The transport of genetic material across biomembranes through pore-forming proteins is a process of great biological and medicinal interest (Szabo et al 1998). Alpha-Hemolysin, a pore-forming protein, was identified as a macromolecular device for DNA and RNA transport and detection. This protein may have a potential use in nanopore sequencing. The nanopore sequencing technique measures the effect of the captured single-stranded (ss) DNA blockade on the ion current across the nanopore. However, designing a nanopore that gives an ideal resolution at the single-base level is challenging due to the absence of detailed information on the behaviour of a DNA within the nanopore. This research project was able to confirm that several factors govern DNA behaviour inside the nanopore. In addition, novel software has been developed and validated for DNA-nanopore studies and for fast screening of multiple mutant nanopores.