Gene design program from Johns Hopkins simplifies, automates and speeds design of 'artificial' genes

Johns Hopkins researchers have announced the development of a Web-based, automated computer program that they say greatly simplifies the time-consuming and error-prone process of manually designing artificial pieces of DNA.

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."

The researchers have so far used GeneDesign to make a variety of synthetic sequences, including a Ty1 element -- a mobile piece of genetic material found in yeast cells. Ty1 elements can move from one yeast cell and "jump" into a specific spot in one of a second yeast's chromosomes. This jumping movement can cause mutations or bring in additional genetic material to the yeast.

GeneDesign consists of six modules that can be used individually or in series to automate the tasks required to design and manipulate synthetic DNA sequences. The program allows the user to start with either the sequence of the amino acid making up the protein or the bases making up the gene that codes for that protein. Then the user moves through a series of steps that guide the design of the gene and vector that will carry the gene into the cell. Users can follow the main "Design a Gene" path or use the modules individually as needed. Vectors are mobile pieces of DNA that are used to carry artificial genes into cells.

A major advantage to GeneDesign is the ability to choose specific codons that work especially well in specific organisms, Boeke said. A codon is a trio of bases in a gene that codes for a specific amino acid building block. Most amino acids are represented by more than one codon. For example, the codons GCU, GCC, GCA, GCG can each code for the amino acid alanine.

Human, bacterial and yeast cells often differ in the codon they prefer to use for a particular amino acid. "GeneDesign automatically chooses the best codon to use depending on whether the gene is supposed to work in a human cell, a bacterium, or a yeast cell," Boeke said. "When you're working with hundreds of codons, that's a significant help."

The program also simplifies the design of genes that will make proteins with desired, specific modifications -- for example, changes that make them work more efficiently.

Another advantage of the GeneDesign is ease of creating restriction sites -- places along the DNA where the gene can be cut, said Sarah M. Richardson, a Ph.D. candidate in the Department of Genetic Medicine at Hopkins and first author of the paper. Scientists use molecular scissors called restriction enzymes to make these cuts, which allow them to do the cutting and pasting needed to put artificial genes into vectors.

"GeneDesign guides the choice of the series of base pairs where the restriction enzymes cut the DNA," Richardson said. "That lets investigators use different restriction enzymes to make cuts exactly where they want to."

If the same restriction site sequence occurred throughout the gene, the specific restriction enzyme that recognizes that site would make multiple cuts, according to Richardson. "That would make it impossible to do the precise cutting and pasting needed to make and use artificial genes," she said.

However, even a successfully designed gene would not benefit researchers if there were only one copy of it. "To make use of artificial genes we need to make millions of copies of them for experiments using a process called polymerase chain reaction," said Boeke. "By putting restriction sites into specific spots along the gene, we can cut it into bite-sized pieces that are easily duplicated millions of times. So the ability to cut and paste genes back together again is critical for designing genes to the right specifications, rapidly replicating them and putting them into vectors to genetically engineer cells."

The other authors of the paper include Sarah J. Wheelan and Robert M. Yarrington of The Johns Hopkins University School of Medicine High Throughput Biology Center.

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This work was supported by National Institutes of Health grants, including a Research Roadmap grant.

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