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On the origin of the unusual behavior in the stretching of single-stranded DNA.

Research paper by Ngo Minh NM Toan, D D Thirumalai

Indexed on: 12 Jul '12Published on: 12 Jul '12Published in: The Journal of chemical physics



Abstract

Force-extension curves (FECs), which quantify the response of a variety of biomolecules subject to mechanical force (f), are often quantitatively fit using worm-like chain (WLC) or freely jointed chain (FJC) models. These models predict that the chain extension, x, normalized by the contour length increases linearly at small f and at high forces scale as x ~ (1 - f(-α)), where α = 0.5 for WLC and unity for FJC. In contrast, experiments on single-stranded DNA (ssDNA) show that over a range of f and ionic concentration, x scales as x ~ ln f, which cannot be explained using WLC or FJC models. Using theory and simulations we show that this unusual behavior in FEC in ssDNA is due to sequence-independent polyelectrolyte effects. We show that the x ~ ln f arises because in the absence of force the tangent correlation function, quantifying chain persistence, decays algebraically on length scales on the order of the Debye length. Our theory, which is most appropriate for monovalent salts, quantitatively fits the experimental data and further predicts that such a regime is not discernible in double-stranded DNA.