Dielectric spectroscopy is used to investigate fundamental length scales of 146 bp short-fragment (nucleosomal) dilute Na-DNA solutions. Two relaxation modes are detected: the high- and the low-frequency mode. Dependence of the corresponding length scales on the DNA and on the (uni-valent) salt concentration is studied in detail, being different from the case of long, genomic DNA, investigated before. In low added salt regime, the length scale of the high-frequency mode scales as the average separation between DNAs, though it is smaller in absolute magnitude, whereas the length scale of the low-frequency mode is equal to the contour length of DNA. These fundamental length scales in low added salt regime do not depend on whether DNA is in a double stranded or single stranded form. On the other hand, with increasing added salt, the characteristic length scale of low-frequency mode diminishes at low DNA concentrations probably due to dynamical formation of denaturation bubbles and/or fraying in the vicinity of DNA denaturation threshold.
We report on a detailed characterization of complex dielectric response of Na-DNA aqueous solutions by means of low-frequency dielectric spectroscopy (40 Hz - 110 MHz). Results reveal two broad relaxation modes of strength 20<Δε_LF<100 and 5<Δε_HF<20, centered at 0.5 kHz<ν_LF<70 kHz and 0.1 MHz<ν_HF<15 MHz. The characteristic length scale of the LF process, 50<L_LF<750nm, scales with DNA concentration as c_DNA^{-0.29\pm0.04} and is independent of the ionic strength in the low added salt regime. Conversely, the measured length scale of the LF process does not vary with DNA concentration but dep…
The nonlinear flow behaviour of a viscoelastic gel formed due to entangled, cylindrical micelles in aqueous solutions of the surfactant CTAT has been studied. On subjecting the system to a step shear rate lying above a certain value, the shear and normal stresses show interesting time dependent behaviour. The analysis of the measured time series shows the existence of a finite correlation dimension and a positive Lyapunov exponent, unambiguously implying that the dynamics can be described by that of a dynamical system with a strange attractor whose dimension increases with the increase in shea…
The low-frequency limit of the electrical conductivity (d.c. conductivity) of differently flexible polyions in aqueous solutions has been measured over an extended polyion concentration range, covering both the dilute and semidilute (entangled and unentangled) regime, up to the concentrated regime. The data have been analyzed taking into account the different flexibility of the polymer chains according to the scaling theory of polyion solutions, in the case of flexible polyions, and according to the Manning model, in the case of rigid polyions. In both cases, the fraction f of free counterions…
Cation accumulation drives the preferential partitioning of DNA in an aqueous two-phase system
The University of Tokyo（东京大学）；Leibniz-Institut für Polymerforschung Dresden e.V.（德累斯顿莱布尼茨聚合物研究所）；Technische Universität Dresden（德累斯顿工业大学）；Keio University（庆应义塾大学）
The effect of magnesium ion Mg2+ on the dielectric relaxation of semidilute DNA aqueous solutions has been studied by means of dielectric spectroscopy in the 100 Hz-100 MHz frequency range. De Gennes-Pfeuty-Dobrynin semidilute solution correlation length is the pertinent fundamental length scale for sufficiently low concentration of added salt, describing the collective properties of Mg-DNA solutions. No relaxation fingerprint of the DNA denaturation bubbles, leading to exposed hydrophobic core scaling, was detected at low DNA concentrations, thus indicating an increased stability of the doubl…
The viscosity of dilute and semidilute unentangled DNA solutions, in steady simple shear flow, has been measured across a range of temperatures and concentrations. For polystyrene solutions, measurements of viscosity have been carried out in the semidilute unentangled regime, while results of prior experimental measurements in the dilute regime have been used for the purpose of data analysis, and for comparison with the behaviour of DNA solutions. Interpretation of the shear rate dependence of viscosity in terms of suitably defined non-dimensional variables, is shown to lead to master plots, i…
The dynamic behavior of semi-dilute polymer solutions is governed by an interplay between solvent quality, concentration, molecular weight, and flow type. Semi-dilute solutions are characterized by large fluctuations in concentration, wherein polymer coils interpenetrate but may not be topologically entangled at equilibrium. In non-equilibrium flows, it is generally thought that polymer chains can self-entangle in semi-dilute solutions, thereby leading to entanglements in solutions that are nominally unentangled at equilibrium. Despite recent progress, we still lack a complete molecular-level …
