By Teri Sprackland
Small Times Correspondent
BOULDER, Colo., Jan. 3, 2002 — After two decades of commercialization, the time has come to improve the chemical process by which DNA is synthesized, according to scientists at Agilent Technologies Inc.
Agilent and the federal Defense Advanced Research Projects Agency (DARPA) have combined forces to reduce the cost and time it takes to synthesize DNA for the microarray market. The two entities are spending $6.1 million to simplify the steps needed to create synthetic DNA. Work will be done in conjunction with the University of Colorado, Boulder, where the original research was completed.
DARPA, the central research and development branch of the U.S. Department of Defense, has provided years of support to high technology industries, resulting in the commercialization of many discoveries. DARPA retains the right to use the results for government applications, while the companies are free to commercialize their results.
Uses for controlled laboratory synthesis of DNA material has spread far and wide into the pharmaceutical and biotechnology industries, facilitating drug research and development. DNA, deoxyribonucleic acid, contains the blueprints of all living organisms.
DNA synthesis was made possible by the work done in the late 1970s and early 1980s by Marvin Caruthers and his team at the University of Colorado’s department of chemistry and biochemistry.
The principal investigator named on the DARPA grant, Douglas Dellinger, did his graduate work under Caruthers. After Dellinger finished his Ph.D. and went to work for Agilent, he continued to collaborate with Caruthers on Agilent’s behalf. He now splits his time between Boulder and Agilent Laboratories in Palo Alto, Calif.
“It was an amazing breakthrough to be able to chemically synthesize DNA. Making DNA is like adding beads on a string.” Dellinger said. “You really need to keep the process efficient, or there is a logarithmic drop in yield. The original breakthrough achieved 99 percent efficiency.”
“Chemical synthesis is broadly used in industry. The genomics revolution was built on the synthesis of DNA.” Chemical synthesis allowed researchers to bypass the need to produce DNA through direct replication. “Now we can make whatever DNA sequence we want ‘de novo,’ ” he said.
Success has brought its own challenges, however. High yields are no longer enough — the process needs to be cheaper so that its end market, the DNA microarray, can be expanded.
Now, said Dellinger, it is time to improve the process.
“Dr. Caruthers and I feel that there is a bottleneck developing in the ability to make lots of DNA cheaply and easily.”
“Now what we want to do is develop a more user-friendly process, one that uses less solvents, fewer reagents,” Dellinger said. The chemical reagents are not only expensive to buy but, because they are hazardous wastes, they are also expensive to get rid of, he noted. Although he did not quantify the savings that the team was hoping to achieve, he noted that it costs as much to dispose of the chemicals as to buy them.
The new process will take about half the number of steps as the original, thus saving time in the process, he added. “We’re out to make better, cheaper, faster arrays for our customers.”
The number of steps will be reduced from four to two, the use of most of the highly toxic reagents and solvents will be eliminated, and chemical waste will be reduced by 75 percent, according to a statement by Agilent. It will be more suitable for chip-sized miniaturization and highly parallel batch processing, the statement said.
Agilent offers the technology and application tools to customers in the pharmaceutical industry. It is specifically targeting research customers in gene expression, genotyping and proteomics research with nanoscale technologies such as microarrays, according to a company statement.
Agilent introduced a series of ready-to-use catalog microarray products, including a human cDNA microarray kit, this year. Agilent also plans to offer automated microarray scanning equipment, an enterprisewide expression analysis informatics platform, and the biological protocols required for gene expression profiling experiments.
FROM SYNTHESIZED DNA TO MICROARRAYS
After DNA is synthesized, it can be deposited on slides known as microarrays. DNA microarrays are tools used in gene expression research, which allows gene-level investigation of the mechanism of diseases. They can be used to determine which genes are turned on or off in a cell or tissue and to evaluate the activity level under different conditions. That can lead researchers to understand the impact of a drug on cells.
DNA can then be incubated on the microarray slide. If sequences in the original sample match up with those on the slide, they bind and produce fluorescence. A laser beam can be used to detect which regions on the chip fluoresce. The resulting data is then sent to a computer database, where patterns of gene expression are identified through software analysis called bioinformatics. These data are used to determine which genes are in use, and to what extent they are active.
By speeding up research during preclinical drug development, DNA microarrays reduce the time it takes to get a drug to market, according to a report by Rob Ellis, an analyst with Front Line Stragetic Consulting Inc. in Foster City, Calif.
According to Ellis, the DNA microarray market will reach $3.6 billion by 2006, with several segments such as the scanner and arrayer markets growing at a compound annual growth rate of 44 percent. Lower prices, greater production needs and increased use will drive the market.
Eventually, according to the report, microarrays will be used in clinical diagnostics to allow physicians to detect genetic predispositions to specific diseases and to customize treatment on the basis of the patient’s genetics.
Prefabricated arrays will become more affordable, leading to wider use, the report stated. Affymetrix, Apogent, and GeneMachines together hold about 73 percent of the arrayer market.
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