New Sequencing Method Brings New Possibilities in Protein Research
UT researchers have developed the first viable alternative to a 75-year-old method for sequencing proteins.
Image of amino acids, the building blocks of proteins.
Scientists at The University of Texas at Austin have added a new tool to the toolbelt for figuring out the building blocks of proteins, something researchers have been doing the same way for 75 years. Their new method, outlined in a paper published this month in the Journal of the American Chemical Society, could advance biomedical research and lead to the development of better medical tests, discoveries of new treatments and a whole new generation of biochemistry tools.
Since 1950, a method called Edman degradation has been used to sequence proteins by chemically chopping off and identifying one amino acid at a time. But that process uses strong acid, which can destroy important parts of a protein or other molecules researchers want to use in experiments, such as fluorescent tags or DNA.
“Edman degradation uses a very harsh acid, and it damages things we now use in modern protein studies,” said Eric Anslyn, Welch Regents Chair in Chemistry at UT Austin. “So, we created a version that uses a base instead. It’s much gentler and keeps sensitive parts like DNA and fluorescent tags intact.”
Proteins are made up of chains of amino acids. Knowing the exact order of those amino acids helps scientists understand how proteins work, how diseases form and how to design new medicines.
The researchers’ new method lets them remove and identify each amino acid, one by one, just like the original method, but without the damage caused by acid. Instead, they use a chemical base and a specially designed reagent called DR3 to do the job.
Fluorescent tags are used in fluorosequencing — a breakthrough in single-molecule protein sequencing first developed in the lab of UT’s Edward Marcotte – and they’re vulnerable to destruction by acid. Researchers using the technology were motivated to find an acid-free alternative, and Anslyn says their new method could help bring about improvements in fluorosequencing such as expanding the ability to distinguish between different amino acids in a mixture and increase the number of proteins that can be sequenced from a single sample.
This opens the door to faster and more accurate snapshots of the proteins in cells and tissues. Expanded distinction could lead to more accurate testing for diseases or health conditions, development of more targeted drug therapies and expanded research capabilities for conditions such as cancer, Alzheimer’s disease, ALS and Parkinson’s.
After lots of testing and fine-tuning, postdoctoral researcher Harnimarta Deol showed that their new technique works on all 20 types of amino acids and can be used on simple or complex protein mixtures.
“What took the most time was perfecting the chemical recipe and the conditions to get good results,” Anslyn said. “The lightbulb moment came while I was teaching my Introduction to Organic Chemistry class. I realized the basic science I was teaching could actually solve this real-world problem.”
Another exciting use for this method is in DNA barcoding, a way to tag proteins with tiny strands of DNA to track or analyze them. Until now, scientists couldn’t combine DNA barcoding with traditional protein sequencing because the acid would ruin the DNA.
“With our method, the DNA tags stay completely safe,” Anslyn said. “That gives scientists a lot more freedom in how they design experiments.”
The research has already caught the attention of scientists around the world. Anslyn shared the findings at a major conference in Italy, where many researchers were eager to try the new technique right away. The new technique could soon make its way into commercially available biotechnology processes and pave the way for more efficient and automated tools.
“I absolutely see this being used in commercial testing and health technologies in the future,” Anslyn said.
Other authors of the paper were Marcotte, Ava Raeisbahrami, Phuoc H.T. Ngo and Ophelia Papoulas at UT and UT Ph.D. graduate Jagannath Swaminathan of Erisyon, Inc., a fluorosequencing startup co-founded by him, Marcotte and Anslyn.
The research was funded by the National Institutes of Health, Erisyon, Inc., the Army Research Office and the Welch Foundation. Anslyn and Deol have applied for a patent on the technique.
