The Nucleotide Capture Region of Alpha Hemolysin: Insights into Nanopore Design for DNA Sequencing from Molecular Dynamics Simulations

Abstract

Nanopore technology for DNA sequencing is constantly being refined and improved. In strand sequencing a single strand of DNA is fed through a nanopore and subsequent fluctuations in the current are measured. A major hurdle is that the DNA is translocated through the pore at a rate that is too fast for the current measurement systems. An alternative approach is “exonuclease sequencing”, in which an exonuclease is attached to the nanopore that is able to process the strand, cleaving off one base at a time. The bases then flow through the nanopore and the current is measured. This method has the advantage of potentially solving the translocation rate problem, as the speed is controlled by the exonuclease. Here we consider the practical details of exonuclease attachment to the protein alpha hemolysin. We employ molecular dynamics simulations to determine the ideal (a) distance from alpha-hemolysin, and (b) the orientation of the monophosphate nucleotides upon release from the exonuclease such that they will enter the protein. Our results indicate an almost linear decrease in the probability of entry into the protein with increasing distance of nucleotide release. The nucleotide orientation is less significant for entry into the protein.

Molecular Mechanics of the Moisture Effect on Epoxy/Carbon Nanotube Nanocomposites

“…To understand the origin of the moisture effect, it is important to study the material behavior in the molecular level, so as to predict the system performance at the larger length and time scales. Molecular dynamics (MD) simulation has been considered as a fundamental and powerful technique for studying the molecular interaction inside the structure [ 14 , 15 , 16 , 17 , 18 ], and it has been widely used to investigate the structure and properties of the polymer, the carbon material, and the polymer composite at the nanoscale [ 19 , 20 , 21 , 22 , 23 ]. Microscopic information about the moisture diffusion and absorption inside the polymer and the nanocomposite has been obtained through observing the molecular motions [ 24 , 25 , 26 ].…”

Translocation of flexible and tensioned ssDNA through in silico designed hydrophobic nanopores with two constrictions

“…Periodic boundary conditions were applied in three dimensions as in our own previous work on pores based on α-hemolysin and the work of other groups studying similar phenomena. 5,[19][20][21] Repeat simulations were performed by extracting system coordinates from random timepoints from the last 100 ps of the equilibration run to initiate the simulations. Therefore, the starting coordinates as well as the initial velocities are different for the repeat runs.…”

Electric-Field-Driven Translocation of ssDNA through Hydrophobic Nanopores

“…Periodic boundary conditions were applied in three dimensions as in our own previous work on pores based on α-hemolysin and the work of other groups studying similar phenomena. 8,10,20,21 Analysis was conducted using GROMACS utilities and locally written code. Pore radius profiles for the pore models were obtained using HOLE.…”

“…The electric field was imposed by a constant voltage drop across the simulation cell. Periodic boundary conditions were applied in three dimensions as in our own previous work on pores based on α-hemolysin and the work of other groups studying similar phenomena. ,,, Analysis was conducted using GROMACS utilities and locally written code. Pore radius profiles for the pore models were obtained using HOLE .…”