Translocation of a Single Stranded DNA Through a Conformationally Changing Nanopore

TL;DR

This paper models the translocation of single-stranded DNA through a conformationally changing nanopore using coupled master equations, revealing complex passage time behaviors influenced by various physical parameters.

Contribution

It introduces a coupled master equation approach to analyze DNA translocation through dynamic nanopores, providing analytical expressions for first passage times and linking theory to experiments.

Findings

First passage time distributions can be mono, double, or triple peaked.

The model predicts two regimes of translocation times in field-free conditions.

Analytical mean first passage time expressions are derived.

Abstract

We investigate the translocation of a single stranded DNA through a pore which fluctuates between two conformations, using coupled master equations. The probability density function of the first passage times (FPT) of the translocation process is calculated, displaying a triple, double or mono peaked behavior, depending on the interconversion rates between the conformations, the applied electric field, and the initial conditions. The cumulative probability function of the FPT, in a field-free environment, is shown to have two regimes, characterized by fast and slow timescales. An analytical expression for the mean first passage time of the translocation process is derived, and provides, in addition to the interconversion rates, an extensive characterization of the translocation process. Relationships to experimental observations are discussed.