Electrophoretic migration behavior of DNA fragments in polymer solution

A newly developed polymer coil shrinking theory is described and compared with the existing entangled solution theory to explain electrophoretic migration behaviour of DNA in hydroxypropylmethylcellulose (HPMC) polymer solution in buffer containing 100 mM tris(hydroxymethyl)aminomethane 100 mM boric acid, 2 mM ethylenediaminetetraacetic acid at pH 8.3. The polymer coil shrinking theory gave a better model to explain the results obtained. The polymer coil shrinking concentration, Cs, was found to be 0.305% and the uniform entangled concentration, C+, 0.806%. The existence of three regions (the dilute, semidilute, and concentrated solution) at different polymer concentrations enables a better understanding of the system to guide the selection of the best conditions to separate DNA fragments. For separating large fragments (700/ 800 bp), dilute solutions (HPMC < 0.3%) should be used to achieve a short migration time (10 min). For small fragments (200/300 bp), concentrated solutions are preferred to obtain constant resolution and uniform separation. The best resolution is 0.6% HPMC due to a combined interaction of the polymer coils and the entangled structure. The possibility of DNA separation in semidilute solution is often neglected and the present results indicate that this region has a promising potential for analytical separation of DNA fragments.     

Mannitol influence on the separation of DNA fragments by capillary electrophoresis in entangled polymer solutions

A new kind of sieving matrix is presented in this paper to allow satisfactory separation of DNA fragments in a relatively low viscous solution. When a certain amount of mannitol was added to cellulose solution not concentrated enough to separate PGEM-3Zf(+)/HaeIII standards well, a polymer solution with low viscosity but with very good separation effects was obtained. The separation result of this sieving buffer was comparable with those using highly concentrated cellulose solutions. The sieving ability of solutions with different cellulose concentrations and different amounts of mannitol has been investigated. It was proved that 0.5% was the minimum hydroxypropylmethylcellulose (HPMC) concentration that could be used to separate DNA fragments satisfactorily. HPMC solutions with a concentration of less than 0.5% could not separate the standard DNA fragments even in the presence of mannitol. It was found that 6% was the optimized mannitol concentration because either more or less mannitol will lead a decrease of resolution. The principle of the positive influence of mannitol has also been discussed.     

Effect of ionic strength, pH and polymer concentration on the separation of DNA fragments in the presence of electroosmotic flow

DNA separations in the presence of electroosmotic flow (EOF) using poly(ethylene oxide) (PEO) solutions have been demonstrated. During the separations, PEO entered capillaries filled with Tris-borate (TB) free buffers by EOF and acted as sieving matrices. We have found that ionic strength and pH of polymer and free solutions affect the bulk EOF and resolution differently from that in capillary zone electrophoresis. The EOF coefficient increases with increasing ionic strength of the free TB buffers as a result of decreases in the adsorption of PEO molecules. In contrast, the bulk EOF decreases with increasing the ionic strength of polymer solutions using capillaries filled with high concentrations of free TB buffers. Although resolution values are high due to larger differential migration times between any two DNA fragments in a small bulk EOF using 10 mM TB buffers, use of a capillary filled with at least 100 mM TB free buffers is suggested for high-speed separations. On the side of PEO solutions, 1.5% PEO solutions prepared in 100 to 200 mM TB buffers are more proper in terms of resolution and speed. The separation of DNA markers V and VI was accomplished less than 29 min in 1.5% PEO solutions prepared in 100 mM TB buffers, pH 7.0 at 500 V/cm using a capillary filled with 10 mM free TB buffers, pH 7.0.     

Ultra-thin-layer agarose gel electrophoresis. I. Effect of the gel concentration and temperature on the separation of DNA fragments

A novel, rapid and efficient separation method is described for the analysis of double stranded (ds) DNA fragments in the form of horizontal ultra-thin-layer agarose gel electrophoresis. This separation technique combines the multilane, high-throughput separation format of agarose slab gel electrophoresis with the excellent performance of capillary electrophoresis. The electrophoretic separation of the fluorophore (Cy5)-labeled dsDNA molecules were imaged in real time by a scanning laser-induced fluorescence/avalanche photodiode detection system. Effects of the gel concentration (Ferguson plot) and separation temperature (Arrhenius plot) on the migration characteristics of the DNA fragments are discussed. An important genotyping application is also shown by characterizing the polymorphic region (2× or 4×48 base pair repeats) of the dopamine D₄ receptor gene (D₄DR, exon III region) for ten individuals, using PCR technology with Cy5-labeled primers and ultra-thin-layer agarose gel electrophoresis.     

