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arXiv · 2411.01097

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

Kunlin Ma·Caleb J. Samuel·Soumyadeep Paul·Fereshteh L. Memarian·Gabrielle Vukasin·Armin Darvish·Juan G. Santiago
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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.

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Kunlin Ma, Caleb J. Samuel, Soumyadeep Paul, Fereshteh L. Memarian, Gabrielle Vukasin, Armin Darvish, Juan G. Santiago. 2024-11-02. Vertex pinning and stretching of single molecule DNA in a linear polymer solution. https://arxiv.org/abs/2411.01097

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