Web program simplifies artificial gene design

2019-03-02 11:02:00

By Will Knight A web-based program that simplifies many tricky steps involved in designing artificial DNA has been released by US microbiologists. The software suite, called GeneDesign, should make it easier for researchers to modify and study DNA. The cost of gene synthesis is rapidly falling with dozens of companies around the world now offering to create genes to order from the chemical components of DNA. GeneDesign was created by researchers led by Jef Boeke at Johns Hopkins University School of Medicine in Baltimore, US. It simplifies and automates several key steps of DNA design. These key steps include translating proteins and amino acids – the building blocks which make proteins – backwards into a DNA sequence. Or the software can manipulate simulated DNA “codons” which can code for an amino acid. DNA codons are made of sets of three nucleotides – the fundamental molecules which link together to form a DNA chain Or the software can be used to identify DNA restriction sites – sections of the DNA which can be spliced or cut in order to mix synthetic and natural DNA. “The ability to order up any piece of DNA you want is empowering, and the design process itself is quite interesting and gives a totally new perspective,” Boeke told New Scientist. “It’s a really nice tool,” says Drew Endy, a bioengineer the Massachusetts Institute of Technology, US. “But you should expect it to be outdated in 18 months.” Endy says the development of more and more advanced gene-design software reflects the increasing technological ease with which genes can be made to order. “We’re at this interesting stage where it’s becoming easy to synthesise DNA,” Endy says. “It is important to have software environments to support this.” But this is also a source of concern. An investigation conducted by New Scientist in November 2005, revealed that few gene synthesis companies check that the genes they are being asked to make are safe, or perform customer background checks after receiving an orders. “Potential for misuse comes with the territory of any powerful new technology,” Boeke says. “The synthetic biology community has prided itself on envisioning the darker side of the technology and building in safeguards wherever possible, to minimise the risks associated with gene synthesis technology.” In the face of such worries, Boeke’s team would like to introduce safeguards to prevent anyone from using their software to design genes that could be used as a bioweapon. However, Boeke says it is crucial to have access to a regularly updated database of suspect genes. He believes gene design software will become more and more powerful. “The next scale will be the synthesis of entire chromosomes and genomes,