Macromolecular crowding impacts on the diffusion and conformation of DNA hairpins

Olivia Stiehl, Kathrin Weidner-Hertrampf, and Matthias Weiss
Phys. Rev. E 91, 012703 – Published 12 January 2015

Abstract

Biochemical reactions in crowded fluids differ significantly from those in dilute solutions. Both, excluded-volume interactions with surrounding macromolecules (“crowders”) and an enhanced rebinding of reaction partners due to crowding-induced viscoelasticity and subdiffusion have been hypothesized to shift chemical equilibria towards the associated state. We have explored the impact of both cues in an experimentally tunable system by monitoring the steady-state fraction of open DNA hairpins in crowded fluids with varying viscoelastic characteristics but similar occupied volume fractions. As a result, we observed an increased fraction of closed DNA hairpins in viscoelastic crowded fluids. Our observations compare favorably to a simple statistical model that considers both facets of crowding, while preferential interactions between crowders and DNA hairpins appear to have little influence.

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  • Received 14 July 2014
  • Revised 27 October 2014

DOI:https://doi.org/10.1103/PhysRevE.91.012703

©2015 American Physical Society

Authors & Affiliations

Olivia Stiehl, Kathrin Weidner-Hertrampf, and Matthias Weiss*

  • Experimental Physics I, University of Bayreuth, Universitätsstrasse 30, D-95440 Bayreuth, Germany

  • *Author to whom correspondence should be addressed: matthias.weiss@uni-bayreuth.de

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Vol. 91, Iss. 1 — January 2015

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