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Johns Hopkins Gene Researcher Tries Cracking the DNA Code to Better Productivity

Posted on: Friday, 3 March 2006, 21:00 CST

By Joe Bacchus

Tedious, frustrating, slow and painful.Designing artificial genes by hand is part of the new wave of biotechnology research, but it is not the most fun project in the world, according to Jef Boeke.Boeke is a professor of molecular biology and the director of the High Throughput Biology Center at the Johns Hopkins University School of Medicine. He's also the senior author on the Hopkins project to create GeneDesign - a way to shorten that unpleasant process.The Web- based program guides researchers through the gene design and development process, helping find best fits while also cutting down on the errors that can occur when the complicated process of DNA sequencing is done by hand, he said.Boeke hopes GeneDesign, which was funded in part by the National Institutes of Health, will be as helpful to other researchers as it was with him and his work. The program has already been used to create several artificial DNA sequences.GeneDesign was born of the same mother of invention that's produced most of the world's advancements - that is, Boeke really, really didn't like doing it the way it had always been done before. Specifically, he didn't like paying graduate students for an entire semester's worth of necessary, but tedious, work

. Especially, he said, when there was an easier path.Boeke said there are other programs which perform similar tasks. However, he said he believed GeneDesign was easier to use and could accomplish more.We sort of built a better mousetrap, he said.Researchers who design artificial DNA sequences on the site can use their results in two different ways. One, they can study the sequences on a computer screen. Two, then can print actual blueprints for the DNA and send them off to laboratories that specialize in synthesizing DNA and genes for research.Boeke said the synthesis process is already relatively inexpensive and will only get cheaper over the coming years.Positive feedbackThe program has been active for several months, but recently saw a surge in page views after it was mentioned on Slashdot.org, a technology news Web site that proudly markets itself to the nerd demographic, he said.After playing with the site's features for several minutes, Boro Dropulic said he can definitely see the allure for researchers. Dropulic is the founder and chief executive officer of Lentigen Corp., a Baltimore-based biotech that has developed a way to send new genetic information into existing cells.Dropulic said he has used similar programs, such as Vector NTI, which assists in the process of cloning DNA strands.He said it seems especially useful for those researchers who don't want to put an unnecessary amount of faith in third-party vendors. The same companies that synthesize artificial DNA and genes also often map the DNA sequences for scientists.I think it is a very useful tool for researchers who want to do it themselves, Dropulic said.Ravinder Dhallan is the founder, chairman and chief executive officer of RavGen, a Columbia company that uses genetic markers for early disease diagnosis. He is also a former student of Boeke's and laughingly said he is sure anything Boeke creates is important and useful.DNA sequencing is a fundamental research step in every molecular biology laboratory in the world, Dhallan said. As such, GeneDesign has the potential to make a major impact on the world of gene design and synthesis as the process becomes more commonplace.I'm glad to see that people at Hopkins are reaching out and trying to help other researchers, he said.Especially in field such as DNA sequencing, which Dhallan agrees is a tedious and time-consuming process.Software tools that make that easier are always useful, he said.Dhallan said he would not use GeneDesign with his work at RavGen, but can understand its importance as a doctor, a scientist and a former graduate student. He said it would be especially useful as scientists used the results of the human genome sequencing process to do more research into the secrets of biology.

Source: The Daily Record (Baltimore)

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