Brownian diffusion and electrophoretic transport of double‐stranded DNA in agarose gels

The field free diffusion constant and the electric field dependence of the electrophoretic mobility and molecular orientation of DNA samples from 5 to 164 kilobase pairs in agarose gels from 0.5 to 2% have been measured by fluorescence recovery after photobleaching and birefringence. In conditions where the reptation predictions hold for the field free diffusion, they partially fail for the DNA size dependence of the low field limit of the electrophoretic mobility. The linear field dependencies of the electrophoretic mobility and orientation factor seem to favor the biased reptation model with fluctuations over the standard biased reptation model, which predicts a quadratic field dependence. The quantitative analysis of the molecular parameters shows, however, that most experiments have been carried out at values of the field where the difference between the two models may be less conclusive. The pore size dependence of the different quantities has been given a particular attention and the role of the distribution of pore sizes in the departures from the reptation predictions is discussed. © 1999 John Wiley & Sons, Inc. Biopoly 50: 45–59, 1999     

An evaluation of the outer membrane charge and softness of<Emphasis Type="Italic">Thiobacillus ferrooxidans</Emphasis> by the Ohshima's electrophoretic model of a “soft” particle

The surface charge of bacterial cells plays an important role in their interfacial physiology and adhesion to substrata mediated by the electrostatic double-layer interaction. The surface charge or potential of biological cells is generally calculated from the experimentally measurable electrophoretic velocity of these cells migrating in an external electric field, applying the well-known Smoluchowski equation which is valid for “hard” particles with a sharp interface. However, bacterial cells possessing a structured outer membrane of a finite thickness (dependent on the ionic strength and pH of the surrounding liquid medium) are expected to obey Ohshima's electrophoretic mobility equation derived recently for ‘soft” particles. The electrophoretic mobility ofThiobacillus ferrooxidans was measured here by the fully automated technique of electrophoretic light scattering, based on the proportionality between the mobility and the Doppler shift in the frequency of light scattered by electrophoresing cells. Agreement was obtained between the experimentally determined electrophoretic mobility expressed as a function of low ionic strength (60–6000 μmol/L) at different pH values and the best-fit theoretical predictions of the “soft” particle electrophoresis theory, which is better than in the case of applying the Smoluchowski formula. The best-fit surface-charge and softness parameters predict a rather rigid and low-charge outer membrane of the bacterium examined, as compared to the parameters obtained for other bacteria in media of high ionic strength.     

Electrophoretic mobility distributions of normal human T and B lymphocytes and of peripheral blood lymphoblasts in acute lymphocytic leukemia: effects of neuraminidase and of solvent ionic strength.

Human T and B lymphocytes were found to be distinguishable on the basis of electrophoretic mobility, with the T cells having the higher mobility, in agreement with previous reports. The effects of the enzyme neuraminidase on the electrophoretic mobilities of T and B lymphocytes were determined. T lymphocytes showed a greater decrease in electrophoretic mobility after neuraminidase treatment; the relative mobilities of T and B cells were reversed by neuraminidase treatment, and the electrophoretic distinguishability was enhanced. The electrophoretic mobility distributions of lymphoblasts from patients with acute lymphocytic leukemia were found to differ from those of normal cells in their response to neuraminidase treatment and to changes in solution ionic strength. These results imply that the surface structure of the leukemic cells differs from that of either T or B lymphocytes from normal donors.     

Translocation of hyaluronic acid in cell surface of cultured mammalian cells after X-irradiation and its recovery by added adenosine triphosphate

To investigate the mechanism of radiation-induced decrease in cell electrophoretic mobility and its recovery by added adenosine triphosphate, specific enzymes and buffer solutions of different ionic strength were utilized. Decrease in the mobility of irradiated cells was detected only with the buffer solution of ionic strengths higher than 0.100. In this range of ionic strengths, removal of hyaluronic acid from cell surface by hyaluronidase had no effect on the electrophoretic mobility of irradiated cells, while the enzyme treatment resulted in 27% mobility reduction in non-irradiated cells. The removal of sialic acid and chondroitin sulfate by their specific enzymes resulted in the similar decrease in mobility either in irradiated and non-irradiated cells. These results suggest that the X-ray induced translocation of hyaluronic acid from the peripheral zone of 0–7.5 Å into the deeper zone of about 10–17 Å, if we use the Debye-Hückel's thickness of ion atmosphere for an approximate estimate of effective depth of electrokinetic plane of shear. Hyaluronic acid reappeared to the peripheral zone by the subsequent incubation after small dose irradiation, or by the addition of 1 mM adenosine triphosphate with Ca²⁺.     