On-column preconcentration and separation of DNA fragments using polymer solutions in the presence of electroosmotic flow

We demonstrated DNA preconcentration and separation in the presence of electroosmotic flow (EOF) using poly(ethylene oxide) (PEO) solutions. After injecting large volumes of DNA samples into a capillary filled with free tris(hydroxymethyl)aminomethane (Tris)-borate (TB) buffers, PEO solutions entered the capillary by EOF and acted as sieving matrices. In contrast to conventional methods (in the absence of EOF), controlling the EOF was also useful for resolution optimization. We have found that PEO adsorption on the capillary wall was more pronounced when low ionic strength buffers were used. Thus, the EOF decreased with increasing injection length, which led to longer migration times and changes in resolution and stacking efficiency. All resolution values were higher than 1.5 when 1.0 microg/mL DNA samples were injected at 240 V/cm for 60 s (0.67 microL). In addition, as low as 0.015 microg/mL DNA samples (an about 66-fold increase in sensitivity) were detected when the injection was performed at 250 V/cm for 60 s.     

Microelectrophoresis for the separation of DNA fragments.

A methodology has been developed which significantly reduces the linear dimension necessary for the electrophoretic separation of DNA fragments and oligonucleotides. DNA fragments are rapidly separated into compact, resolvable microscopic banding patterns which can be detected using a high-resolution electronic imaging system. Separations can be carried out in either capillary tube or thin-layer (slab) microgel formats of one centimeter or less in length. The complete separation of all eleven fragments (1353 to 72 base pairs) of the pi X174 DNA/HaeIII restriction ladder was achieved in a total running distance of less than 2 mm and in less than 2 min. The observed band widths for the larger fragments (1353-603 bp) ranged from 18 to 25 microns, with the intermediate and smaller fragments (310 to 72 bp) ranging from 30 microns to 60 microns. The ethidium bromide-stained microgels were analyzed using an epifluorescent microscope combined with an intensified charged coupled device imaging system. In other experiments, single-base resolution of fluoresceinated oligonucleotides in the 20-30 nucleotide range was demonstrated. DNA sequencing may be possible with further optimization. This new methodology departs from the conventional gel formulations and electrophoretic procedures used for the separation DNA fragments. High voltage gradients and the use of highly concentrated and crosslinked homogeneous polyacrylamide gels effects the rapid separation of DNA fragments in very short distances. Analysis of the microgels with proteins of known size (Stokes radius) indicates that separations are occurring in gels with pore sizes close to the diameter of double-stranded DNA.(ABSTRACT TRUNCATED AT 250 WORDS)     

Size exclusive capillary electrophoresis separation of DNA oligonucleotides in small size linear polyacrylamide polymer solution

The mobility of analytes in capillary electrophoresis using polymer gels and solutions is usually described as having an inverse relationship with the molecular size (mobility decreases as molecular size increases). The most commonly used models for predicting such mobility are the Ogston model and the Reptation model. However, in this study a new separation phenomenon was observed in which the mobility of DNA oligonucleotides increased with molecular size in a capillary electrophoresis phase (CEP) coated capillary column. The polymer system used was a 11% linear polyacrylamide (Mr = 1500) solution. The log-transformed number of base pairs (log N) of three double stranded oligonucleotides had an inverse linear relationship (r2 > 0.9981) with their migration time in the capillary column. Such a relationship is similar to that observed with size exclusive chromatography.     

基于微芯片电泳的脱氧核糖核酸片段的浓缩和分离

采用超负荷电动供给(electrokinetic supercharging, EKS)预浓缩技术,在微芯片电泳(MCE)上对脱氧核糖核酸（DNA）片段进行浓缩和分离。EKS是集合样品电动进样(EKI)和过渡等速电泳(tITP)的一种在线浓缩方法。研究表明：采用该方法后,在40.5 mm长的单通道芯片上能够实现对低浓度样品的大量进样、浓缩和基线分离。在普通的紫外检测条件(检测波长为260 nm)下,对DNA片段的平均检出限(S/N=3)约为0.07 mg/L,仅为十字芯片上的微芯片电泳检出限的1/40。本文还对浓缩过程中的一些关键因素和定性分析进行了探讨。     

Interaction of DNA fragments with counterions in aqueous solution

Monte Carlo simulation of the hydration of metal ion—DMP⁻ and metal ion—9-methylguanine complexes was performed. A comparative analysis of the results for Na⁺ and K⁺ ions was carried out. The main stages of dissociation were revealed. The energy effects of dissociation were evaluated. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 2174–2177, November, 1998.     

Effects of polymer chain length and stiffness on phase separation dynamics of semidilute polymer solution

Three-dimensional dissipative particle dynamics (DPD) simulations were performed to investigate the phase separation dynamics of semidilute polymer solutions with different polymer chain length and stiffness. For the polymer solution composed of shorter and more flexible chains, a crossover of the domain growth exponent from 1/3 to 2/3 was observed during the course of phase separation, indicating that the growth mechanism altered from diffusion to interfacial-tension driven flow. When the chain flexibility was kept the same but the chain was lengthened to allow for the chain entanglement to occur, the growth exponent changed to 1/4 in the diffusion-dominating coarsening regime while the growth exponent remained 2/3 in the flow-dominating regime. When the chain length was kept short but the stiffness was increased, the growth exponent became 1/6 in the diffusion-dominating regime and little effect was observed in the flow-dominating coarsening regime. The slow down of the phase separation dynamics in the diffusion-dominating coarsening could be explained by that the polymer chains could only perform wormlike movement when chain entanglements occurred or when the chain motion was limited by chain stiffness during phase separation. Moreover, when both the effects of chain length and stiffness were enhanced, polymer networks composed of longer and stiffer chains appeared and imposed an energy barrier for phase separation to occur. As a result, the polymer solution with stiffer and longer chains required a larger quench depth to initiate the phase separation and caused the delay in crossover of the coarsening mechanism from diffusion to flow.     

