Deconvoluting chain heterogeneities from driven translocation through a nano-pore

TL;DR

This study investigates how chain heterogeneities affect driven translocation through nanopores, revealing how mechanical properties can be extracted from translocation dynamics for biomolecular analysis.

Contribution

It introduces a model for translocation of semi-flexible chains with heterogeneities, enabling deconvolution of mechanical properties from translocation data.

Findings

Different translocation scenarios depend on chain heterogeneity and viscosity.

Waiting time distributions reveal information about chain stiffness and flexibility.

Method can be used to probe biomolecules like DNA, RNA, and proteins.

Abstract

We study translocation dynamics of a driven compressible semi-flexible chain consisting of alternate blocks of stiff ($S$) and flexible ($F$) segments of size $m$ and $n$ respectively for different chain length $N$ in two dimension (2D). The free parameters in the model are the bending rigidity $\kappa_b$ which controls the three body interaction term, the elastic constant $k_F$ in the FENE (bond) potential between successive monomers, as well as the segmental lengths $m$ and $n$ and the repeat unit $p$ ($N=m_pn_p$) and the solvent viscosity $\gamma$. We demonstrate that due to the change in entropic barrier and the inhomogeneous viscous drag on the chain backbone a variety of scenarios are possible amply manifested in the waiting time distribution of the translocating chain. These information can be deconvoluted to extract the mechanical properties of the chain at various length scales and thus can be used to nanopore based methods to probe bio-molecules, such as DNA, RNA and proteins.