Electrophoretic mobility of lambda phage HIND III and HAE III DNA fragments in agarose gels: a detailed study

The electrophoretic mobility (μ) of DNA fragments from λ phage and ΦX 174, split by restriction enzyme to molecular lengths from 3 × 10² to 2.36 × 10⁴ base pairs, has been investigated in 0.6–4% agarose gels at various field strengths, ionic strengths, and temperatures. As already observed, μ is seen to be very sensitive to the field, increasing with field strength. The sensitivity increases with the molecular length of the DNA and decreases at high gel concentration. Our data are in qualitative agreement with recent theoretical predictions that concern the influence of the electric field on electrophoretic mobility. Mobility data have been extrapolated to zero field. This enables a comparison of our experimental results with theoretical predictions on the dependence of μ on the molecular weight of the DNA fragments. Our data fit, quite closely, a reptation model, where the tube path is described as a semiflexible entity with a persistence length equal to the pore diameter. The influence of the agarose concentration and the ionic strength of the buffer on the two parameters of the model—intrinsic electrophoretic mobility (μ₀) and the number of base pairs per element of the tube (g)—are well described by the model. The temperature dependence of the electrophoretic mobility, together with the influence of the agarose concentration on μ₀, indicate that the hydrodynamic drag is the leading frictional force on the DNA molecules in the gel.     

Steady-state gel electrophoresis of long polymer molecules: a theoretical study

The velocity of long polymer molecules in a gel and the liquid flow profile in the vicinity of a molecule's surface were studied theoretically by combining the Navier-Stokes equation with the Poisson-Boltzmann equation. The electrophoretic mobility has been calculated in dependence of the ionic strength of the electrolyte solution, its viscosity, the gels' volume friction coefficient, the surface charge and the radius of the polymer molecule. The results are presented in a non-dimensional form and depend on two dimensionless parameters only. The first parameter is the radius of the polymer molecule in units of the Debye length. The second is a parameter comprising the electrolyte's viscosity and the gel density. Thus, by similarity theory, the results apply to any given experimental arrangement. Received: 10 May 1999 / Revised version: 17 November 1999 / Accepted: 6 December 1999     

Differences in the mode of iodination of H2a variants in chromatin

Modification of H2a variants with radioactive iodine was used to study under different ionic conditions the accessibility of their tyrosine residues in chromatin, in monosomes and when free in solution. The modification of tyrosine 57 in the hydrophobic part of H2a was found responsible for the appearance of new fractions with a reduced electrophoretic mobility in the presence of Trition X 100, detected only by autoradiography (radioactive "ghosts"). At low ionic strength a very small number of molecules were iodinated in chromatin, the modification affecting only their hydrophobic region. At moderate ionic strength the tyrosine residues near the N-terminal region of the molecule were predominantly modified. In chromatin the accessibility of the tyrosine residues of H2a1 was much greater than that of H2a2, a difference not observed with free histones.     

Electrophoretic detection of reversible chlorpromazine · HCl binding at the human erythrocyte surface

