Discrimination of Polynucleotide Transport through a Highly Hydrophobic Uncharged Nanopore

The importance of DNA structures in medicine has motivated researchers to develop sequencing methods with low costs and high speeds. The potential use of nanofluidics for the analysis of the translocation of polynucleotides through a nanopore is a very interesting solution. Herein, we demonstrate both by experiments and by explicit solvent molecular dynamics simulations that the translocation of polyadenylic acid and polycytidylic acid can significantly affect the ionic flux behavior. In particular, the nanochannel enhances the velocity difference between polynucleotides during the trans location process. Our results revealed the important role of the strand structures during their translocation, as already observed in biochannels. The folding unfolding process leads to stronger interactions with the nanopore wall that decrease the velocity of the strands. This behavior could lead to the detection of different polynucleotides in mixture.