Vertex pinning and stretching of single molecule DNA in a linear polymer solution

TL;DR

This study demonstrates a method to trap, stretch, and image single DNA molecules in a linear polymer solution using electric fields, revealing dynamics of pinning and relaxation with potential for high-throughput analysis.

Contribution

It introduces a simple fluidic approach to achieve vertex pinning and stretching of DNA molecules, enabling detailed study of their dynamics in polymer solutions.

Findings

DNA pinning occurs above a threshold electric field.

Pinned DNA relaxes to a Brownian coil within seconds.

Method allows high-quality, high-throughput imaging of single DNA molecules.

Abstract

Trapping, linearization, and imaging of single molecule DNA is of broad interest to both biophysicists who study polymer physics and engineers who build nucleic acid analyzing methods such as optical mapping. In this study, single DNA molecules in a neutral linear polymer solution were driven with an axial electric field through microchannels and their dynamics were studied using fluorescence microscopy. We observed that above a threshold electric field, individual DNA molecules become pinned to the channel walls at a vertex on each molecule and are stretched in the direction opposite to the electric field. Upon removal of the electric field, pinned DNA molecules undergo relaxation within a few seconds to a Brownian coil around the vertex. After 10s of seconds, DNA is released and free to electromigrate. The method enables high quality imaging of single-molecule DNA with high throughput using simple-to-fabricate fluidic structures. We analyze the conditions needed for trapping, relaxation dynamics, and the repeatability of vertex pinning. We hypothesize DNA entangles with neutral linear polymers adsorbed to walls. We hypothesize that a sufficiently high electric force on the DNA is required to expel a hydration layer between the DNA and the wall-adsorbed neutral linear polymers. The elimination of the hydration layer may increase the friction between charged DNA and the uncharged polymer, promoting vertex pinning of DNA.