The binding of chlorpromazine · HCl at the human erythrocyte surface has been detected through its effect on cellular electrophoretic mobility. Incubation of erythrocytes (approx. 5 · 10⁶/ml) in 23 μM chlorpromazine · HCl resulted in a reduction of negative electrophoretic mobility from the control value of $\text{?1.11 ± 0.01}$ (μm · s^?1)/(V · cm^?1) to $\text{?1.00 ± 0.02}$ (μm · s^?1)/(V · cm^?1) (pH 7.2, ionic strength 0.155). This mobility change was completely reversed when chlorpromazine · HCl was removed by centrifugal washing. Increasing the drug concentration to 70μM did not affect the mobility change, indicating saturation of the electrophoretically detectable drug binding sites over chlorpromazine · HCl concentration range studied here. The effect of the 23 μM chlorpromazine · HCl on electrophoretic mobility was also measured in isotonic media of reduced ionic strength. The drug-induced reduction in negative surface charge density was found to be independent of ionic strength over the range 0.155 (Debye length, 0.8 nm) to 0.00310 (Debye length, 5.7 nm).Fixation of erythrocytes with glutaraldehyde affected neither the normal electrophoretic mobility of discocytes nor the reduced electrophoretic mobility of chlorpromazine · HCl-induced stomatocytes. When these stomatocytes were first fixed with glutaraldehyde, then washed free of chlorpromazine · HCl, they retained the stomatocyte form while regaining a normal control electrophoretic mobility. Conversely, when discocytes fixed in that form were treated with chlorpromazine · HCl, they showed the same mobility change as did fixed or unfixed stomatocytes. The drug-induced mobility change is therefore independent of the shape change, but reflects a contribution to cellular surface charge density from the membrane-bound chlorpromazine · HCl molecules. From the charge reduction, it is estimated that about 10⁶ chlorpromazine · HCl molecules are bound at the electrokinetic cell surface and occupy approximately 0.4% of the total surface area.     

Size-dependent mobile surface charge model of cell electrophoresis

A model that accurately predicts the effects of cellular size and electric field strength on electrophoretic mobility has been developed. Previous models have predicted that electrophoretic mobility (EPM) is dependent only on cell surface charge, bath viscosity and ionic strength of the electrolyte. However, careful analysis of experimental data from the literature shows that these models do not accurately depict the relationship between chemically determined surface charge and observed mobility. We propose a new model that accounts for electrically driven redistribution of mobile surface charge islands, such as the recently proposed lipid raft structures. This model predicts electrophoretic mobility as a function of a new dimensionless quantity, A, that incorporates the cell radius, the electric field strength, and the average diameter of charged membrane complexes.     

Factors affecting resolution, band width, number of theoretical plates, and apparent diffusion coefficients in polyacrylamide gel electrophoresis

A systematic study of several variables affecting band width and resolution in polyacrylamide gel electrophoresis (PAGE) has been carried out. This makes it possible to determine resolution, number of theoretical plates, and an apparent diffusion coefficient in PAGE. Measurement of band position yields a linear relationship between logarithm of electrophoretic mobility and gel concentration when other variables are held constant. Similarly, measurement of band width yields a linear relationship between the logarithm of the dispersion coefficient (D′) and gel concentration. This makes it possible to extrapolate to 0 gel concentration and to obtain as estimate of a free dispersion coefficient (D′₀) which is usually one or two orders of magnitude greater than the free diffusion coefficient (D_20,w). D′ depends on protein concentration (which is a function of sample load and time), on ionic strength (I), and on duration of electrophoresis (dependent on field strength which in turn depends on ionic strength and current). Since these several variables introduce nonlinear and interrelated correction factors, extrapolation to “infinite ionic strength,” “zero concentration,” and “infinite time” becomes difficult although it is potentially feasible at both the experimental and the theoretical level, and thus it may be possible to determine diffusion coefficients in PAGE on microgram amounts of material without the need for preliminary purification. Alternatively, PAGE in a nonsieving, anticonvectant gel at high ionic strength and for long duration may be able to provide an estimate of D_20,w. The results also support the validity of previously developed approximations for the relationship between band width and gel concentration, and for the relationship between band dispersion and electrophoretic mobility.     

Influence of Pretreatment and Experimental Conditions on Electrophoretic Mobility and Hydrophobicity of Cryptosporidium parvum Oocysts

