Sometimes DNA just needs to be slowed down. When the concept of nanopore-based sequencing was developed, the idea was that an electrical field would apply a force to get the strands of DNA to pass through the small nanopore opening while that same electrical field would read the sequence off the strands. "The idea of the nanopore sequencing as originally proposed … is very enticing in its simplicity, that you read off the genetic sequence by measuring current or voltage," says Brown University physicist Xinsheng Sean Ling. "That's very appealing to physicists."
But the electric force needed to get DNA through the pore makes it move too fast for the sequence to be determined; it needed to be slowed down. "The only way to get the DNA into the nanopore is by cranking up voltage, to have a large electric field. And then the large electric field also pushes DNA too quickly. So you can't win. It's a real Catch-22," Ling says.
To slow down the movement of DNA through the nanopore, Ling and his graduate student Hongbo Peng, who is now at IBM, decided to separate out the force driving the DNA's movement from the reading mechanism. In their experiment, the motion of the DNA is controlled by a magnetic field, while the reading of the sequence is still done by electrical field. They coated a commercially available magnetic bead, 2.8 microns in diameter, with streptavidin. That streptavidin then attached to the biotin they added to the end of the DNA. As in the original experiments, they drove the DNA through the 10 nanometer-sized nanopore using the electric field. However, the magnetic bead got stuck in the pore. The researchers then used a magnet to pull the bead out of the pore, thus pulling the DNA slowly backward and out of the pore. "The DNA translocates against the electrical field," Ling says. They were able to slow the movement of the DNA by 2,000-fold compared to the original technique.
There's still a long way to go for this technique to be used for sequencing, such as scaling it up and using different-sized pores. "For sequencing you need to demonstrate this on multiple pores. I think on 10 simultaneously would be very nice. That's not something I'm doing myself here," Ling says. "I'm hoping that a company will pick it up and do that."