The program, called GeneDesign, guides the design of blueprints for DNA segments to the exacting specifications required for studying gene function and genetically engineering cells. The blueprints are then used by companies or other investigators to synthesize the gene.
A report on the program appears in the April 2006 issue of Genome Research and online in mid-February. The publicly accessible Web site can be found at http://slam.bs.jhmi.edu/gd.
GeneDesign automates the process of determining which base pairs -- the building blocks of DNA -- should be linked together in a particular order to make a gene, according to Jef Boeke, Ph.D., professor of molecular biology and genetics and director of the High Throughput Biology Center at The Johns Hopkins University School of Medicine. A gene codes for a specific protein, and the order of the hundreds or thousands of base pairs making up that gene determines the order of the amino acid building blocks making up that protein. Boeke is senior author of the paper.
"GeneDesign not only guides the user in designing the gene, but also automatically diagnoses design flaws in the sequence of bases making up the gene," said Boeke.
Simplifying creation of so-called designer or artificial genes is important because slight changes in the choice of base pairs making up specific parts of the gene can have significant effects on how the gene works and how efficiently it can be inserted into cells. "In the past," said Boeke, "researchers had to use many different programs to address all the requirements of the separate steps of synthetic gene design."