Surface properties of Cryptosporidium parvum oocysts were investigated by using electrophoretic mobility and hydrophobicity measurements. Oocysts purified from calf feces by several sucrose flotation steps and deionized water (DI) washes (DIS method) had an electrophoretic mobility (neutral surface charge) near 0.0 m² V⁻¹ s⁻¹ over a pH range of 2 to 10. The mean electrophoretic mobility of oocysts stored in DI containing a mixture of antibiotics had a lower standard deviation (ς = 0.36) than that of oocysts stored in DI without antibiotics (ς = 0.53); their electrophoretic mobility remained unchanged up to 121 days after collection. The electrophoretic mobility of oocysts purified on a cold Percoll-sucrose gradient after the feces was defatted with ethyl acetate (EAPS method) varied linearly with pH from 0.0 m² V⁻¹ s⁻¹ at pH 2.4 to −3.2 × 10⁻⁸ m² V⁻¹ s⁻¹ at pH 10 (ς = 0.52), thus displaying the negative surface charge at neutral pH observed by other researchers. The hydrophobicity of oocysts and two types of polystyrene beads was measured as a function of ionic strength by adhesion to polystyrene. Oocysts were purified by the DIS method. The ionic strength of the suspending solution was varied from 0 to 95 mmol liter⁻¹. Two-week-old oocysts exhibited strong adhesion (~85%) at ionic strengths of 0 to 10 mmol liter⁻¹ and moderate adhesion (~20%) at ionic strengths of 20 to 95 mmol liter⁻¹. Two-month-old oocysts exhibited high adhesion (~60 to 80%) at all ionic strengths. These results show that adhesion properties governed by the electrophoretic mobility of purified C. parvum oocysts can be altered by the method of purification and that hydrophobicity can change as oocysts age.     

Comparison of mammalian mitochondrial ribosomal ribonucleic acid from different species

Mitochondrial ribosomal RNA species from mouse L cells, rat liver, rat hepatoma, hamster BHK-21 cells and human KB cells were examined by electrophoresis on polyacrylamide-agarose gels and sedimentation in sucrose density gradients. The S(E) (electrophoretic mobility) and S values of mitochondrial rRNA of all species were highly dependent on temperature and ionic strength of the medium; the S(E) values increased and the S values decreased with an increase in temperature at a low ionic strength. At an ionic strength of 0.3 at 23-25 degrees C or an ionic strength of 0.01 at 3-4 degrees C the S and S(E) values were almost the same being about 16.2-18.0 and 12.3-13.6 for human and mouse mitochondrial rRNA. The molecular weights under these conditions were calculated to be 3.8x10(5)-4.3x10(5) and 5.9x10(5)-6.8x10(5), depending on the technique used. At 25 degrees C in buffers of low ionic strength mouse mitochondrial rRNA species had a lower electrophoretic mobility than those of human and hamster. Under these conditions the smaller mitochondrial rRNA species of hamster had a lower electrophoretic mobility than that of human but the larger component had an identical mobility. Mouse and rat mitochondrial rRNA species had identical electrophoretic mobilities. Complex differences between human and mouse mitochondrial rRNA species were observed on sedimentation in sucrose density gradients under various conditions of temperature and ionic strength. Mouse L-cell mitochondrial rRNA was eluted after cytoplasmic rRNA on a column of methylated albumin-kieselguhr.     

Calculation of the Electrophoretic Mobility of a Particle Bearing Bound Polyelectrolyte Using the Nonlinear Poisson-Boltzmann Equation

A numerical method for determining the electrophoretic mobility of a polyelectrolyte-coated particle is presented. The particle surface is modeled as having a permeable layer of polyelectrolyte molecules anchored to its surface. Fluid flow within the polyelectrolyte layer is subject to Stokes drag arising from the polyelectrolyte segments. The method allows arbitrary distribution of polymer segments and charge density normal to the surface to be used. The hydrodynamic plane of shear may also be varied. The potential profile is determined by a numerical solution to the nonlinearized Poisson-Boltzmann equation. The potential profile is then used in a numerical solution to the Navier-Stokes equation to give the required mobility. The use of the nonlinearized Poisson-Boltzmann equation extends the results to higher charge density/lower ionic strength conditions than previous treatments. The surface potentials and mobilities for three limiting charge distributions are compared for both the linear and nonlinear treatments to delimit the range of validity of the linear treatment. The utility of the numerical, nonlinear treatment is demonstrated by an improved fit to the electrophoretic mobility of human erythrocytes as a function of ionic strength in the range 10 to 150 mM.     

