Correlation-induced DNA adsorption on like-charged membranes

The adsorption of DNA or other polyelectrolyte molecules on charged membranes is a recurrent motif in soft matter and bionanotechnological systems. Two typical situations encountered are the deposition of single DNA chains onto substrates for further analysis, e.g., by force microscopy, or the pulling of polyelectrolytes into membrane nanopores, as in sequencing applications. In this paper, we present a theoretical analysis of such scenarios based on the self-consistent field theory approach, which allows us to address the important effect of charge correlations. We calculate the grand potential of a stiff polyelectrolyte immersed in an electrolyte in contact with a negatively charged dielectric membrane. For the sake of conciseness, we neglect conformational polymer fluctuations and model the molecule as a rigid charged line. At strongly charged membranes, the adsorbed counterions enhance the screening ability of the interfacial region. In the presence of highly charged polymers such as double-stranded DNA molecules close to the membrane, this enhanced interfacial screening dominates the mean-field level DNA-membrane repulsion and results in the adsorption of the DNA molecule to the surface. This picture provides a simple explanation for the recently observed DNA binding onto similarly charged substrates [G. L.-Caballero et al., Soft Matter 10, 2805 (2014)] and points out charge correlations as a non-negligible ingredient of polymer-surface interactions

Structure and mechanical characterization of DNA i-motif nanowires by molecular dynamics simulation

We studied the structure and mechanical properties of DNA i-motif nanowires by means of molecular dynamics computer simulations. We built up to 230 nm long nanowires, based on a repeated TC5 sequence from crystallographic data, fully relaxed and equilibrated in water. The unusual stacked C*C+ stacked structure, formed by four ssDNA strands arranged in an intercalated tetramer, is here fully characterized both statically and dynamically. By applying stretching, compression and bending deformation with the steered molecular dynamics and umbrella sampling methods, we extract the apparent Young's and bending moduli of the nanowire, as wel as estimates for the tensile strength and persistence length. According to our results, the i-motif nanowire shares similarities with structural proteins, as far as its tensile stiffness, but is closer to nucleic acids and flexible proteins, as far as its bending rigidity is concerned. Furthermore, thanks to its very thin cross section, the apparent tensile toughness is close to that of a metal. Besides their yet to be clarified biological significance, i-motif nanowires may qualify as interesting candidates for nanotechnology templates, due to such outstanding mechanical properties.Comment: 25 pages, 1 table, 7 figures; preprint submitted to Biophysical Journa

Ionic current inversion in pressure-driven polymer translocation through nanopores

We predict streaming current inversion with multivalent counterions in hydrodynamically driven polymer translocation events from a correlation-corrected charge transport theory including charge fluctuations around mean-field electrostatics. In the presence of multivalent counterions, electrostatic many-body effects result in the reversal of the DNA charge. The attraction of anions to the charge-inverted DNA molecule reverses the sign of the ionic current through the pore. Our theory allows for a comprehensive understanding of the complex features of the resulting streaming currents. The underlying mechanism is an efficient way to detect DNA charge reversal in pressure-driven translocation experiments with multivalent cations.Comment: This version is accepted for publication in Physical Review Letter

Comment on "Nonlocal statistical field theory of dipolar particles in electrolyte solutions" by Y.A. Budkov

The article by Budkov introduces a nonlocal field-theoretic model of solvent-explicit electrostatics. Despite giving a detailed introduction to the early literature on the topic, the article misses out on a series of articles that we published several years ago. Consequently, the manuscript essentially rederives without mention several results that were derived by us for the first time

Histone mark recognition controls nucleosome translocation via a kinetic proofreading mechanism: Confronting theory and high-throughput experiments

International audienceChromatin remodelers are multi-domain enzymatic motor complexes that displace nucleosomes along DNA and hence 'remodel chromatin structure', i.e., they dynamically reorganize nucleosome positions in both gene activation and gene repression. Recently, experimental insights from structural biology methods and remodeling assays have substantially advanced the understanding of these key chromatin components. Here we confront the kinetic proofreading scenario of chromatin remodeling, which proposes a mechanical link between histone residue modifications and the ATP-dependent action of remodelers, with recent experiments. We show that recent high-throughput data on nucleosome libraries assayed with remodelers from the ISWI family are in accord with our earlier predictions of the kinetic proofreading scenario. We make suggestions for new experimentally verifiable predictions of the kinetic proofreading scenarios for remodelers from other families

Active noise-driven particles under space-dependent friction in one dimension

We study a Langevin equation describing the stochastic motion of a particle in one dimension with coordinate $x$, which is simultaneously exposed to a space-dependent friction coefficient $\gamma(x)$, a confining potential $U(x)$ and non-equilibrium (i.e., active) noise. Specifically, we consider frictions $\gamma(x)=\gamma_0 + \gamma_1 | x |^p$ and potentials $U(x) \propto | x |^n$ with exponents $p = 1,2$ and $n = 0, 1, 2$. We provide analytical and numerical results for the particle dynamics for short times and the stationary probability density functions (PDFs) for long times. The short-time behaviour displays diffusive and ballistic regimes while the stationary PDFs display unique characteristic features depending on the exponent values $(p, n)$. The PDFs interpolate between Laplacian, Gaussian and bimodal distributions, whereby a change between these different behaviours can be achieved by a tuning of the friction strengths ratio $\gamma_0/\gamma_1$. Our model is relevant for molecular motors moving on a one-dimensional track and can also be realized for confined self-propelled colloidal particles.Comment: 10 page, 9 figure