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.”
The Latest on: Synthetic Biology
via Google News
The Latest on: Synthetic Biology
- Gore-Tex Is Betting Big On Synthetic Biologyon November 19, 2019 at 9:41 am
It was just this April that Checkerspot raised a $13 million Series A to develop this platform to produce synthetic biology-enabled performance materials. Gore has decades of experience in making high ...
- Revolutionizing agriculture with synthetic biologyon November 18, 2019 at 8:28 am
Synthetic biology is here to stay and will transform agriculture if given the chance. The huge challenges facing food, fuel and chemical production make it vital to give synthetic biology that ...
- Synthetic Biology Market is Estimated to Achieve $ 14 Billion by 2026on November 17, 2019 at 11:37 pm
The report is readily available and can be dispatched immediately after payment confirmation.
- Synthetic Biology Market Comprehensive Insights Of Recent Developmentson November 14, 2019 at 5:12 am
The global Synthetic Biology Market is set to surpass US$ 14 billion by the year end of 2026. According to a study produced by Acumen Research and Consulting, The industry also reflects the CAGR of 26 ...
- Synthetic Biology Market Anticipated to Witness Enhanced Applications Into Agricultural, Healthcare & Food Sectors Till 2020 | Million Insightson November 13, 2019 at 4:19 pm
FELTON, California, Nov. 13, 2019 /PRNewswire/ -- The global Synthetic Biology Market is expected to witness a stupendous CAGR in the years to come. This could be attributed to its presence across ...
- Camena flies the flag for new wave of synthetic biology trailblazerson November 12, 2019 at 9:26 am
Quizzed about the science and technology sectors destined to have the most impact globally in future years, Cambridge entrepreneur Dr Hermann Hauser placed synthetic biology in his top three. Business ...
- Former Google CEO Eric Schmidt Talks Synthetic Biologyon November 11, 2019 at 9:05 am
Having helped develop both the gene-editing tool CRISPR and the first method for sequencing a genome, his work has largely defined 21st-century biology. His current projects include growing human ...
- Twist Biopharma Implements Genedata Biologics to Advance Synthetic Biology-driven Antibody Discoveryon November 8, 2019 at 5:05 am
“Twist Biopharma is leading the way in industrializing synthetic biology and we are thrilled that they have chosen Genedata to make the most of their technology for next-generation biopharma R&D,” ...
- Synthetic Biology Market Worldwide Growth, Trends, Forecasts by 2019-2024on November 6, 2019 at 2:08 am
Nov 06, 2019 (Heraldkeepers) -- New York, November 06, 2019: The report covers detailed competitive outlook including the market share and company profiles of the key participants operating in the ...
- Gene-OFF switches tool up synthetic biologyon November 4, 2019 at 8:16 am
Only if a certain combination of input signals is present, does the device produce a desired output protein. Another desirable regulatory element for synthetic biology would be a device that can do ...
via Bing News