Computer simulation studies of aqueous solutions of argon are performed from ambient to supercritical conditions by using a recent polarizable potential model (BSV) and the non polarizable simple point charge extended (SPC/E) model. At T=673 K we compare the water-solute pair correlation functions of the argon-water mixture with recent experimental results obtained from neutron scattering experiments. The comparison shows that the introduction of the polarizable effects decreases the solute-water repulsion and improves the agreement with the experiment at supercritical conditions. In particula…
The swelling of the viscosity radius, $α_η$, and the universal viscosity ratio, $U_{ηR}$, have been determined experimentally for linear DNA molecules in dilute solutions with excess salt, and numerically by Brownian dynamics simulations, as a function of the solvent quality. In the latter instance, asymptotic parameter free predictions have been obtained by extrapolating simulation data for finite chains to the long chain limit. Experiments and simulations show a universal crossover for $α_η$ and $U_{ηR}$ from $θ$ to good solvents in line with earlier observations on synthetic polymer-solvent…
The effects of ionic ordering in DNA water solutions are studied by conductivity experiments. The conductivity measurements are performed for the solutions of DNA with KCl salt in the temperature range from 28 to 70 C. Salt concentration vary from 0 to 2 M. The conductivity of solutions without DNA but with the same concentration of KCl salt are also performed. The results show that in case of salt free solution of DNA the melting process of the double helix is observed, while in case of DNA solution with added salt the macromolecule denaturation is not featured. For salt concentrations lower …
We study the rheology of semi-dilute solutions of the sodium salt of calf-thymus DNA in the linear and nonlinear regimes. The frequency response data can be fitted very well to the hybrid model with two dominant relaxation times $τ_{\circ}$ and $τ_{1}$. The ratio $\frac{τ_{\circ}}{τ_{1}} \sim$ 5 is seen to be fairly constant on changing the temperature from 20$^{\circ}$C to 30$^{\circ}$C. The shear rate dependence of viscosity can be fitted to the Carreau model.
A series of amphiphilic LC block copolymers, in which the hydrophobic block is a smectic polymer poly(4-methoxyphenyl 4-(6-acryloyloxy-hexyloxy)-benzoate) (PA6ester1) and the hydrophilic block is polyethyleneglycol (PEG), were synthesized and characterized. The self-assembly of one of them in both the pure state and the dilute aqueous solution was investigated in detail. Nano-structures in the pure state were studied by SAXS and WAXS on samples aligned by a magnetic field. A hexagonal cylindrical micro-segregation phase was observed with a lattice distance of 11.2 nm. The PEG blocks are in the…
We quantified the Manning free (uncondensed) counterions fraction $θ$ for dilute solutions of rod-like polyions - 150bp DNA fragments, in very low salt $<0.05$mM. Conductivity measurements of aqueous DNA solutions in the concentration range $0.015\leq c \leq 8$~mM (bp) were complemented by fluorescence correlation spectroscopy (FCS) measurements of the DNA polyion diffusion coefficient $D_p(c)$. We observed a crossover in the normalized conductivity $σ(c)/c$ which nearly halved across $c=0.05-1$ mM range, while $D_p(c)$ remained rather constant, as we established by FCS. Analyzing these data w…
We propose an efficient numerical algorithm for solving integral equations of the theory of liquids in the Reference Interaction Site Model (RISM) approximation for infinitely dilute solution of macromolecules with a large number of atoms. The algorithm is based on applying the nonstationary iterative methods for solving systems of linear algebraic equations. We calculate the solvent-solute atom-atom correlation functions for a fragment of the B-DNA duplex d(GGGGG).d(CCCCC) in infinitely dilute aqueous solution. The obtained results are compared with available experimental data and results fro…
According to classical electrolyte theories interactions in dilute (low ion density) electrolytes decay exponentially with distance, with the Debye screening length the characteristic length-scale. This decay length decreases monotonically with increasing ion concentration, due to effective screening of charges over short distances. Thus within the Debye model no long-range forces are expected in concentrated electrolytes. Here we reveal, using experimental detection of the interaction between two planar charged surfaces across a wide range of electrolytes, that beyond the dilute (Debye-Huucke…
When multivalent salts are added to dilute DNA solution, the DNA chains condense into bundles of a well-defined size. We explore two physical problems motivated by this phenomenon: the origin of the attractive interactions between the highly-negatively charged DNA chains that cause them to concentrate into bundles, and the mechanism that provents the bundles from growing indefinitely large.
