Modeling transport through synthetic nanopores: Simulating biomolecules in synthetic nanopores presents various challenges

Synthetic nanopores have arisen as a convenient means of characterizing single molecules, with DNA being one of the most popular subjects. By applying an electric field, ions and charged biomolecules like DNA can be compelled to interact with, or translocate through, nanopores in thin membranes. The use of the nanopore method for characterizing nucleic acids gained initial momentum in 1996 with a landmark paper by Kasianowicz et al. [1]. The researchers observed step-like reductions of ionic current through a pore furnished by the protein α-hemolysin, apparently associated with the passage of single nucleic acid molecules. The duration of the reductions was found to be proportional to the length of the molecules. Subsequent research showed that different DNA homopolymers and block copolymers [2] and, later, molecules differing by a single nucleotide [3] could be discriminated by the values of the ionic current. It was also possible to determine the orientation of the DNA (led by the 5′- or 3′-end) [4] in this way.