Nanotechnology pulls DNA through nanopore slowly enough to read sequence

Using a magnetic bead to slowly pull a DNA molecule through a solid-sate nanopore looks promising as the basis for a very fast and efficient nanotech DNA sequencing method. If this method is perfected (no DNA sequence obtained by this method has been published yet) sequencing an individual human genome may become cheap enough to make practical personalized medicine that accounts for individual genetic differences. From Brown University, via AAAS EurekAlert “Brown researchers create novel technique to sequence human genome“:

Since the human genome was sequenced six years ago, the cost of producing a high-quality genome sequence has dropped precipitously. More recently, the National Institutes of Health called for cutting the cost to $1,000 or less, which may enable sequencing as part of routine medical care.

The obstacles to reaching that goal have been primarily technological: Scientists have struggled to figure out how to accurately read the 3 billion base pairs – the amount of DNA found in humans and other mammals – without time-consuming, inefficient methods.

Physicists at Brown University may have an answer. They introduce a novel procedure to vastly slow the DNA’s movement through openings that are used to read the code. In the journal Nanotechnology [abstract], the physicists report the first experiment to move DNA through a solid-state nanopore 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 that 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, who joined the Brown faculty in 1996. “This is a step in that direction.”

The idea of reading DNA by threading strands through tiny openings is not new. Scientists have shown that an applied electric field can drive the DNA molecules through a nanopore, a tiny hole in a membrane. 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 explained, the same field moves the DNA too quickly, a classic scientific Catch-22.

The trick is to figure out how to slow the strands’ movement through the opening so the base pairs (A, T, C, and G) can be read. To solve that, Ling and Hongbo Peng, the lead author who performed the work as a graduate student at Brown and who now works at IBM, attached the DNA strand to a bead using a streptavidin-biotin bond. Like previous researchers, they used an electric field to drive the DNA strand toward the pore. But while the strand could pass through the pore, the bead, with a 2.8-micron diameter, was too large for the pore, which has a diameter of only 10 nanometers. So the bead was stuck in the hole with the attached DNA strand suspended on the other side of the membrane.

The Brown researchers then used magnets — they call them “magnetic tweezers” — to draw the iron-oxide 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 scientists named their process “reverse DNA translocation” because, as Ling explained, “the DNA is essentially caught in a tug-of-war. And the speed of translocation will be controlled not solely by the electric field but 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 Brown method sends multiple strands through the nanopores simultaneously. “It is scalable,” Ling said.

The researchers expect to test their technique in experiments using bacterial DNA.

This research (519 KB PDF) and other papers published in Nanotechnology and other IOP journals are freely available for 30 days after publication. Electron beams from a transmission electron microscope were used to drill 12-nm-diameter nanopores in a 60-nm-thick silicon dioxide/silicon nitride/silicon dioxide membrane. Bacteriophage lambda DNA molecules (about 48,500 base pairs long) were attached to 2800-nm-diameter magnetic beads by the (non-covalent) association of biotin molecules linked to the DNA and streptavidin protein coating the magnetic beads. When an electric field was applied, the DNA molecules rapidly threaded through the nanopores but became immobilized because the beads were too large to fit through the pores. By pulling back with a carefully calibrated magnetic force, the DNA was reverse-threaded through the nanopore at a speed slow enough (19 ms to traverse the 60-nm channel) to read the sequence. The principal technical problems were the capture of multiple DNA molecules in one nanopore and the breakage of the non-covalent biotin-streptavidin bond. Nevertheless the authors believe the method can be scaled so that large numbers of nanopores can be individually addressed to read multiple DNA sequences as different DNA molecules are pulled from different nanopores at slightly different times.

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