DNA Barcodes using a Double Nanopore System

TL;DR

This paper investigates the challenges in accurately reading DNA barcodes using a double nanopore system, highlighting the impact of tension propagation on measurement errors and proposing an interpolation method to improve accuracy.

Contribution

It introduces a simulation-based analysis of DNA translocation dynamics, revealing the role of tension propagation and proposing an interpolation scheme for better barcode decoding.

Findings

Velocity variation causes measurement errors in DNA length estimation.

Tension propagation along DNA influences translocation dynamics.

Proposed interpolation scheme improves barcode decoding accuracy.

Abstract

The potential of a double nanopore system to determine DNA barcodes has been demonstrated experimentally. By carrying out Brownian dynamics simulation on a coarse-grained model DNA with protein tag (barcodes) at known locations along the chain backbone, we demonstrate that due to large variation of velocities of the chain segments between the tags, it is inevitable to under/overestimate the genetic lengths from the experimental current blockade and time of flight data. We demonstrate that it is the tension propagation along the chain's backbone that governs the motion of the entire chain and is the key element to explain the non uniformity and disparate velocities of the tags and DNA monomers under translocation that introduce errors in measurement of the length segments between protein tags. Using simulation data we further demonstrate that it is important to consider the dynamics of the entire chain and suggest methods to accurately decipher barcodes. We introduce and validate an interpolation scheme using simulation data for a broad distribution of tag separations and suggest how to implement the scheme experimentally.