Researchers at the National Institute of Standards and Technology (NIST) have simulated a new concept for rapid, accurate gene sequencing by pulling a DNA molecule through a tiny hole in graphene and detecting changes in electrical current. This new method might ultimately be faster and cheaper than conventional DNA sequencing.
The study suggests that the method could identify about 66 billion bases (the smallest units of genetic information) per second with 90% accuracy and no false positives. Conventional sequencing involves separating, copying, labeling and reassembling pieces of DNA to read the genetic information. The new NIST way offers a twist on the more recent "nanopore sequencing" idea of pulling DNA through a hole in specific materials, originally a protein. This concept is based on the passage of electrically charged particles (ions) through the pore and poses challenges such as unwanted electrical noise and inadequate selectivity.
The new NIST method is to create temporary chemical bonds and rely on graphene's capability to convert the mechanical strains from breaking those bonds into measurable changes in electrical current. In the method, a graphene nanoribbon (4.5 by 15.5 nanometers) has several copies of a base attached to the nanopore (2.5 nm wide).
The researchers see it as a tiny strain sensor of sorts, and state that no new complete technology was invented, but instead - a new physical principle that can potentially be far superior to other existing concepts. In simulations of how the sensor would perform at room temperature in water, cytosine is attached to the nanopore to detect guanine. A single-strand (unzipped) DNA molecule is pulled through the pore. When guanine passes by, hydrogen bonds form with the cytosine. As the DNA continues moving, the graphene is removed and then slips back into position as the bonds break.
The NIST study focused on how this strain affects graphene's electronic properties and found that temporary changes in electrical current indeed indicate that a target base has just passed by. To detect all four bases, four graphene ribbons, each with a different base inserted in the pore, could be stacked vertically to create an integrated DNA sensor.
The researchers combined simulated data with theory to estimate levels of measurable signal variations. Signal strength was in the milliampere range, stronger than in the earlier ion-current nanopore methods. Based on the performance of 90% accuracy without any false positives (i.e., errors were due to missed bases rather than wrong ones), the researchers suggest that four independent measurements of the same DNA strand would produce 99.99 percent accuracy, as required for sequencing the human genome.
The researchers concluded that the proposed method shows "significant promise for realistic DNA sensing devices" without the need for advanced data processing, microscopes, or highly restricted operating conditions. Other than attaching bases to the nanopore, all sensor components have been demonstrated experimentally by other research groups. Theoretical analysis suggests that basic electronic filtering methods could isolate the useful electrical signals. The proposed method could also be used with other strain-sensitive membranes, such as molybdenum disulfide.