title: Effect of confinement on DNA, solvent and counterion dynamics in a model biological nanopore.
abstract: The application of recent advances in nanopore technology to high-throughput DNA sequencing requires a more detailed understanding of solvent, ion and DNA interactions occurring within these pores. Here we present a combination of atomistic and coarse-grained modeling studies of the dynamics of short single-stranded DNA (ssDNA) homopolymers within the alpha-hemolysin pore, for the two single-stranded homopolymers poly(dA)40 and poly(dC)40. Analysis of atomistic simulations along with the per-residue decomposition of protein-DNA interactions in these simulations gives new insight into the very complex issues that have yet to be fully addressed with detailed MD simulations. We discuss a modification of the solvent properties and ion distribution around DNA within nanopore confinement and put it into the general framework of counterion condensation theory. There is a reasonable agreement in computed properties from our all-atom simulations and the resulting predictions from analytical theories with experimental data, and our equilibrium results here support the conclusions from our previous non-equilibrium Brownian dynamics studies with a recently developed BROMOC protocol that cations are the primary charge carriers through alpha-hemolysin nanopores under an applied voltage in the presence of ssDNA. Clustering analysis led to an identification of distinct conformational states of captured polymer and depth of the current blockade. Therefore, our data suggest that confined polymer may act as a flickering gate, thus contributing to excess noise phenomena. We also discuss the extent of water structuring due to nanopore confinement and the relationship between the conformational dynamics of a captured polymer and the distribution of blocked current.
authors: Centre for Molecular Simulation, Department of Biological Sciences, 2500 University Drive, Calgary, AB T2N 2N4, Canada. snoskov@ucalgary.ca.
authors: Suren
authors: S
authors: Markosyan
authors: Pablo M
authors: PM
authors: De Biase
authors: Luke
authors: L
authors: Czapla
authors: Olga
authors: O
authors: Samoylova
authors: Gurpreet
authors: G
authors: Singh
authors: Javier
authors: J
authors: Cuervo
authors: D Peter
authors: DP
authors: Tieleman
authors: Sergei Yu
authors: SY
authors: Noskov
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D004277:DNA, Single-Stranded / Q000737:chemistry; D004594:Electrophysiology; D006460:Hemolysin Proteins / Q000737:chemistry*; D007477:Ions; D008051:Lipid Bilayers; D056004:Molecular Dynamics Simulation; D058608:Nanopores; D009690:Nucleic Acid Conformation; D011108:Polymers / Q000737:chemistry; D017433:Protein Structure, Secondary; D012997:Solvents / Q000737:chemistry*; D013696:Temperature
chemical_list: D004277:DNA, Single-Stranded; D006460:Hemolysin Proteins; D007477:Ions; D008051:Lipid Bilayers; D011108:Polymers; D012997:Solvents; D004247:DNA