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

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.

iopart, 14 pages, 13 figures, to appear in J. Phys.: Condens. Matter

References in corpus (9)

• Theory of High-Force DNA Stretching and Overstretching
• From polymers to proteins -- novel phases of short compact tubes
• The Electrostatic Persistence Length Calculated from Monte Carlo, Variational and Perturbation Methods
• Stretching an heteropolymer
• Elastic moduli renormalization in self interacting stretchable polyelectrolytes
• Elasticity of semiflexible polymers with and without self-interactions
• Inferring the diameter of a biopolymer from its stretching response
• Semi-Flexible Polymer in a Uniform Force Field in Two Dimensions
• Stretching DNA: Role of electrostatic interaction

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• Stretching Semiflexible Polymer Chains: Evidence for the Importance of Excluded Volume Effects from Monte Carlo Simulation
• Cooperativity-Dependent Folding of Single-Stranded DNA
• Stacking correlation length in single-stranded DNA