The researchers showed that modestly charged nanocarriers can be used to detect and capture DNA or RNA molecules of any length or secondary structure. Such selective, molecular detection technologies would greatly improve the real-time analysis of complex clinical samples for cancer detection and other diseases.
Aksimentiev used TACC's Stampede supercomputer, as well as Blue Waters at the National Center for Supercomputing Applications, to design and virtually test the behavior of these nanopores systems.
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"In the development of nanosensors, such as the nanopore single-molecule sensor for genetic diagnosis of cancer, we can experimentally discover various clinically useful phenomena at the nanometer scale. But our collaborator, Dr. Aksimentiev can utilize their superior computational power to accurately dig out the molecular mechanisms behind these experimental observations," said Gu. "These new nano-mechanisms can guide the design of a new generation of nanopore sensors for genetic marker-based cancer diagnostics, which we believe will play an important role in precision oncology."
(This work was supported by grants from the National Institutes of Health (R01-GM079613, R01-GM114204). The simulation studies led to the development of a patent, which was published in May 2017.)
DIAGNOSING BIOMARKERS IN THE BLOODSTREAM WITH A MICROSCOPIC LAB-ON-A-CHIP
Researchers from Lamar University, including Tao Wei, Ian Lian and Yu-Hwa Lo, are exploring a different approach to nanoscale cancer diagnostics. In place of nanopores, they are using lab-on-a-chip techniques invented by Lo's group that can recognize short nucleic acid fragments -- which act as biomarkers for diseases -- in the bloodstream.
The detection is based on the hybridization of nucleic acid fragments grafted on the substrate surface inside an evaporating droplet. Hybridization occurs when nucleic acids form hydrogen bonds. This process is influenced by the molecular geometry of the nucleic acid fragments that spontaneously self-organize into an ordered structure on the surface, also known as self-assembling monolayers (SAMs).
The sensitivity of such biochips is dependent on the degree to which the target material can bind to the surface of the biochip. Various factors affect the binding processes, including the structure of SAMs surface, the ion strength, the target DNA concentration and the surface packing density.
Wei and his collaborators used Stampede to perform molecular dynamics simulations and free energy computations to study the DNA hybridization process in detail.
