Computer program scrambles genetic codes for production of repetitive DNA and synthetic molecules
Researchers have created a computer program that will open a challenging field in synthetic biology to the entire world.
In the past decade, billions of dollars have been spent on technology that can quickly and inexpensively read and write DNA to synthesize and manipulate polypeptides and proteins.
That technology, however, stumbles when it encounters a repetitive genetic recipe. This includes many natural and synthetic materials used for a range of applications from biological adhesives to synthetic silk. Like someone struggling with an “impossible” jigsaw puzzle, synthesizers have trouble determining which genetic piece goes where when many of the building blocks look the same.
Scientists from Duke University have removed this hurdle by developing a freely available computer program based on the “traveling salesman” mathematics problem. Synthetic biologists can now find the least-repetitive genetic code to build the molecule they want to study. The researchers say their program will allow those with limited resources or expertise to easily explore synthetic biomaterials that were once available to only a small fraction of the field.
The results appear in Nature Materials, January 4, 2016.
“Synthesizing and working with highly repetitive polypeptides is a very challenging and tedious process, which has long been a barrier to entering the field,” said Ashutosh Chilkoti, the Theo Pilkington Professor of Biomedical Engineering and chair of the biomedical engineering department at Duke. “But with the help of our new tool, what used to take researchers months of work can now be ordered online by anyone for about $100 and the genes received in a few weeks, making repetitive polypeptides much easier to study.”
Every protein and polypeptide is based on the sequencing of two or more amino acids. The genetic recipe for an individual amino acid—called a codon—is three letters of DNA long. But nature has 61 codons that produce 20 amino acids, meaning there are multiple codons that yield a given amino acid.
Because synthetic biologists can get the same amino acid from multiple codons, they can avoid troublesome DNA repeats by swapping in different codons that achieve the same effect. The challenge is finding the least repetitive genetic code that still makes the desired polypeptide or protein.
“I always thought there was a potential solution, that there must be a way of mathematically figuring it out,” said Chilkoti. “I had offered this problem to graduate students before, but nobody wanted to tackle it because it requires a particular combination of high-level math, computer science and molecular biology. But Nicholas Tang was the right guy.”
After studying the problem in detail, Nicholas Tang, a doctoral candidate in Chilkoti’s laboratory, discovered that the solution is a version of the “traveling salesman” mathematics problem. The classic question is, given a map with a set of cities to visit, what is the shortest route possible that hits every city exactly once before returning to the original city?
After writing the algorithm, Tang put it to the test. He created a laundry list of 19 popular repetitive polypeptides that are currently being studied in laboratories around the world. After passing the codes through the program, he sent them for synthesis by commercial biotechnology outfits—a task that would be impossible for any one of the original codes.
Without the help of commercial technology, researchers spend months building the DNA that cells use to produce the proteins being studied. It’s a tedious, repetitive task—not the most attractive prospect to a young graduate student. But if the new program worked, the process could be reduced to a few weeks of waiting for machines to deliver the goods instead.
When Tang received his DNA, they each were introduced into living cells to produce the desired polypeptide as hoped.
“He made 19 different polymers from the field in one shot,” said Chilkoti. “What probably took tens of researchers years to create, he was able to reproduce in a single paper in a matter of weeks.”
Chilkoti and Tang are now working to make the new computer program available online for anybody to use through a simple web form, opening a new area of synthetic biology for all to explore.
“This advance really democratizes the field of synthetic biology and levels the playing field,” said Tang. “Before, you had to have a lot of expertise and patience to work with repetitive sequences, but now anyone can just order them online. We think this could really break open the bottleneck that has held the field back and hopefully recruit more people into the field.”
Read more: Traveling Salesman Uncorks Synthetic Biology Bottleneck
The Latest on: Synthetic Biology
[google_news title=”” keyword=”Synthetic Biology” num_posts=”10″ blurb_length=”0″ show_thumb=”left”]
via Google News
The Latest on: Synthetic Biology
- Programmable Living Materials Created Using Synthetic Biology and 3D Printingon May 2, 2024 at 2:07 am
Scientists are harnessing cells to make new materials that can grow, repair themselves and even respond to their environment.
- Twist Bioscience: Strong Demand and Strategic Positioning Fuel Buy Ratingon May 1, 2024 at 11:38 pm
Analyst Catherine Ramsey Schulte from Robert W. Baird maintained a Buy rating on Twist Bioscience (TWST – Research Report) and keeping ...
- Marriage of synthetic biology and 3D printing produces programmable living materialson May 1, 2024 at 6:42 am
Scientists are harnessing cells to make new types of materials that can grow, repair themselves and even respond to their environment. These solid "engineered living materials" are made by embedding ...
- Engineered living materials: Scientists 3D print with bio-ink made from tobacco cellson May 1, 2024 at 5:03 am
Also known as EPLMs, “engineered plant living materials” are a new frontier that marries synthetic biology and 3D printing, an invention that’s inspired many improvements to the mechanism itself as ...
- Crafting Programmable Living Materials With Synthetic Biology & 3D Printingon May 1, 2024 at 4:59 am
New study uses 3D printing and genetically modified plant cells to create complex, self-repairing materials that could revolutionize biomanufacturing and construction. Scientists are harnessing cells ...
- Vaccine Developers Leverage mRNA and Other Powerful Technologieson April 30, 2024 at 5:00 pm
Grint is entrepreneur in residence at the University of California, San Diego, and holds board-level positions in several companies, including Codagenix, which combines live, attenuated virus design ...
- Ansa Biotechnologies to Showcase Early Access Customer Success at Upcoming Global Synthetic Biology Conferenceon April 30, 2024 at 5:03 am
Ansa Biotechnologies, Inc., the trusted partner for complex DNA synthesis, today announced its speaker lineup for presentations at the upcoming Global Synthetic Biology (SynBioBeta) Conference in San ...
- Self-assembling synthetic cells act like living cells with extra abilitieson April 23, 2024 at 5:00 pm
Blurring the line between artificial and living materials, these cells can be reprogrammed to perform multiple functions, opening the door to new synthetic biology tech that goes beyond nature’s ...
- Inside the new Seattle Hub for Synthetic Biology, which uses DNA to ‘record biology over time’on April 1, 2024 at 6:20 pm
Scientist Sundarshan Pinglay shows off a liquid handling instrument that automatically dispenses reagents, at the Seattle Hub for Synthetic Biology. (GeekWire Photo / Charlotte Schubert ...
- Synthetic Biology Comes of Ageon March 22, 2024 at 6:25 pm
Murphy Professor of Chemical and Biological Engineering and Charles Deering McCormick Professor of Teaching Excellence at the McCormick School of Engineering, this burgeoning field within synthetic ...
via Bing News