Ribosomal type RNA of rat liver mitochondria

A method for the isolation and purification of rat liver mitochondria in the presence of an extract of natural RNAase inhibitor is described. Mitochondria free from contamination and undegraded mitochondrial ribosomal type RNA are obtained. Sedimentation coefficient measurements and base composition analysis showed significant differences between homologous mitochondrial and cytoplasmic rRNA's. The mitochondrial low molecular weight rRNA showed a higher electrophoretic mobility through 2.4% polyacrylamide gel at different ionic strengths than the homologous cytoplasmic component.     

ELECTROPHORETIC STUDIES ON HUMAN RED BLOOD CELLS

1. The electrophoretic mobility of unhemolyzed human red cells has been determined as a function of ionic strength at approximately constant pH in isotonic mixtures of glucose solution and saline-phosphate buffer solution. 2. Above an ionic strength of about 0.02 the cells behave as particles with a smooth surface of large radius of curvature. Below an ionic strength of about 0.02, changes of the surface occur, probably involving a decrease of charge density and perhaps connected with injury of the surface. 3. The mobility as a function of pH at an ionic strength of 0.172 has been determined for human red cells, for the lipid extract of the cells, and for the stroma protein of the cells. The isoelectric points of cells, lipid, and protein have been found to be about 1.7, 2.6, and 4.7 respectively. 4. The pH-mobility data lead to the conclusion that a red cell surface is composed largely of lipid and dominated by strong acid groups, possibly the phosphoric acid groups of cephalin molecules.     

Interpretation of the mechanism of changes in electrophoretic motility after exposure to physical fields in a solid liquid mosaic model of the erythrocyte

A decrease of electrophoretic mobility of the blood red cell under the influence of the microwave and thermal field is determined by the mechanism based on two effects--change of the ionic conductivity and visco-elastic properties of the membrane.     

Probing the electrostatic shielding of DNA with capillary electrophoresis

The free solution mobility of a 20-bp double-stranded DNA oligomer has been measured in diethylmalonate (DM) and Tris-acetate buffers, with and without added NaCl or TrisCl. DM buffers have the advantage that the buffering ion is anionic, so the cation composition in the solution can be varied at will. The results indicate that the free solution mobility of DNA decreases linearly with the logarithm of ionic strength when the ionic strength is increased by increasing the buffer concentration. The mobility also decreases linearly with the logarithm of ionic strength when NaCl is added to NaDM buffer or TrisCl is added to TrisDM buffer. Nonlinear effects are observed if the counterion in the added salt differs from the counterion in the buffer. The dependence of the mobility on ionic strength cannot be predicted using the Henry, Debye-Hückel-Onsager, or Pitts equations for electrophoresis. However, the mobilities observed in all buffer and buffer/salt solutions can be predicted within approximately 20% by the Manning equation for electrophoresis, using no adjustable parameters. The results suggest that the electrostatic shielding of DNA is determined not only by the relative concentrations of the various ions in the solution, but also by their equivalent conductivities.     

Electrophoretic mobility of bimolecular lipid membranes

The floating membrane vesicle is fixed by the counter solution flow in different points along the radius of a cylinder electrophoretic chamber, which permits to measure the vesicle electrophoretic mobility (EM). Close state condition of the chamber is provided for by the capillary system successively connected with the chamber. Relationship between EM of bimolecular lipid membranes (BLM) and pH and ionic concentration of aqueous solution qualitatively coincides with similar relationship for liposomes. The EM value of BLM essentially decreases in solution containing polyene antibiotics nystatine and levorin when derivative of cholesterol having 3betaOH-groups is present in the membrane.     

Surface potential and surface charge density of the cerebral-cortex synaptic vesicle and stability of vesicle suspension

Using a microelectrophoresis instrument employing the Lazer-Zee system, the electrophoretic mobility of synaptic vesicles isolated from Guinea-pig brain cortex was measured under several conditions. The mobility was found to depend on both pH and ionic concentration of the solution. The surface of the synaptic vesicle was shown to be negatively charged under physiological conditions. The isoelectric point was observed at pH 4.0 in 0.01 M NaCl solution. Effects of divalent cations were examined and reversal of surface charge was observed in 0.1 M CaCl₂ solution. Interaction of vesicles was also considered on the basis of the DLVO theory of colloid stability by using calculated values of surface charge density and surface potential of the synaptic vesicle.