68 research outputs found
Helical Structure Determines Different Susceptibilities of dsDNA, dsRNA, and tsDNA to Counterion-Induced Condensation
AbstractRecent studies of counterion-induced condensation of nucleic acid helices into aggregates produced several puzzling observations. For instance, trivalent cobalt hexamine ions condensed double-stranded (ds) DNA oligomers but not their more highly charged dsRNA counterparts. Divalent alkaline earth metal ions condensed triple-stranded (ts) DNA oligomers but not dsDNA. Here we show that these counterintuitive experimental results can be rationalized within the electrostatic zipper model of interactions between molecules with helical charge motifs. We report statistical mechanical calculations that reveal dramatic and nontrivial interplay between the effects of helical structure and thermal fluctuations on electrostatic interaction between oligomeric nucleic acids. Combining predictions for oligomeric and much longer helices, we also interpret recent experimental studies of the role of counterion charge, structure, and chemistry. We argue that an electrostatic zipper attraction might be a major or even dominant force in nucleic acid condensation
Electrotunable friction with ionic liquid lubricants: how important is the molecular structure of the ions?
Using non-equilibrium molecular dynamics simulations and a coarse grained
model of ionic liquids, we have investigated the impact that the shape and the
intramolecular charge distribution of the ions have on the electrotuneable
friction with ionic-liquid nanoscale films. We show that the electric-field
induces significant structural changes in the film, leading to dramatic
modifications of the friction force. Comparison of the present work with
previous studies using different models of ionic liquids indicate that the
phenomenology presented here applies to a wide range of ionic liquids. In
particular, the electric-field-induced shift of the slippage plane from the
solid-liquid interface to the interior of the film and the non-monotonic
variation of the friction force are common features of ionic lubricants under
strong confinement. We also demonstrate that the molecular structure of the
ions plays an important role in determining the electrostriction and
electroswelling of the confined film, hence showing the importance of
ion-specific effects in electrotuneable friction
Theory of The Double Layer in Water-in-Salt Electrolytes
One challenge in developing the next generation of lithium-ion batteries is
the replacement of organic electrolytes, which are flammable and most often
contain toxic and thermally unstable lithium salts, with safer, environmentally
friendly alternatives. Recently developed Water-in-Salt Electrolytes (WiSEs)
were found to be a promising alternative, having also enhanced electrochemical
stability. In this work, we develop a simple modified Poisson-Fermi theory,
which demonstrates the fine interplay between electrosorption, solvation, and
ion correlations. The phenomenological parameters are extracted from molecular
simulations, also performed here. The theory reproduces the electrical double
layer structure of WiSEs with remarkable accuracy.Comment: 29 pages, 8 figure
Correlated Ion Transport and the Gel Phase in Room Temperature Ionic Liquids
Here we present a theory of ion aggregation and gelation of room temperature
ionic liquids (RTILs). Based on it, we investigate the effect of ion
aggregation on correlated ion transport - ionic conductivity and transference
numbers - obtaining closed-form expressions for these quantities.The theory
depends on the maximum number of associations a cation and anion can form, and
the strength of their association. To validate the presented theory, we perform
molecular dynamics simulations on several RTILs, and a range of temperatures
for one RTIL. The simulations indicate the formation of large clusters, even
percolating through the system under certain circumstances, thus forming a gel,
with the theory accurately describing the obtained cluster distributions in all
cases. We discuss the possibility of observing a gel phase in neat RTILs, which
has hitherto not been discussed in any detail.Comment: 44 pages, 11 figure
Which way up? Recognition of homologous DNA segments in parallel and antiparallel alignment
Homologous gene shuffling between DNA promotes genetic diversity and is an
important pathway for DNA repair. For this to occur, homologous genes need to
find and recognize each other. However, despite its central role in homologous
recombination, the mechanism of homology recognition is still an unsolved
puzzle. While specific proteins are known to play a role at later stages of
recombination, an initial coarse grained recognition step has been proposed.
