New DNA-Sequencing Technique May Lower Cost of Genome Analysis

Method allows more-accurate reading of DNA code.

Magnetic tweezers slow the movement of DNA through a nanopore, allowing its base pairs to be read.

Since the human genome was spelled out six years ago, DNA sequencing costs have fallen more than 50-fold, fueled in large part by tools, technologies and process improvements. But it still costs as much as $5 million to sequence 3 billion base pairs — the amount of DNA found in the genomes of humans and other mammals.

More recently, the National Institutes of Health called for cutting the cost to $1,000 or less, which may enable sequencing to be part of routine medical care—tailoring diagnosis, treatment and prevention to each person’s unique genetic profile.

But scientists have struggled to figure out how to accurately read the 3 billion base pairs without time-consuming and expensive methods.

To help solve the problem, physicists at Brown University have developed a new procedure that moves DNA through an electrified nanopore sieve using magnets. The approach is promising because it allows multiple segments of a DNA strand to be threaded simultaneously through numerous tiny pores and for each fragment to move slowly enough through the opening so the base pairs can be accurately read.

“When it comes to sequencing anyone’s genome, you need to do it cheaply, and you need to do it quickly,” explained Xinsheng Sean Ling, professor of physics at Brown. “This is a step in that direction.”

Appying an electric field to drive DNA molecules through a nanopore—a tiny hole in a membrane—is not new. But in those experiments, the base pairs moved too quickly through the openings for the code to be read accurately. So, while a large electric field is needed to draw the DNA molecules into the pore, Ling said, the same field moves the DNA too quickly.

It’s a classic scientific Catch-22, Ling said.

To slow the strands’ movement through the opening so the base pairs (A, T, C, and G) can be read, Ling and his coworker Hongbo Peng attached the DNA strand to an iron bead using a special chemical bond. They used an electric field to drive the beaded DNA strand toward the pore. But while the strand could pass through the pore, the bead was too large, and lodged in the pore with the attached DNA strand suspended on the other side of the membrane.

The researchers then used “magnetic tweezers” to draw the bead away from the pore. As the bead moves toward the magnets, the attached DNA strand moves through the pore — slowly enough so that the base pairs can be read.

“The DNA is essentially caught in a tug-of-war,” Ling explained. “The speed will be controlled by striking some balance between the magnetic and the electric fields. From there, we can tune it to dictate the speed.”

The scientists report their technique reduces the average speed of the DNA strand’s passage by more than 2,000-fold. “It can be slower even. There is no limit,” Ling said.

A similar experiment has been done using optical tweezers, Ling said, but it involves only one DNA strand at a time. The new method sends multiple strands through the nanopores simultaneously. “It is scalable,” Ling said.

The researchers plan to test their technique on bacterial genomes first.

The research was funded by the National Human Genome Research Institute and the National Science Foundation's Nanoscale Interdisciplinary Research Teams. It was publish in an April edition of the journal Nanotechnology.

—By Leslie Fink/NSF from materials provided by Brown University.