Sequence dependence of DNA translocation through a nanopore

Abstract

We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are built from two types of bases $A$ and $C$, which has been shown previously to have different interactions with the pore. We study DNA with repeating blocks $A_n{C}_n$ for various values of $n$, and find that the translocation time depends strongly on the {\em block length} $2n$ as well as on the {\em orientation} of which base entering the pore first. Thus, we demonstrate that the measurement of translocation dynamics of DNA through nanopore can yield detailed information about its structure. We have also found that the periodicity of the block sequences are contained in the periodicity of the residence time of the individual nucleotides inside the pore.

4 pages, 4 figures, minor changes

References in corpus (16)

• Fast DNA translocation through a solid-state nanopore
• Polymer Translocation througha Pore in a Membrane
• Driven Polymer Translocation Through a Narrow Pore
• Unzipping Kinetics of Double-Stranded DNA in a Nanopore
• Anomalous Dynamics of Translocation
• Anomalous Dynamics of Forced Translocation
• Influence of polymer-pore interactions on translocation
• Langevin Dynamics Simulations of Polymer Translocation through Nanopores
• Polymer translocation through a nanopore: a two-dimensional Monte Carlo simulation
• Polymer translocation through a nanopore under an applied external field
• When translocation dynamics becomes anomalous
• Dynamics of Molecular Motors and Polymer Translocation with Sequence Heterogeneity
• Polymer translocation through a nanopore under a pulling force
• Heteropolymer translocation through nanopores
• Directed motion emerging from two coupled random processes: Translocation of a chain through a membrane nanopore driven by binding proteins
• Effect of Inhomogeneity in Translocation of Polymers through Nanopores

Cited by in corpus (35)

• Driven polymer translocation through nanopores: slow versus fast dynamics
• Comment on ``Passage Times for Unbiased Polymer Translocation through a Narrow Pore''
• Dynamical Scaling Exponents for Polymer Translocation through a Nanopore
• Active polymer translocation through flickering pores
• Chaperone-assisted translocation of a polymer through a nanopore
• Out of Equilibrium Characteristics of a Forced Translocating Chain through a Nanopore
• Polymer translocation into a fluidic channel through a nanopore
• Polymer translocation under time-dependent driving forces: resonant activation induced by attractive polymer-pore interactions
• Translocation Dynamics with Attractive Nanopore-Polymer Interactions
• Theory of pore-driven and end-pulled polymer translocation dynamics through a nanopore: An overview
• Theory of polymer translocation through a flickering nanopore under an alternating driving force
• Dynamics of DNA translocation through an attractive nanopore
• The chain sucker: translocation dynamics of a polymer chain into a long narrow channel driven by longitudinal flow
• Effects of Surface Trapping and Contact Ion Pairing on Ion Transport in Nanopores
• Stochastic sensing of polynucleotides using patterned nanopores
• Polymer translocation out of confined environments
• Translocation through environments with time dependent mobility
• Particle diode: Rectification of interacting Brownian ratchets
• Sequencing of semiflexible polymers of varying bending rigidity using patterned pores
• Dynamics of polymer translocation into a circular nanocontainer through a nanopore
• Polymer translocation into laterally unbounded confined environments
• Ejection dynamics of a ring polymer out of a nanochannel
• The circular Kardar-Parisi-Zhang equation as an inflating, self-avoiding ring polymer
• Translocation through a narrow pore under a puling force
• Chain conformation of ring polymers under a cylindrical nanochannel confinement
• Tug-of-War in a Double-Nanopore System
• Translocation of stiff polymers through a nanopore driven by binding particles
• Noise driven translocation of short polymers in crowded solutions
• On the Lubensky-Nelson model of polymer translocation through nanopores
• Pulling a DNA molecule through a nanopore embedded in an anionic membrane: tension propagation coupled to electrostatics
• Free Energy Evaluation in Polymer Translocation via Jarzynski Equality
• Deconvoluting chain heterogeneities from driven translocation through a nano-pore
• Markovian Description of Unbiased Polymer Translocation
• Markov Chain Modeling of Polymer Translocation Through Pores
• Environmental Noise and Nonlinear Relaxation in Biological Systems