This relies on the sequence dependence of the DNA structural parameters, such
as twist and rise, mediated by intermolecular interactions, in particular
electrostatic ones. In this proposed mechanism, sequences having the same base
pair text, or are homologous, have lower interaction energy than those
sequences with uncorrelated base pair texts; the difference termed the
recognition energy. Here, we probe how the recognition energy changes when one
DNA fragment slides past another, and consider, for the first time, homologous
sequences in antiparallel alignment. This dependence on sliding was termed the
recognition well. We find that there is recognition well for anti-parallel,
homologous DNA tracts, but only a very shallow one, so that their interaction
will differ little from the interaction between two nonhomologous tracts. This
fact may be utilized in single molecule experiments specially targeted to test
the theory. As well as this, we test previous theoretical approximations in
calculating the recognition well for parallel molecules against MC simulations,
and consider more rigorously the optimization of the orientations of the
fragments about their long axes. The more rigorous treatment affects the
recognition energy a little, when the molecules are considered rigid. However
when torsional flexibility of the DNA molecules is introduced, we find
excellent agreement between analytical approximation and simulation.Comment: Paper with supplemental material attached. 41 pages in all, 4 figures
in main text, 3 figures in supplmental. To be submitted to Journa
Theory of Ion Aggregation and Gelation in Super-Concentrated Electrolytes
In concentrated electrolytes with asymmetric or irregular ions, such as ionic
liquids and solvent-in-salt electrolytes, ion association is more complicated
than simple ion-pairing. Large branched aggregates can form at significant
concentrations at even moderate salt concentrations. When the extent of ion
association reaches a certain threshold, a percolating ionic gel networks can
form spontaneously. Gelation is a phenomenon that is well known in polymer
physics, but it is practically unstudied in concentrated electrolytes. However,
despite this fact, the ion-pairing description is often applied to these
systems for the sake of simplicity. In this work, drawing strongly from
established theories in polymer physics, we develop a simple thermodynamic
model of reversible ionic aggregation and gelation in concentrated electrolytes
accounting for the competition between ion solvation and ion association. Our
model predicts the populations of ionic clusters of different sizes as a
function of salt concentration, it captures the onset of ionic gelation and
also the post-gel partitioning of ions into the gel. We discuss the
applicability of our model, as well as the implications of its predictions on
thermodynamic, transport, and rheological properties
Double layer in ionic liquids: Overscreening vs. crowding
We develop a simple Landau-Ginzburg-type continuum theory of solvent-free
ionic liquids and use it to predict the structure of the electrical double
layer. The model captures overscreening from short-range correlations, dominant
at small voltages, and steric constraints of finite ion sizes, which prevail at
large voltages. Increasing the voltage gradually suppresses overscreening in
favor of the crowding of counterions in a condensed inner layer near the
electrode. The predicted ion profiles and capacitance-voltage relations are
consistent with recent computer simulations and experiments on room-temperature
ionic liquids, using a correlation length of order the ion size.Comment: 4 pages + supplementary informatio
Helical coherence of DNA in crystals and solution
The twist, rise, slide, shift, tilt and roll between adjoining base pairs in DNA depend on the identity of the bases. The resulting dependence of the double helix conformation on the nucleotide sequence is important for DNA recognition by proteins, packaging and maintenance of genetic material, and other interactions involving DNA. This dependence, however, is obscured by poorly understood variations in the stacking geometry of the same adjoining base pairs within different sequence contexts. In this article, we approach the problem of sequence-dependent DNA conformation by statistical analysis of X-ray and NMR structures of DNA oligomers. We evaluate the corresponding helical coherence length—a cumulative parameter quantifying sequence-dependent deviations from the ideal double helix geometry. We find, e.g. that the solution structure of synthetic oligomers is characterized by 100–200 Å coherence length, which is similar to ∼150 Å coherence length of natural, salmon-sperm DNA. Packing of oligomers in crystals dramatically alters their helical coherence. The coherence length increases to 800–1200 Å, consistent with its theoretically predicted role in interactions between DNA at close separations
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