Nanoscale holes in solid-state membranes, so-called nanopores, furnish nanosensors for probing biological molecules such as DNA and protein. Under electric fields, charged molecules like DNA are pushed through these pores and the flow of ions surrounding the translocating DNA can be recorded to recognize individual DNA bases, and in turn, the sequence of DNA. Traditional nanopore sensors often use solid-state membranes, which are too thick to recognize single bases on a DNA strand. This limitation can be overcome by using two-dimensional materials such as graphene or MoS$_2$. Only a single base pair of DNA fits into the thin two-dimensional material nanopores at any time, such that these nanopores can potentially provide single-base resolution for DNA sensing. In addition, graphene and MoS$_2$ are both lectrically conductive, thereby allowing the use of electric current in the layer to detect and characterize the DNA in the pore. Instead of actually building and testing the device experimentally, molecular dynamics simulations can assist and enable a bottom-up design of two-dimensional material nanopore devices by unveiling the atomic-level processes occurring during nanopore sensing.
Threading DNA electrically through nanometer-sized pores, so-called
holds promise for detecting and sequencing DNA (see Nov
2005 and Oct
Nanopore measurements tend to be the more sensitive the smaller the pores are.
The material graphene, which is just one atom thick and looks like a
two-dimensional ``honeycomb" made up of carbon atoms, offers the ultimate
physical resolution for measuring DNA (the stacking distance between
base-pairs in DNA is about 0.35 nm). As reported recently, molecular dynamics
simulations using NAMD revealed the motion of DNA being threaded through
graphene nanopores at atomic level resolution. Simulations not only agree
qualitatively with previous experiments on DNA translocation through graphene
nanopores, but go one step further than the experiments and suggest how
individual base pairs can be discriminated. The recent computational study is
one further example for the guidance
that molecular dynamics simulations provide in nanosensor development (see a
information can be found on our graphene
Computer modeling in biotechnology, a partner in development.
Aleksei Aksimentiev, Robert Brunner, Jordi Cohen, Jeffrey Comer, Eduardo Cruz-Chu, David Hardy, Aruna Rajan, Amy Shih, Grigori Sigalov, Ying Yin, and Klaus Schulten. In Protocols in Nanostructure Design, Methods in Molecular Biology, pp. 181-234. Humana Press, 2008.