Orientation-Dependent Electric Potential and Ionic Current Model of a Nucleotide in a Silicon Dioxide Nanopore

Nanopore sensing and detection over the last few years has become an integral and useful method for identification and separation of biomolecules and DNA chains. In order to better identify DNA molecules with very slight variations in nucleotide composition, it is imperative to study the ionic current variations caused by individual nucleotides placed in a solid-state nanopore. In this work, we perform a systematic study, using a self-consistent method of computation, of the dependence of ionic current variations on the orientation of the translocating nucleotide. We simulate ionic current and electric potential trends for an individual nucleotide placed in a silicon dioxide nanopore for certain pre-defined orientations in different planes of rotations. We illustrate how slight variations in the nucleotide's orientation can alter the measured ionic current and electric potential and obscure the variations caused by the nucleotide substitution.