Identification of nucleobases of single stranded DNA by nanopore force resolution at different film thickness

The model of the molecular translocation of all types of DNA base molecules of cytosine, thymine, adenine and guanine through the nanoporous membrane of a solid thin film has been considered from the point of view of improving the resolution of forces by changing parameters of the membrane itself. The results of simulation of translocation process were compared for all four DNA nucleotides. The molecular dynamics (MD) method with the force field potential has been used for the atomic level modeling of the cytosine(C), thymine(T), adenine(A), and guanine(G) molecules and a configuration of the nanoporous Si membrane. With the planar structure of base molecules and cylindrical symmetry of pore, the two-dimensional projection was used in the simulation. The force field between the base molecule and atoms of nanopore has been estimated. Influence of the Si surface hydrogenization and film thickness on the force resolution for each nucleobase was evaluated vs. possible signal resolution. At 5 layer thickness of the film it was possible to cut thermal fluctuations and distinguish four nucleobase types.