89 research outputs found
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
The Inclusion of Water Molecules in Residue Interaction Networks Identifies Additional Central Residues
International audienceThe relevance of water molecules for the recognition and the interaction of biomolecules is widely appreciated. In this paper we address the role that water molecules associated to protein complexes play for the functional relevance of residues by considering their residue interaction networks (RINs). These are commonly defined on the basis of the amino acid composition of the proteins themselves, disregarding the solvation state of the protein. We determine properties of the RINs of two protein complexes, colicin E2/Im2 and barnase/barstar, with and without associated water molecules, using a previously developed methodology and its associated application RINspector. We find that the inclusion of water molecules in RINs leads to an increase in the number of central residues which adds a novel mechanism to the relevance of water molecules for protein function
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