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Stretching and Sequencing DNA


  • Title: Assistant Professor, North Carolina State University
  • Education: PhD, University of Cambridge, 2003
  • Recommended by: Robert Austin, Alan Guttmacher

Many approaches to DNA sequencing rely on fluorescent tags to signal the different bases contained in a given stretch of DNA. Instead of using tags, North Carolina State's Robert Riehn thinks that the electrical properties of DNA can be harnessed to determine its sequence — and he's putting his background in nanotechnology to use to find sequence-specific electric signals from DNA. "What I'm doing is very basic: trying to show there is a signal and trying to show that we can make this signal sequence-specific," Riehn says.

In his microfluidic device, Riehn uses nanofluidic channels with cross-sections smaller than 50 nanometers and a few hundred microns long. Strands of DNA are then stretched out in these channels and placed between two electrodes. "The DNA is directly between two opposing electrodes, and the two opposing electrodes try to attract the DNA," Riehn says. His team members are currently working on measuring how current flows sideways through DNA. They hope that if they choose the conditions properly, they will be able to detect a sequence-dependent signal. "Chemically, the bases have different chemical structure," Riehn says. "What we hope is that by choosing the conditions of the electrical field correctly, or of the energies of the electrons correctly, that we can gain some insight into the electrical energy structure of the molecular orbitals inside the molecule. And then, hopefully, if we choose correctly, the different bases have different signatures."

The challenges, he adds, are getting that sequence-dependent signal and knowing how fast the strands of DNA are flowing through the nanochannels. Though all the bases are different, they are still fairly similar, hanging off the same sugar phosphate backbones; Riehn says that only about a third of the base accounts for the difference. Then, you have to know how fast the DNA moves through the channel because if you don't know that, "you still don't know what the sequence is," he says.

Riehn's interest in this area was piqued by working in Robert Austin's lab at Princeton University. Riehn says that Austin's rigorous way of asking questions has shaped how he does his own research. "His approach definitely is not one of incremental research. He has more of an approach of trying to do something big — try to do something big and you may fail and you may not fail," Riehn says. "I like that."

Looking ahead

In the next five years, Riehn says, the goal of sequencing a human genome for $1,000 will most likely be met. However, he thinks that sequencing will still be performed in large diagnostic laboratories. Further down the line, in about 10 years, he thinks that doctors' offices may have sequencers that could provide low or medium-quality readouts to be used as a screening tool, say for a microbial or viral infection. "We wouldn't necessarily be seeing the resequencing everything to true fidelity, but simply a screening for a large number of common questions," Riehn says.

Publications of note

In a PNAS paper from 2005 called "Restriction mapping in nanofluidic devices," Riehn and his coauthors restriction-mapped DNA stretched in their nanochannel. Riehn says that restriction mapping is one of the more basic tools in the field, but the effort showed "that we can really do biology on our microfluidic devices, that they are not just applicable to a very narrow range of applications, that we can do real biology on the stretch-out DNA inside the nanochannels."

And the Nobel goes to …

"A very large-scale issue would be the eradication of transmittable diseases," Riehn says. "That would be one thing that I would do if I could, really — diagnose every person instantly for exactly which pathogen they are carrying."

The Scan

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