Natalia Ziebacz

Comparative analysis of viscosity of complex liquids and cytoplasm of mammalian cells at the nanoscale.

We present a scaling formula for size-dependent viscosity coefficients for proteins, polymers, and fluorescent dyes diffusing in complex liquids. The formula was used to analyze the mobilities of probes of different sizes in HeLa and Swiss 3T3 mammalian cells. This analysis unveils in the cytoplasm two length scales: (i) the correlation length ξ (approximately 5 nm in HeLa and 7 nm in Swiss 3T3 cells) and (ii) the limiting length scale that marks the crossover between nano- and macroscale viscosity (approximately 86 nm in HeLa and 30 nm in Swiss 3T3 cells). During motion, probes smaller than ξ experienced matrix viscosity: η(matrix) ≈ 2.0 mPa·s for HeLa and 0.88 mPa·s for Swiss 3T3 cells. Probes much larger than the limiting length scale experienced macroscopic viscosity, η(macro) ≈ 4.4 × 10(-2) and 2.4 × 10(-2) Pa·s for HeLa and Swiss 3T3 cells, respectively. Our results are persistent for the lengths scales from 0.14 nm to a few hundred nanometers.

Incorporation of carbon nanotubes into a lyotropic liquid crystal by phase separation in the presence of a hydrophilic polymer.

Single-walled carbon nanotubes (SWNTs) were incorporated into a lyotropic liquid crystal (LLC) matrix formed by n-dodecyl octaoxyethene monoether (C(12)E(6)) at room temperature through spontaneous phase separation induced by nonionic hydrophilic polymer poly(ethylene glycol) (PEG). The quality of SWNTs/LLC composite was evaluated by polarized microscopy observations and small-angle X-ray scattering (SAXS) measurements. The results obtained clearly indicated that SWNTs have been successfully incorporated into the LLC matrix up to a considerable high content without destroying the LLC matrix, although interesting changes of the LLC matrix were also induced by SWNTs incorporation. By varying the ratio of PEG to C(12)E(6), the type of LLC matrix can be controlled from hexagonal phase to lamellar phase. Temperature was found to have a significant influence on the quality of SWNTs/LLC composite, and tube aggregation can be induced at higher temperature. When SWNTs were changed to multiwalled carbon nanotubes (MWNTs), they became difficult to be incorporated into LLC matrix because of an increase in the average tube diameter.

Crossover regime for the diffusion of nanoparticles in polyethylene glycol solutions: influence of the depletion layer

The viscosity in soft matter systems is a scale dependent quantity. In polymer solutions the viscosity of nanoprobes of size R approaches the macroscopic viscosity when R exceeds the radius of gyration of the polymer, Rg. The nano to macroviscosity crossover occurs for R ∼ Rg. Here we analyze diffusion in a polymer (polyethylene glycol) solution of nanoparticles in the crossover regime. We report a scale dependent diffusion coefficient in this regime due to non-uniform viscosity in the depletion layer around particles. The phenomenological scaling of the slow diffusion coefficient as a function of probe size is compared to the same scaling for macroscopic viscosity as a function of polymer size.

Formation and structure of PEI/DNA complexes: quantitative analysis

Controlled formation of gene delivery complexes (DNA and a vector, usually a cationic polymer) is one of the key challenges in developing efficient gene delivery systems. The researchers focused their procedures on the ratio of vector to DNA, neglecting the influence of concentration on the complex formation process. In this study we show, by studying the association of polyethylenimine (PEI) and 66-base pair (bp) DNA fragments, that the concentration of the gene delivery system greatly influences the formation of PEI/DNA complexes even at a fixed PEI/DNA ratio. We find that the charge and the size of PEI/DNA complexes are increasing functions of their concentration even in a highly dilute regime of concentrations. The number of PEI/DNA molecules in a complex was calculated from the measured charge and electrophoretic mobility. We established a model, on the basis of Smoluchowski theory, to explain the relation between the concentration and the size of PEI/DNA complexes. We analyzed the structure of the complexes and found out that a large proportion of space in the PEI/DNA complexes is occupied by the solvent. This study indicates that the influence of concentration should be seriously considered in gene delivery studies, since large PEI/DNA complexes can be prepared by scaling up their concentration simultaneously without increasing the dosage of PEI.

