Single-Stranded DNA within Nanopores: Conformational Dynamics and Implications for Sequencing; a Molecular Dynamics Simulation Study

Abstract

Engineered protein nanopores, such as those based on α-hemolysin from Staphylococcus aureus have shown great promise as components of next-generation DNA sequencing devices. However, before such protein nanopores can be used to their full potential, the conformational dynamics and translocation pathway of the DNA within them must be characterized at the individual molecule level. Here, we employ atomistic molecular dynamics simulations of single-stranded DNA movement through a model α-hemolysin pore under an applied electric field. The simulations enable characterization of the conformations adopted by single-stranded DNA, and allow exploration of how the conformations may impact on translocation within the wild-type model pore and a number of mutants. Our results show that specific interactions between the protein nanopore and the DNA can have a significant impact on the DNA conformation often leading to localized coiling, which in turn, can alter the order in which the DNA bases exit the nanopore. Thus, our simulations show that strategies to control the conformation of DNA within a protein nanopore would be a distinct advantage for the purposes of DNA sequencing.

The NMR structure of the II–III–VI three-way junction from the Neurospora VS ribozyme reveals a critical tertiary interaction and provides new insights into the global ribozyme structure

“…The following NMR structures of isolated subdomains were used: the cleavage site internal loop of the SLI substrate in its active form (PDB ID code 1OW9) (Hoffmann et al 2003), the terminal loop of SLV in the presence of Mg 2+ (PDB ID code 1YN1) (Campbell et al 2006), the I/V kissing-loop interaction (PDB ID code 2MI0) (Bouchard and Legault 2014b), the A730 loop of SLVI (PDB ID code 2L5Z) (Desjardins et al 2011), the III-IV-V junction (PDB ID code 2MTJ) (Bonneau and Legault 2014b) and the II-III-VI junction (PDB ID code 2N3Q). The initial model was then minimized with the molecular dynamics package GROMACS (Pronk et al 2013) and the Amber99SB force field with the ParmBSC0 nucleic acid parameters and using explicit aqueous solvent (Hornak et al 2006;Perez et al 2007;Guy et al 2012).…”

Diffusive dynamics of DNA unzipping in a nanopore

“…The coarse-grained (CG) models, where superatoms represent groups of atoms or even whole molecules, decrease the computational cost significantly. [23][24][25][26][27][28] The dynamics of single-stranded DNA translocation through a nanopore were studied by Guy et al [29] However, that model was not optimized to study the unzipping process. Therefore, we explored the kinetics of DNA unzipping using our CG model, [30] which allows simulations with explicit solvent and ions.…”

A nucleotide-level coarse-grained model of RNA

“…36,37 Moreover, while the forcefields are improving, they are still under development so that different versions can generate different behavior. [38][39][40] In order to access longer time scales relevant to rare events, such as the breaking of base pairs or the formation of large structures, one needs to use a more coarse-grained description. In this approach, atoms are incorporated into a reduced set of degrees of freedom that experience effective interactions.…”