subscribe: Daily Newsletter

 

Breakthrough in DNA diagnostics

0 comments
Breakthrough in DNA diagnostics

If NASA is going to send astronauts on years-long missions, the agency will need new and better tools to monitor whether the men and women are healthy along the way. One company has developed a tool that could make comprehensive diagnostics at long distances a reality for NASA — and it has big potential to advance medicine on Earth, too.
Currently, Earth-based researchers keep track of things like white blood cell counts and cholesterol and cortisol levels, dubbed “biomarkers”, with tests that use special proteins called antibodies. But the antibodies have a short, three- to six-month shelf life and can be ruined by the high levels of radiation in space, making them ill-suited for such missions.
Research from the 1990s suggested an alternative: single strands of RNA and DNA that can be folded into three-dimensional structures and, like antibodies, bind to specific molecules. These structures, called aptamers, can be stored at ambient temperatures without degrading and are impervious to radiation.
There are, however, drawbacks to using aptamers for diagnostics. For one, making them is a time-consuming, complicated process. Furthermore, until recently aptamers haven’t been as good as antibodies at sticking to target molecules.
“They didn’t bind well enough — they weren’t specific enough for their targets,” explains Mark Shumbera, president of AM Biotechnologies. “Certain chemical modifications needed to be added to their DNA to make them work better.”
A standard aptamer process starts by placing a target molecule into a solution holding one hundred trillion random RNA/DNA sequences. Some sequences will bond well with the target molecule, while others won’t — or will bond only weakly. The successful sequences are then separated and copied through a chain reaction to create another, more refined solution, in a process that is repeated up to 15 times.
This technique, called systemic evolution of ligands by exponential enrichment (Selex) often requires many chemical modifications to best tailor aptamers to bind to target substances. However, scientists are limited in how many chemical modifications they can make, in part because the chain reaction “doesn’t work very efficiently like that”, says Shumbera. “So typically, people only use one, and maybe two modifications at a time.”
In part through NASA Small Business Innovation Research funding from Johnson Space Center, in 2007 AM Biotechnologies advanced a faster, simplified method for creating aptamers that bond strongly to their target molecule. The company calls these next-generation aptamers X-Aptamers.
The new, faster method uses a proprietary process to synthesize a library of 10-billion RNA/DNA sequences, including both natural and heavily modified sequences, onto microbeads, which are then used to develop aptamers with an affinity for particular molecules, such as the biomarkers NASA is interested in. The bead-based method removes the previous limitations on allowable chemical modifications and simplifies the manufacturing process.
“You can have 50 modifications in a sequence – there is virtually no limit,” Shumbera says. “This method allows for the DNA or RNA to be more chemically diverse, meaning there’s a better chance of creating a molecule with a particularly high affinity and specificity for the target.”
The process is now in use by the company, which has also made it commercially available so anyone can make their own aptamers. The kit is so simple that anyone with basic biochemistry lab skills can use it easily, Shumbera says. “We have university customers, our prototype users, who have freshmen undergraduates select X-Aptamers using our kits. The bead-based process simplifies aptamer selection tremendously.”
In addition to helping diagnose diseases, X-Aptamers could also be used to carry and attach a chemotherapy drug to a tumor, sparing other parts of the body from receiving the treatment. “It could help usher in the next big revolution in terms of how we diagnose and treat patients,” Shumbera says.
One aptamer drug, Pegaptanib, has already gotten FDA approval, and Shumbera believes diagnostic applications aren’t far behind. He sees a bright future for aptamers, especially for NASA uses. The agency is working with other companies to create a hardware platform that can perform analysis in space, helping to diagnose and possibly treat ailments while astronauts are thousands or millions of miles from Earth.