The effect of depletion layer on diffusion of nanoparticles in solutions of flexible and polydisperse polymers

We introduce a model of diffusion of nanoparticles in solutions of flexible, polydisperse polymers. The model takes into account the effect of depletion layer with soft boundaries. The presence of depletion layer leads to nonlinear dependence of the mean square displacement (MSD) on time. Our model may be an alternative choice for the study of those experimental systems where the crossover between subdiffusion and normal diffusion is observed. Its advantage is mathematical simplicity: it allows easy identification of the crossover times and distances, which are here associated with the depletion layer thickness. The soft boundaries of the depletion layer, generated by the flexible and polydisperse polymers, are here approximated by two shells enclosed one in another, which may be interpreted as approximations of polymer density profiles around the probe. We show a very good agreement of the model with dynamic light scattering (DLS) measurements of diffusion of nanoparticles in solutions of polyethylene glycol (PEG).

Characterization of Caulobacter crescentus FtsZ Protein Using Dynamic Light Scattering

Background: Self-assembly of the tubulin-homologue FtsZ is critical in bacterial cell division. Results: Dynamic light scattering (DLS) measurements provide insight into the kinetics and stable length of Caulobacter crescentus FtsZ in vitro. Conclusion: C. crescentus FtsZ forms short linear polymers in solution with the assembly rate depending on the concentrations of GTP and GDP. Significance: DLS is a valuable technique for studying the polymerization of cytoskeletal proteins. The self-assembly of the tubulin homologue FtsZ at the mid-cell is a critical step in bacterial cell division. We introduce dynamic light scattering (DLS) spectroscopy as a new method to study the polymerization kinetics of FtsZ in solution. Analysis of the DLS data indicates that the FtsZ polymers are remarkably monodisperse in length, independent of the concentrations of GTP, GDP, and FtsZ monomers. Measurements of the diffusion coefficient of the polymers demonstrate that their length is remarkably stable until the free GTP is consumed. We estimated the mean size of the FtsZ polymers within this interval of stable length to be between 9 and 18 monomers. The rates of FtsZ polymerization and depolymerization are likely influenced by the concentration of GDP, as the repeated addition of GTP to FtsZ increased the rate of polymerization and slowed down depolymerization. Increasing the FtsZ concentration did not change the size of FtsZ polymers; however, it increased the rate of the depolymerization reaction by depleting free GTP. Using transmission electron microscopy we observed that FtsZ forms linear polymers in solutions which rapidly convert to large bundles upon contact with surfaces at time scales as short as several seconds. Finally, the best studied small molecule that binds to FtsZ, PC190723, had no stabilizing effect on Caulobacter crescentus FtsZ filaments in vitro, which complements previous studies with Escherichia coli FtsZ and confirms that this class of small molecules binds Gram-negative FtsZ weakly.

Influence of nano-viscosity and depletion interactions on cleavage of DNA by enzymes in glycerol and poly(ethylene glycol) solutions: qualitative analysis

Biochemical reactions in living systems take place in an environment crowded by various macromolecules and ligands. Therefore experimental data obtained in buffer do not reflect in vivo conditions. We have used glycerol, poly(ethylene glycol) (PEG) 6000 and PEG 8 M solutions to investigate the influence of the crowded environment on cleavage of plasmid DNA by restriction enzyme HindIII. PEG 6000 solution can effectively slow down the cleavage process. However, neither PEG 8 M solution of the same viscosity as PEG 6000 solution nor glycerol solution of the same concentration as PEG 6000 solution slows the cleavage of DNA appreciably. The viscosity experienced by the biomolecules (here called nano-viscosity) and aggregation induced by the depletion interactions between DNA molecules in polymer solution (PEG 6000) are two factors responsible for slow cleavage of DNA. We have ruled out the change of pH and denaturation of HindIII as possible sources for the effect.

Thousand‐Fold Acceleration of Phase Decomposition in Polymer/Liquid Crystal Blends

The phase separation pro-cess is slow, both in the sense of actual time (of minutes tohours) and—as it is controlled by diffusion—in the sense ofthe power law evolution of the mean size of the domains. Inaddition to the traditional adjustment of the natural parame-ters of the process (temperature, composition), conceptuallynew advances attempt to affect the phase separation with anexternal electric field (EF). The use of an EF brings into focusthe role of ionic constituents. Tsori et al.