Inferring the effective thickness of polyelectrolytes from stretching measurements at various ionic strengths: applications to DNA and RNA

TL;DR

This paper introduces a thick-chain model to analyze how the stretching response of DNA and RNA polymers depends on their effective thickness, influenced by ionic strength, with implications for understanding their electrostatic properties.

Contribution

The study develops an analytic expression from stochastic simulations to infer the effective diameter of polyelectrolytes from stretching data, linking molecular flexibility and ionic conditions.

Findings

Electrostatic contribution to DNA's effective radius is about five times the Debye length.

Poly-U RNA exhibits a smaller electrostatic contribution compared to DNA.

The model successfully fits experimental stretching data across various ionic strengths.

Abstract

By resorting to the thick-chain model we discuss how the stretching response of a polymer is influenced by the self-avoidance entailed by its finite thickness. The characterization of the force versus extension curve for a thick chain is carried out through extensive stochastic simulations. The computational results are captured by an analytic expression that is used to fit experimental stretching measurements carried out on DNA and single-stranded RNA (poly-U) in various solutions. This strategy allows us to infer the apparent diameter of two biologically-relevant polyelectrolytes, namely DNA and poly-U, for different ionic strengths. Due to the very different degree of flexibility of the two molecules, the results provide insight into how the apparent diameter is influenced by the interplay between the (solution-dependent) Debye screening length and the polymers' ``bare'' thickness. For DNA, the electrostatic contribution to the effective radius, $\Delta$, is found to be about 5 times larger than the Debye screening length, consistently with previous theoretical predictions for highly-charged stiff rods. For the more flexible poly-U chains the electrostatic contribution to $\Delta$ is found to be significantly smaller than the Debye screening length.