Modulation of HU-DNA interactions by salt concentration and applied force.

HU is one of the most abundant proteins in bacterial chromosomes and participates in nucleoid compaction and gene regulation. We report experiments using DNA stretching that study the dependence of DNA condensation by HU on force, salt and HU concentration. Previous experiments at sub-physiological salt levels revealed that low concentrations of HU could compact DNA, whereas larger HU concentrations formed a DNA-stiffening complex. Here we report that this bimodal binding behavior depends sensitively on salt concentration. Only the compaction mode was observed for 150 mM and higher NaCl levels, i.e. for physiological salt concentrations. Similar results were obtained for the more physiological salt K-glutamate. Real-time studies of dissociation kinetics revealed that HU unbound slowly (minutes to hours under the conditions studied) but completely for salt concentrations at or above 100 mM NaCl; the lifetime of HU complexes was observed to increase with the HU concentration at which the complexes were formed, and to decrease with salt concentration. Higher salt levels of 300 mM NaCl completely eliminated observable HU binding to DNA. Finally, we observed that the dissociation kinetics depend on force applied to the DNA: increased applied force in the sub-piconewton range accelerates dissociation, suggesting a mechanism for DNA tension to regulate chromosome structure and gene expression

More on phase diagram of Laponite

The phase diagram of a charged colloidal system (Laponite) has been investigated by dynamic light scattering in a previously unexplored range of salt and clay concentrations. Specifically the clay weight and salt molar concentrations have been varied in the ranges Cw=0.004- 0.025, Cs=(1x 10^-3- 5x 10^-3) M respectively. As in the case of free salt water samples (Cs= 1x 10^-4 M) an aging dynamics towards two different arrested phases is found in the whole examined Cw and Cs range. Moreover a transition between these two different regimes is found for each investigated salt concentration. It is clear from these measurements that a revision of the phase diagram is necessary and a new "transition" line between two different arrested states is drawn.Comment: 16 pages, 5 figures, submitted to Langmui

Effect of ionic ordering in conductivity experiments of DNA aqueous solutions

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 than some critical one (0.4 M) the conductivity of DNA solution is higher than the conductivity of KCl water solution without DNA. Starting from the critical concentration the conductivity of KCl solution is higher than the conductivity of DNA solution with added salt. For description of the experimental data phenomenological model is elaborated basing on electrolyte theory. In framework of the developed model a mechanism of counterion ordering is introduced. According to this mechanism under the low salt concentrations electrical conductivity of the system is caused by counterions of DNA ion-hydrate shell. Increasing the amount of salt to the critical concentration counterions condense on DNA polyanion. Further increase of salt concentration leads to the formation of DNA-salt complexes that decreases the conductivity of the system.Comment: 12 pages, 6figures. Ukr. J. Phys. (2014

Relaxation Behavior by Time-Salt and Time-Temperature Superpositions of Polyelectrolyte Complexes from Coacervate to Precipitate

Complexation between anionic and cationic polyelectrolytes results in solid-like precipitates or liquid-like coacervate depending on the added salt in the aqueous medium. However, the boundary between these polymer-rich phases is quite broad and the associated changes in the polymer relaxation in the complexes across the transition regime are poorly understood. In this work, the relaxation dynamics of complexes across this transition is probed over a wide timescale by measuring viscoelastic spectra and zero-shear viscosities at varying temperatures and salt concentrations for two different salt types. We find that the complexes exhibit time-temperature superposition (TTS) at all salt concentrations, while the range of overlapped-frequencies for time-temperature-salt superposition (TTSS) strongly depends on the salt concentration (Cs) and gradually shifts to higher frequencies as Cs is decreased. The sticky-Rouse model describes the relaxation behavior at all Cs. However, collective relaxation of polyelectrolyte complexes gradually approaches a rubbery regime and eventually exhibits a gel-like response as Cs is decreased and limits the validity of TTSS.Comment: 12 pages, 5 figures, Follow Gels journal link for latest versio

DNA Binding in High Salt: Analysing the Salt Dependence of Replication Protein A3 from the Halophile Haloferax volcanii

Halophilic archaea maintain intracellular salt concentrations close to saturation to survive in high-salt environments and their cellular processes have adapted to function under these conditions. Little is known regarding halophilic adaptation of the DNA processing machinery, particularly intriguing since protein-DNA interactions are classically salt sensitive. To investigate such adaptation, we characterised the DNA-binding capabilities of recombinant RPA3 from Haloferax volcanii (HvRPA3). Under physiological salt conditions (3M KCl), HvRPA3 is monomeric, binding 18 nucleotide ssDNA with nanomolar affinity, demonstrating that RPAs containing the single OB-fold/zinc finger architecture bind with broadly comparable affinity to two OB-fold/zinc finger RPAs. Reducing the salt concentration to 1M KCl induces dimerisation of the protein, which retains its ability to bind DNA. On circular ssDNA, two concentration-dependent binding modes are observed. Conventionally, increased salt concentration adversely affects DNA binding but HvRPA3 does not bind DNA in 0.2M KCl, although multimerisation may occlude the binding site. The single N-terminal OB-fold is competent to bind DNA in the absence of the C-terminal zinc finger, albeit with reduced affinity. This study represents the first quantitative characterisation of DNA binding in a halophilic protein in extreme salt concentrations

Estimating the Application Rate of Liquid Chloride Products Based on Residual Salt Concentration on Pavement

This technical report summarizes the results of laboratory testing on asphalt and concrete pavement. A known quantity of salt brine was applied as an anti-icer, followed by snow application, traffic simulation, and mechanical snow removal via simulated plowing. Using a sample from this plowed snow, researchers measured the chloride concentration to determine the amount of salt brine (as chloride) that remained on the pavement surface. Under the investigated scenarios, the asphalt samples showed higher concentrations of chloride in the plowed-off snow, and therefore lower concentrations of chlorides remaining on the pavement surface. In comparison, the concrete samples had much lower chloride concentrations in the plowed-off snow, and much higher chloride concentrations remaining on the pavement surface. An interesting pattern revealed by the testing was the variation in the percentage of residual chloride on the pavement surface with changes in temperature. When pavement type was not considered, more residual chloride was present at warmer temperatures and less residual chloride was present at colder temperatures. This observation warrants additional testing to determine if the pattern is in fact a statistically valid trend. The findings from the study will help winter maintenance agencies reduce salt usage while meeting the defined Level of Service. In addition, findings will contribute to environmentally sustainable policies and reduce the level of salt usage (from snow- and ice-control products) introduced into the environment

Why is the condensed phase of DNA preferred at higher temperature? DNA compaction in the presence of a multivalent cation

Upon the addition of multivalent cations, a giant DNA chain exhibits a large discrete transition from an elongated coil into a folded compact state. We performed single-chain observation of long DNAs in the presence of a tetravalent cation (spermine), at various temperatures and monovalent salt concentrations. We confirmed that the compact state is preferred at higher temperatures and at lower monovalent salt concentrations. This result is interpreted in terms of an increase in the net translational entropy of small ions due to ionic exchange between higher and lower valence ions.Comment: 4pages,3figure