Simultaneous measurements of the electrophoretic mobility,diffusion coefficient and orientation of dsDNA during electrophoresis in polymer solutions

We determined simultaneously the electrophoretic mobility, diffusion coefficient D and molecular orientation during electrophoresis of dsDNAs in polymer solutions ranging from the dilute to the semidilute regime. We established, for the first time, master scaling laws for the diffusion coefficient showing a universal behavior. A model found in the literature designed for the dilute regime allows, surprisingly, to describe the mobility data over the whole range of concentrations studied and at the same time the biased reptation with fluctuations (BRF) failed for the semidilute regime, even when constraint release of the network was taken into account. These quantitative determinations of D are of practical interest to evaluate band broadening during capillary electrophoresis and provide data for stimulating investigation of the physics of DNA electrophoretic motion.     

Capillary gel electrophoresis of oligonucleotides using polymer solutions

Summary Capillary gel electrophoresis (CGE) has been recognized as an effective method for the analysis of oligonucleotides. CGE using polymer solutions is especially useful and effective compared with that using crosslinked gels, because of easy change of media. Replacement of media leads to the reproducible separation of analytes. We have investigated CGE analysis of oligonucleotides of less than 20 bases employing various kinds of polymers. Polyacrylamide, dextrin, dextran, pullakin, and poly(ethylene glycol) were used as sieving matrixes at concentrations of 0–30 %. Polydeoxythymidylic acids [p(dT)_11–20] were used as a test sample. These small oligonucleotides were successfully resolved on the basis of their base number by CGE using some of these polymer solutions. In particular, dextran was found to be effective and baseline separation was observed when a 30 % dextran solution was employed. Some validations such as linearity and reproducibility were also established and this method was found to be an adequate quality control method for small oligonucleotides. Finally, CGE using a 30 % dextran solution was successfully applied to impurity profiling of some synthetic oligonucleotides.     

Capillary electrophoresis of DNA in entangled polymer solutions.

Electrophoretic separations of DNA restriction fragments were performed in solutions of hydroxyethylcellulose (HEC) using capillary electrophoresis. Rheological studies confirmed that the entanglement threshold (phi*) for the solution is ca. 0.003 g/ml, in good agreement with theoretical predictions. A mesh size an order of magnitude smaller than that found in agarose gels was calculated using polymer-entanglement theory and was confirmed by electrophoretic measurements. Electrophoretic migration was shown to follow the Ogston regime under most conditions. An approach for obtaining smaller mesh sizes is presented.     

Capillary electrophoresis of RNA in dilute and semidilute polymer solutions

We report separations of RNA molecules (281-6583 nucleotides) by capillary electrophoresis in dilute and semidilute solutions of aqueous hydroxyethylcellulose (HEC) ether in varying buffers. RNA mobility and peak band widths are examined under both nondenaturing and also denaturing conditions. From studies of sieving polymer concentration and chain length, it is found that good separations can be obtained in semidilute solutions as well as in dilute solutions. The dependence of RNA mobility on its chain length is consistent with separation by a similar to transient entanglement mechanism in dilute solutions. In semidilute entangled solutions the separation proceeds by segmental motion.     

Electrophoretic mobility of linear and star-branched DNA in semidilute polymer solutions

Electrophoresis of large linear T2 (162 kbp) and 3-arm star-branched (N(Arm) = 48.5 kbp) DNA in linear polyacrylamide (LPA) solutions above the overlap concentration c* has been investigated using a fluorescence visualization technique that allows both the conformation and mobility mu of the DNA to be determined. LPA solutions of moderate polydispersity index (PI approximately 1.7-2.1) and variable polymer molecular weight Mw (0.59-2.05 MDa) are used as the sieving media. In unentangled semidilute solutions (c* < c < c(e)), we find that the conformational dynamics of linear and star-branched DNA in electric fields are strikingly different; the former migrating in predominantly U- or I-shaped conformations, depending on electric field strength E, and the latter migrating in a squid-like profile with the star-arms outstretched in the direction opposite to E and dragging the branch point through the sieving medium. Despite these visual differences, mu for linear and star-branched DNA of comparable size are found to be nearly identical in semidilute, unentangled LPA solutions. For LPA concentrations above the entanglement threshold (c > c(e)), the conformation of migrating linear and star-shaped DNA manifest only subtle changes from their unentangled solution features, but mu for the stars decreases strongly with increasing LPA concentration and molecular weight, while mu for linear DNA becomes nearly independent of c and Mw. These findings are discussed in the context of current theories for electrophoresis of large polyelectrolytes.     

