How capture affects polymer translocation in a solitary nanopore

TL;DR

This study uses simulations to analyze how electric field gradients influence DNA capture and translocation through nanopores, revealing factors affecting translocation success, fold formation, and the impact of charged tags on sequencing efficiency.

Contribution

It provides new insights into the effects of electric field gradients and DNA stiffness on translocation, and demonstrates how charged tags improve sequencing-related translocation metrics.

Findings

Field gradient elongates DNA and promotes translocation.

Finite probability of hairpin-loop capture for flexible chains.

Charged tags increase translocation rate and directionality.

Abstract

DNA capture with high fidelity is an essential part of nanopore translocation. We report several important aspects of the capture process and subsequent translocation of a model DNA polymer through a solid-state nanopore in presence of an extended electric field using the Brownian dynamics simulation that enables us to record statistics of the conformations at every stage of the translocation process. By releasing the equilibrated DNAs from different equipotentials, we observe that the capture time distribution depends on the initial starting point and follows a Poisson process. The field gradient elongates the DNA on its way towards the nanopore and favors a successful translocation even after multiple failed threading attempts. Even in the limit of an extremely narrow pore, a fully flexible chain has a finite probability of hairpin-loop capture while this probability decreases for a stiffer chain and promotes single file translocation. Our in silico studies identify and differentiate characteristic distributions of the mean first passage time due to single file translocation from those due to translocation of different types of folds and provide direct evidences of the interpretation of the experimentally observed folds [M. Gershow et al., Nat. Nanotech. 2, 775 (2007) and M. Mihovilovic et al. Phys. Rev. Letts. 110, 028102 (2013)] in a solitary nanopore. Finally, we show a new finding, - that a charged tag attached at the $5^{\prime}$ end of the DNA enhances both the multi-scan rate as well as the uni-directional translocation ($5^{\prime} \rightarrow 3^{\prime}$) probability that would benefit the genomic barcoding and sequencing experiments.