Simulations show new phenomenon with nanopore DNA sequencing

Any truck operator knows that hydraulics do the heavy lifting. Water does the work because it’s nearly incompressible at normal scales. But things behave strangely in nanotechnology, the control of materials at the scale of atoms and molecules. Using supercomputers, scientists found a surprising amount of water compression at the nanoscale. These findings could help advance medical diagnostics through creation of nanoscale systems that detect, identify, and sort biomolecules.

“We found that an electric field can compress water locally, and that water compression would prevent molecules from being transported through small pores,” Aksimentiev said. “This is a very counterintuitive effect, because usually it is assumed that a higher electric field would propel molecules faster through the pore. But because the electric field also compresses water, the outcome would be the opposite. That is, the higher electric field would not allow molecules to pass through.” In effect, the water compression generated by the higher electric field pushed DNA molecules away from the nanopore channels.

Aksimentiev and Wilson worked with a one-atom-thick graphene membrane. They poked a hole in it 3.5 nanometers wide, just wide enough to let a strand of DNA through. An external electric field pulled the DNA through the hole, like threading a needle. The nucleotide letters A-C-T-G that make the rungs of the double stranded DNA produce signals as they go through the pore, analogous to playing a tape in a tape recorder. This method being developed, called nanopore sequencing, is an alternative to conventional sequencing. It doesn’t depend on polymerase chain reaction enzymes to amplify DNA and in theory allows for much longer reads.


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