In the prestigious journal, Kosuri’s team of scientists report on the innovative low-cost method of building gene sequences which they developed.
The new technique could enable scientists in any typical biochemistry laboratory to make their own gene sequences for only about $2 per gene. Researchers now generally buy gene sequences from commercial vendors for $50 to $100 per gene.
The team’s paper titled “Multiplexed gene synthesis in emulsions for exploring protein functional landscapes” was published in the January 19, 2018 issue of the journal Science. Postdoctoral researcher Dr. Calin Plesa (UCLA Department of Chemistry and Biochemistry) and graduate student Angus Sidore (UCLA Chemical and Biomolecular Engineering) were first co-authors on the paper. Other authors were graduate student Nathan Lubock (UCLA Department of Chemistry and Biochemistry) and former collaborator Di Zhang, now at the University of Pennsylvania. Kosuri was the senior author.
(From left) First co-authors of the Science paper Angus Sidore and Dr. Calin Plesa, and co-author Nathan Lubock.
From UCLA Newsroom (by Sarah C. P. Williams):
UCLA scientists develop low-cost way to build gene sequences
DropSynth can make thousands of genes at once for just a few dollars apiece
UCLA scientists used DropSynth to make thousands of bacterial genes with different versions of phosphopantetheine adenylyltransferase, or PPAT (pictured). Sriram Kosuri/UCLA
A new technique pioneered by UCLA researchers could enable scientists in any typical biochemistry laboratory to make their own gene sequences for only about $2 per gene. Researchers now generally buy gene sequences from commercial vendors for $50 to $100 per gene.
The approach, DropSynth, which is described in the January issue of the journal Science, makes it possible to produce thousands of genes at once. Scientists use gene sequences to screen for gene’s roles in diseases and important biological processes.
“Our method gives any lab that wants the power to build its own DNA sequences,” said Sriram Kosuri, a UCLA assistant professor of chemistry and biochemistry and senior author of the study (pictured below). “This is the first time that, without a million dollars, an average lab can make 10,000 genes from scratch.”
Increasingly, scientists studying a wide range of subjects in medicine — from antibiotic resistance to cancer — are conducting “high-throughput” experiments, meaning that they simultaneously screen hundreds or thousands of groups of cells. Analyzing large numbers of cells, each with slight differences in their DNA, for their ability to carry out a behavior or survive a drug treatment can reveal the importance of particular genes, or sections of genes, in those abilities.
Such experiments require not only large numbers of genes but also that those genes are sequenced. Over the past 10 years, advances in sequencing have enabled researchers to simultaneously determine the sequences of many strands of DNA. So the cost of sequencing has plummeted, even as the process of generating genes has remained comparatively slow and expensive.
“There’s an ongoing need to develop new gene synthesis techniques,” said Calin Plesa, a UCLA postdoctoral research fellow and co-first author of the paper. “The more DNA you can synthesize, the more hypotheses you can test.”
The current methods for synthesizing genes, he said, either limit the length of a gene to about 200 base pairs — the sets of nucleotides that made up DNA — or are prohibitively expensive for most labs.
The new method involves isolating small sections of thousands of genes in tiny droplets of water suspended in an oil. Each section of DNA is assigned a molecular “bar code,” which identifies the longer gene to which it belongs.
Then, the sections, which initially are present in only very small amounts, are copied many times to increase their number. Finally, small beads are used to sort the mixture of DNA fragments into the right combinations to make longer genes, and the sections are combined. The result is a mixture of thousands of the desired genes, which can be used in experiments.
To show that technique worked, the scientists used DropSynth to make thousands of bacterial genes — each as long as 669 base pairs in length. Each gene encoded a different bacterium’s version of the metabolic protein phosphopantetheine adenylyltransferase, or PPAT, which bacteria need to survive. Because PPAT is critical to bacteria that cause everything from sinus infections to pneumonia and food poisoning, it’s being studied as a potential antibiotic target.
The researchers created a mixture of the thousands of versions of PPAT with DropSynth, and then added each gene to a version of E. coli that lacked PPAT and tested which ones allowed E. coli to survive. The surviving cells could then be used to screen potential antibiotics very quickly and at a low cost.
DropSynth could potentially also be useful in engineering new proteins. Currently, scientists can use computer programs to design proteins that meet certain parameters, such as the ability to bind to certain molecules, but DropSynth could offer researchers hundreds or even thousands of options from which to choose the proteins that best fit their needs.
The team is still working on reducing DropSynth’s error rate. In the meantime, though, the scientists have made the instructions publicly available on their website. All of the chemical substances needed to replicate the approach are commercially available.
The study’s other authors are graduate students Nathan Lubock and Angus Sidore of UCLA, and Di Zhang of the University of Pennsylvania.
Funding for the study was provided by the Netherlands Organisation for Scientific Research, the Human Frontier Science Program, the National Science Foundation, the National Institutes of Health, the Searle Scholars Program, the U.S. Department of Energy, and Linda and Fred Wudl.
The team’s research has been featured in several publications, including:
- ACS Chemical & Engineering News: Stepping up gene synthesis
- Chemistry World: Synthetic gene cost slashed to $2
- EurekAlert (American Association for the Advancement of Science): UCLA scientists develop low-cost way to build gene sequences
- Fierce Biotech: DIY DNA sequencing for $2 a gene
- Genomeweb: This Week in Science
- Nature Nanotechnology: Gene synthesis: A multiplexing approach
- Nature Reviews Genetics: Functional genomics: A drop in an ocean of gene variants
- Phys.org: DropSynth, a one-pot approach to gene synthesis
- RSC Chemistry World: Synthetic gene cost slashed to $2
- Science Codex: UCLA scientists develop low-cost way to build gene sequences
- Science Daily: Low-cost way to build gene sequences
- My Science: Scientists develop low-cost way to build gene sequences
- Technology.Org: UCLA scientists develop low-cost way to build gene sequences
- Technology Networks: Dropsynth Technique Slashes Cost of Gene Generation
- UCLA Daily Bruin – UCLA researchers devise efficient, low-cost method for gene synthesis