Reducing the variance in the translocation times by pre-stretching the polymer

TL;DR

This study uses simulations to show that pre-stretching polymers reduces variability in translocation times, which could improve nanopore sequencing accuracy by controlling initial conformations and thermal fluctuations.

Contribution

The paper introduces a method of pre-stretching polymers to independently control initial conformations and thermal noise, reducing translocation time variability in simulations.

Findings

Pre-stretching reduces conformational variability.

Reduced conformational spread leads to less translocation time variation.

Stretching DNA prior to translocation can enhance nanopore sequencing.

Abstract

Langevin Dynamics simulations of polymer translocation are performed where the polymer is stretched via two opposing forces applied on the first and last monomer before and during translocation. In this setup, polymer translocation is achieved by imposing a bias between the two pulling forces such that there is net displacement towards the \textit{trans}-side. Under the influence of pre-stretching forces, the elongated polymer ensemble contains less variations in conformations compared to an unstretched ensemble. Simulations demonstrate that this reduced spread in initial conformations yields a reduced variation in translocations times relative to the mean translocation time. This effect is explored for different ratios of the amplitude of thermal fluctuations to driving forces to control for the relative influence of the thermal path sampled by the polymer. Since the variance in translocation times is due to contributions coming from sampling both thermal noise and initial conformations, our simulations offer independent control over the two main sources of noise, and allow us to shed light on how they both contribute to translocation dynamics. Experimentally relevant conditions are highlighted and shown to correspond to a significant decrease in the spread of translocation times, thus indicating that stretching DNA prior to translocation could assist in nanopore-based sequencing and sizing applications.