and two weeks to produce.

Creating and copying novel pieces of DNA quickly
and inexpensively could have broad implications in the production and screening
of new drugs, as well as replacing current technologies for genetic cloning,
the researchers said.

DNA is the genetic material -- or software -- in
all living things that acts as a blueprint for the production of proteins, the
building blocks of life. An improved ability to create and test these
protein-producing molecules could be a boon to the new field of synthetic
biology, where scientists design new genes to produce novel proteins, which can
be used in such fields as medicine and environmental monitoring.

"Using current technology, it takes between
about 50 cents to a dollar to create each base pair of DNA; using the new chip
reduces costs to less than half of 1 cent per base pair," said Jingdong
Tian, assistant professor of biomedical engineering at Duke's Pratt School of

The results of the Duke experiments were
published in the journal Nature Biotechnology.

"In addition, current methods create many mistakes
that must be accounted for,” Tian continued. ”The chip-based method is
self-correcting, so that whenever an error in copying is detected, it is
automatically fixed."

As an example of how time-consuming and expensive
current technology is, Tian cited the recent cloning of the entire genome of a single
bacterium which took more than four years to complete, with a price tag of more
than $40 million. The new chip system would have reduced that to a small
fraction of the time and expense, Tian said.

Gene synthesis involves a number of steps,
including synthesis, purification and assembly of oligonucleotides or oligos,
short snippets of DNA, usually less than 50 base pairs. Each of these steps
currently takes one to two days to complete. The new chip performs all three of
these activities.

The chip itself has row upon row of tiny
indentations, or wells. The biochemical equivalent of an inkjet printer shoots
the desired DNA bases into each well. The bases assemble within the well and
since it is a enzymatic reaction, harsh chemicals are not needed to release the
DNA strand, as it done now, from the walls of the well.

"The chip basically combines the three steps
into one, which can be completed in less than two days, and without all the
labor currently needed," Tian said. "Also, since the wells are so
small, significantly smaller amounts of expensive chemicals are needed to run
the reactions."

The final step involves checking the product for
any errors, which are usually  missing or
altered base pairs. This can be a time-consuming process, sometimes taking up
to a week to complete.

"Using the chip-based system, we add an
enzyme that can recognize when a base pair is not where it should be, cut the
defect out, and reassemble the strand," Tian said. The researchers tested
the chip on genes from E. coli and found that the error rate was much
lower using the chip compared to traditional methods.

Because researchers can produce so many oligos so
quickly, they can screen many versions with subtle differences to see which
particular version produces the most of a desired protein, Tian said.

Tian's research was supported by the Beckman
Foundation, the Hartwell Foundation, and the Duke-Coulter Translational

Other members of the team were, from Duke,
Jiayuan Quan, Ishtiaq Saaem, Nicholas Tang, and Hui Gong. Nicolas Negre and
Kevin White, from the University of Chicago, were also members of the team.

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"Parallel on-chip gene synthesis and application to optimization of
protein expression", Jiayuan Quan, Ishtiaq Saaem, Nicholas Tang, Siying
Ma, Nicolas Negre, Hui Gong, Kevin P White and Jingdong Tian. Nature
Biotechology 29 (2011). doi:10.1038/nbt.1847