Thermal diffusion of dilute polymer solutions: the role of solvent viscosity

We have performed measurements of the thermal diffusion coefficient D(T) in the dilute limit on polystyrene in cyclo-octane, cyclohexane, benzene, toluene, tetrahydrofuran, ethyl acetate, and methyl ethyl ketone and of poly(dimethyl-siloxane) in toluene. These data have been combined with literature data to test various theoretical predictions. The viscosity is identified as the dominating and only relevant solvent parameter. On the polymer side, the size or mass of an effective correlated segment determines the strength of the Soret effect. Large and heavy effective segments, as found in stiffer chains, lead to higher D(T).     

Capillary zone electrophoresis for the determination of average hydrodynamic velocity and diffusion coefficient

The determination of the average hydrodynamic velocity and diffusion coefficient by capillary zone electrophoresis is described. The present simple method only requires basic experimental data, such as peak area, peak height and migration time to complete the task of determining the diffusion coefficient and the average hydrodynamic velocity.     

Capillary zone electrophoresis for the determination of average hydrodynamic velocity and diffusion coefficient

The determination of the average hydrodynamic velocity and diffusion coefficient by capillary zone electrophoresis is described. The present simple method only requires basic experimental data, such as peak area, peak height and migration time to complete the task of determining the diffusion coefficient and the average hydrodynamic velocity. Received: 29 September 1998 / Revised: 14 May 1999 / Accepted: 19 May 1999     

Lanthanide transport in stabilized zirconias: interrelation between ionic radius and diffusion coefficient

The diffusion of all stable lanthanides was measured both in calcia stabilized zirconia (CSZ) and in yttria stabilized zirconia (YSZ) in the temperature range between 1,286 and 1,600 degrees C. The lanthanide diffusion coefficients obtained increase with increasing ionic radius. The experimental activation enthalpy of diffusion is near 6 eV for CSZ and between 4 and 5 eV for YSZ and is not strongly affected by the type of lanthanide. The results were correlated with defect energy calculations of the lanthanide diffusion enthalpy using the Mott-Littleton approach. An association enthalpy of cation vacancies with oxygen vacancies of about 1 eV (96 kJ/mol) was deduced in the case of CSZ, while there is no association in the case of YSZ. Furthermore, the change in diffusion coefficients can be correlated to the interaction parameter for the interaction between the lanthanide oxide with zirconia: The higher the interaction parameter, the higher the lanthanide diffusion coefficient.     

Solvent extraction of ionic solutes in aqueous solutions

Extraction of ionic solutes in aqueous solutions into various organic solvents is reviewed by showing several examples. The extraction of strong acids into polar organic solvents and nonpolar solvents containing hydrogen-bonding extractants is described as the first example and the extraction of simple metal salts into strongly dielectric or solvating polarsolvents and nonpolar solvents containing solvating extractants is then reported. Finally, the solvent extraction of anionic metal complexes with bulky cations into nonpolar solvents as ion-paris is described and the statistical method for such extraction equilibria is considered.     

离子液体的黏度与其扩散系数和电导率的新型关系方程

离子液体的传递性质对其在化学化工等领域的研究和应用至关重要,但迄今文献中缺乏可靠的理论预测模型或传递性质间的相互关系式,因此,有必要建立传递性质间的相互关系以便应用.本文建立了离子液体黏度与扩散系数或电导率间的定量关系,并利用文献实验数据进行了系统检验.结果表明,新方程可由离子液体黏度数据准确预测其扩散系数和电导率.与Stokes-Einstein方程相比,新方程不仅可解释离子液体中的许多实验现象,而且实现了定量预测(无需离子的有效流体力学半径数据).     