We study aqueous xanthan solutions at shear rates up to about 105 s-1. At these shear rates, the salt-free solutions show a second Newtonian branch. Depending on the xanthan concentration, we find two different regimes with scaling laws well-known for the zero viscosity of dilute and semidilute particle solutions: The crossover concentration is considerably higher than in the first Newtonian branch, which can be related to the orientation of the polyelectrolytes. In the second regime, the normal stress differences increase with an exponent of about 1, indicating that the polymer solution behav…
Dielectric spectroscopy is used to investigate fundamental length scales describing the structure of hyaluronic acid sodium salt (Na-HA) semidilute aqueous solutions. In salt-free regime, the length scale of the relaxation mode detected in MHz range scales with HA concentration as $c_\mathrm{HA}^{-0.5}$ and corresponds to the de Gennes-Pfeuty-Dobrynin correlation length of polyelectrolytes in semidilute solution. The same scaling was observed for the case of long, genomic DNA. Conversely, the length scale of the mode detected in kHz range also varies with HA concentration as $c_\mathrm{HA}^{-0…
The dynamics of flexible polymers in dilute solution is usually described in terms of the pure Rouse or Zimm bead-spring models assuming continuous distribution of the internal relaxation modes. We show that this approach may lead to misleading interpretation of experimental data. The more correct description should come from the joint Rouse-Zimm (RZ) theory that contains the Rouse and Zimm models as limiting cases. The internal modes are discrete with respect to the mode number, and the type of the bead motion changes in the time from the Rouse to Zimm behavior. We demonstrate this interpreti…
We have simulated structure and dynamics of water in the grooves of a DNA duplex using moleculear dynamics simulations. We find signatures of a dynamical transition in both translational and orientational dynamics of water molecules in both the major and the minor grooves of a DNA duplex. The transition occurs at a slightly higher temperature ($T_{GL} \approx $ 255 K) than the temperature ($T_L\approx$ 247 K) where the bulk water is conjectured to undergo a dynamical transition. Groove water, however, exhibits markedly different temperature dependence of its properties from the bulk. Entropy c…
We use optical and fluorescence microscopy, densitometry, cryo-transmission electron microscopy (cryo-TEM), spectroscopy, and synchrotron X-ray scattering, to study the phase behavior of the reversible self-assembled chromonic aggregates of an anionic dye Sunset Yellow (SSY) in aqueous solutions crowded with an electrically neutral polymer polyethylene glycol (PEG) and doped with the salt NaCl. PEG causes the isotropic SSY solutions to condense into a liquid-crystalline region with a high concentration of SSY aggregates, coexisting with a PEG-rich isotropic (I) region. PEG added to the homogen…
The DNA duplex may be locally strongly bent in complexes with proteins, for example, with polymerases or in a nucleosome. At such bends, the DNA helix is locally in the non-canonical forms A (with a narrow major groove and a large amount of north sugars) or C (with a narrow minor groove and a large share of BII phosphates). To model the formation of such complexes by molecular dynamics methods, the force field is required to reproduce these conformational transitions for a naked DNA. We analyzed the available experimental data on the B-C and B-A transitions under the conditions easily implemen…
