Determination of Free Energy Profiles for Polynucleotides Translocation through Mutant α-Hemolysin Nanopores

Abstract

The understanding of nucleotides' interaction with the Staphilococcus aureus α-hemolysin nanopore is of special interest because some studies suggest several methods for using this nanopore incorpored in a planar lipid bilayer as a real time DNA sequencer. The main operational difficulty to obtain a DNA sequencer is the high DNA translocation speed through the nanopore, which hinders proper base discrimination. Strategies for producing increasing the residence time of the DNA and the interaction energy with the nanopore include site directed mutations and chemical functionalization. In this work we used nonequilibrium molecular dynamics simulations and Jarzynsnki's relation (JR) to obtain the free energy profiles of DNA translocation through α-hemolysin nanopores, in its native form or mutated by cysteine in strategic positions previously selected by molecular modeling investigations: G133 and L135. Compared to the native form, there was a considerable increase in the minimum energy needed for DNA transport; we also observe, in the point of mutation, a PMF increase in L135C and decrease in G133C.View Large Image | View Hi-Res Image | Download PowerPoint SlideWe intend use the obtained information about the interactions of DNA-nanopore to theoretically predict promising nanopores to be tested experimentally.