Mechanical Engineering Faculty Publications and Presentations
Document Type
Article
Publication Date
8-25-2025
Abstract
DNA flow-stretching is a widely employed, powerful technique for investigating the mechanisms of DNA-binding proteins involved in compacting and organizing chromosomal DNA. We combine single-molecule DNA flow-stretching experiments with Brownian dynamics simulations to study the effect of the crowding agent polyethylene glycol (PEG) in these experiments. PEG interacts with DNA by an excluded volume effect, resulting in compaction of single, free DNA molecules in PEG solutions. In addition, PEG increases the viscosity of the buffer solution. By stretching surface-tethered bacteriophage lambda DNA in a flow cell and tracking the positions of a quantum dot labeled at the free DNA end using total internal reflection fluorescence (TIRF) microscopy, we find that higher PEG concentrations result in increased end-to-end length of flow-stretched DNA and decreased fluctuations of the free DNA end. To better understand our experimental results, we perform Brownian dynamics simulations of a bead-spring chain model of flow-stretched DNA in a viscous buffer that models the excluded volume effect of PEG by an effective attractive interaction between DNA segments. We find quantitative agreement between our model and the experimental results for suitable PEG-DNA interaction parameters.
Recommended Citation
Zohra, Fatema Tuz, Huda Al-Zuhairi, Jefferson Reinoza, HyeongJun Kim, and Andreas Hanke. 2025. “Probing the Effect of PEG-DNA Interactions and Buffer Viscosity on Tethered DNA in Shear Flow.” PLOS ONE 20 (8): e0329961. https://doi.org/10.1371/journal.pone.0329961.
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
Publication Title
PLoS One
DOI
10.1371/journal.pone.0329961
Comments
Copyright: © 2025 Zohra et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.