Influence of electric field intensity, ionic strength, and migration distance on the mobility and diffusion in DNA surface electrophoresis

In order to increase the separation rate of surface electrophoresis while preserving the resolution for large DNA chains, e.g., genomic DNA, the mobility and diffusion of Lambda DNA chains adsorbed on flat silicon substrate under an applied electric field, as a function of migration distance, ionic strength, and field intensity, were studied using laser fluorescence microscope. The mobility was found to follow a power law with the field intensity beyond a certain threshold. The detected DNA peak width was shown to be constant with migration distance, slightly smaller with stronger field intensity, but significantly decreased with higher ionic strength. The molecular dynamics simulation demonstrated that the peak width was strongly related with the conformation of DNA chains adsorbed onto surface. The results also implied that there was no diffusion of DNA during migration on surface. Therefore, the Nernst-Einstein relation is not valid in the surface electrophoresis and the separation rate could be improved without losing resolution by decreasing separation distance, increasing buffer concentration, and field intensity. The results indicate the fast separation of genomic DNA chains by surface electrophoresis is possible.     

Capillary zone electrophoresis of proteins in semidilute polymer solutions: inter- and intra-polymer predictability of size-dependent retardation.

The retardation of three "spherical" proteins with Stokes' radii of 2.0, 2.4, and 3.0 nm (35-104 kDa) was studied in capillary zone electrophoresis (CZE), using semidilute solutions of polyethylene glycol (PEG), linear polyacrylamide (PA), and polyvinyl alcohol (PVA). The purpose was to test the models predicting that the ratio of particle radius, R, to the mesh size of polymer network (the correlation or screening length of a semidilute polymer solution), xi, directly governs the size-dependent retardation in the form: mu/muo = exp (-R/xi). Here xi = kc-0.75, where c is polymer concentration and the numerical factor kcan be calculated based on polymer molecular weight. In application to polymers in a "good solvent" (PA and PEG in the aqueous buffer) and to proteins of 2.4 and 3.0 nm radius, that relation between relative mobility and R/xi was found to be obeyed for PA, while for PEG the value of k derived from retardation experiments significantly exceeded that which was theoretically calculated. Thus, the retardation appears to be polymer-specific, rather than universal, even for polymers in a "good solvent". It is suggested that, in that case, retardation of proteins of R > 2 nm be quantitatively described in the form mu/muo = exp[-p(R/xi], where p is a parameter depending on monomer type and/or polymer polydispersity. For PVA, the logarithm of mu/muo was found to be linearly related to c (in line with the prediction that the aqueous buffer is a "poor solvent" for this polymer) and to be near-independent of R.     

Capillary electrophoresis monitoring of halide impurities in ionic liquids

Quantification of impurities in ionic liquids is a crucial task in assessing the reliability of physical constants and solvent properties: taking into account the particularities of the ionic matrix, a simple routine method using capillary electrophoresis (CE) is developed to determine the halide content at the ppm level in water-immiscible ionic liquids.     

Capillary electrophoresis in sieving matrices: selectivity per base, mobility slope, and inflection slope

We compare the migration behavior of DNA sequencing fragments in hydroxyethyl cellulose (HEC) to the theoretical model of migration in the reptation mode. Good agreement was found for the mobility curve. We derived empirical equations for the relationship between selectivity per base and sieving matrix concentration and between the mobility slope and matrix concentration. We propose the inflection slope, i.e., the slope of the log-log mobility curve at its inflection point, as the quantitative parameter of sieving performance.     

