New Chip Produces DNA Faster, Less Expensively

By Richard Merritt

DURHAM, N.C. –Duke University bioengineers have designed a one-by-three inch chip that can produce custom-made segments of DNA in two days in what it now takes many large pieces of equipment and significant manpower to produce in two weeks.

Creating and then making copies of 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. The ability to quickly create and test these protein-producing molecules could also 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.

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. It is measured in pairs of two of four different nucleotides, the arrangement and sequence of these base pairs determines the uniqueness of an individual. Typical genes are made up of between 100 and 1,000 base pairs

“Using current technology, it takes between about fifty cents to a dollar to create each base pair – using the new chip reduces costs to less than half of one cent per base pair,” said Jingdong Tian, assistant professor of biomedical engineering at Duke’s Pratt School of Engineering. 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, in 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 genetic makeup, or genome, of single bacteria 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.

The gene synthesis process involves a number of steps, including oligonucleotide synthesis, purification and assembly, with each step taking one to two days to complete. An oligonucleotide, or oligo, is a snippet of DNA, usually less than 50 base pairs. 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 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 less amounts of expensive chemicals are needed to run the reactions.”

The final step involves checking the final product for any errors, which are usually base pairs that are missing or altered. 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, or expresses, the desired protein, Tian said.

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

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.