Capillary zone electrophoresis of linear and branched oligosaccharides

The electrophoretic behavior of derivatized linear and branched oligosaccharides from various sources was examined in capillary zone electrophoresis with polyether-coated fused-silica capillaries. Two UV-absorbing (also fluorescent) derivatizing agents (2-amino-pyridine and 6-aminoquinoline) were utilized for the electrophoresis and sensitive dtection of neutral oligosaccharides, e.g., N-acetylchitooligosaccharides, high-mannose glycans and xyloglucan oligosaccharides. The oligosaccharides labelled with 6-aminoquinoline yielded eight times higher signal than those tagged with 2-aminopyridine. Plots of logarithmic electrophoretic mobilities of labelled N-acetylchitooligosaccharides with 6-aminoquinoline or 2-aminopyridine versus the number of sugar residues in the homologous series yielded straight lines in the size range studied, the slopes of which were independent of the tagging functions. The slopes of these lines are referred to as the N-acetylglucosaminyl group mobility decrement. The oligosaccharides were better resolved in the presence of tetrabutylammonium bromide in the running electrolyte. Furthermore, the electrophoretic mobilities of branched oligosaccharides were indexed with respect to linear homooligosaccharides, an approach that may prove valuable in correlating and predicting the mobilities of complex oligosaccharides.     

Capillary zone electrophoresis of sub-microm-sized particles in electrolyte solutions of various ionic strengths: size-dependent electrophoretic migration and separation efficiency

To gain insight into the mechanisms of size-dependent separation of microparticles in capillary zone electrophoresis (CZE), sulfated polystyrene latex microspheres of 139, 189, 268, and 381 nm radius were subjected to CZE in Tris-borate buffers of various ionic strengths ranging from 0.0003 to 0.005, at electric field strengths of 100-500 V cm(-1). Size-dependent electrophoretic migration of polystyrene particles in CZE was shown to be an explicit function of kappaR, where kappa(-1) and rare the thickness of electric double layer (which can be derived from the ionic strength of the buffer) and particle radius, respectively. Particle mobility depends on kappaR in a manner consistent with that expected from the Overbeek-Booth electrokinetic theory, though a charged hairy layer on the surface of polystyrene latex particles complicates the quantitative prediction and optimization of size-dependent separation of such particles in CZE. However, the Overbeek-Booth theory remains a useful general guide for size-dependent separation of microparticles in CZE. In accordance with it, it could be shown that, for a given pair of polystyrene particles of different sizes, there exists an ionic strength which provides the optimal separation selectivity. Peak spreading was promoted by both an increasing electric field strength and a decreasing ionic strength. When the capillary is efficiently thermostated, the electrophoretic heterogeneity of polystyrene microspheres appears to be the major contributor to peak spreading. Yet, at both elevated electric field strengths (500 V/cm) and the highest ionic strength used (0.005), thermal effects in a capillary appear to contribute significantly to peak spreading or can even dominate it.     

Capillary electrophoresis of macromolecules in 'syrupy' solutions: facts and misfacts.

'Syrupy' solutions of liquid linear polyacrylamide (> or = 10%T, 0%C) appear to be excellent for fractionation of oligonucleotides and, potentially, for DNA sequencing. For such analyses, the silica wall must be coated by covalently bound strings of polyacrylamide; otherwise, the electroosmotic flow will slowly pump out the viscous electrolyte solution. Due to the enormous viscosity (100 Pa s for an 8% T solution) the polymer strings must be prepared in situ, by filling the capillary with the appropriate monomer solution. The reaction, however, cannot be driven to better than 80-85% conversion: in 10%T, the concentration of unreacted monomers will thus be 200-300 mM. This will give a substantial background absorbance (even at 254 nm) and leave a huge amount of potentially harmful reacting species in the background electrolyte. A chemical scavenging method is proposed here: after polymerization, a 100 mM solution of cysteine is driven in from the cathode and allowed to react for up to 10 h. At the end of the reaction period, the excess cysteine and its acrylamido adduct are driven out electrophoretically and the column is reconstituted with its normal background electrolyte. Columns thus preconditioned have been found to perform extremely well and to last as long as the inner coating (and the linear polymer filling) will last. No 'carry over' from run to run was experienced.