Theory for the capillary electrophoretic separation of DNA in polymer solutions

We present a mathematical model based on the models of Hubert et al. [Macromolecules 29 (1996) 1006] and Sunada and Blanch [Electrophoresis, 19 (1998) 3128] to describe the electrophoretic mobility of DNA by a transient entanglement coupling mechanism. The proposed model takes into account the interactions between molecules in the capillary and the cross-section of collision between DNA and polymer molecules. The results show that the calculated values agree remarkably well with our electrophoretic mobility data.     

Improved separation of double-stranded DNA fragments by capillary electrophoresis using poly(ethylene oxide) solution containing colloids

The analysis of double-stranded (ds) DNA fragments by capillary electrophoresis (CE) using poly(ethylene oxide) (PEO) solution containing gold nanoparticles (GNPs) is presented, focusing on evaluating size dependence of the GNPs and PEO on resolution and speed. To prevent the interaction of the capillary wall with DNA, the capillary was dynamically coated with polyvinylpyrrolidone. Using different PEO solutions containing GNPs ranging in diameter from 3.5 to 56 nm, we have achieved reproducible, rapid, and high-resolution DNA separations. The results indicate that the sizes of PEO and GNPs as well as the concentration of PEO affect resolution. The separation of DNA ranging in size from 8 to 2176 base pairs (bp) was accomplished in 5 min using 0.2% PEO (8 MDa) containing 56 nm GNPs. We have also demonstrated the separations of the DNA fragments ranging from 5 to 40 kbp using 0.05% PEO (2 MDa) containing 13 nm GNPs or 0.05% PEO (4 MDa) containing 32 nm GNPs. With very low viscosity (< 15 cP), automatic replacement of the sieving matrices is easy, indicating a great potential for high-throughput DNA analysis using capillary array electrophoresis systems.     

Separation of long DNA fragments by inversion field capillary electrophoresis

This study reports improved pulsed field capillary electrophoresis (PFCE) for separation of large DNA ladders. Important analytical conditions, including gel polymer concentration, ratio of forward to backward pulse duration, and separation potential, were investigated for their effects on the separation performance of DNA ranging in size from 0.1 to 10.0 kilo base pairs (kbp). Results show that DNA fragments from 0.1 to 8.0 kbp can be resolved with high resolution, simultaneously, in a short time. The ratio of forward to backward pulse duration affects the separation performance for DNA fragments greater than 1.5 kbp, and 3 or 4 is the optimum value of the ratio for separation of DNA up to 10 kbp. Furthermore, the separations that were obtained with 74–19,329 bp λ-DNA restriction fragments clearly demonstrate a dramatic improvement in the separation time and resolution over the conventionally used square-wave PFCE. The inversion field capillary electrophoresis reported here may help enable future DNA analysis studies to be performed quickly and effectively.     

Effect of test temperature on separation number

The separation number is affected by a variety of extra-column factors (e.g. the injection process, the nature of the sample, and plumbing defects in the inlet and detector) as well as factors related to column efficiency. The magnitude of the separation number, as affected by the column, varies inversely with column temperature and directly with the partition ratios of the test compounds. The interrelationships of column temperature and partition ratios are explored.     

Micropreparative fractionation of DNA fragments on metathesis-based monoliths: influence of stoichiometry on separation

New antibiotics were recently developed, among which are the (fluoro)quinolones. This paper presents an analytical method which allows the determination of 11 (fluoro)quinolones in swine kidneys: norfloxacin, ofloxacin, cinoxacin, oxolinic acid, nalidixic acid, flumequine, enrofloxacin, enoxacin, ciprofloxacin, danofloxacin and marbofloxacin. The procedure involves a rapid and efficient pre-treatment by solid-phase extraction (recoveries 83-98%), followed by the sensitive and selective determination of all compounds in a single run using LC-ESI-MS-MS. Multiple reaction monitoring (MRM) was used for selective detection of each (fluoro)quinolone. Quinine was selected as internal standard. The accuracy of the method, expressed as recovery, was between 89 and 109%; the repeatability had a maximum RSD lower than 15%. The limits of detection (LOD) were much lower than the respective Maximum Residue Limits (MRL)/4.     

Diffusion and phase separation in polymer solution during asymmetric membrane formation

Most of the commercially available polymeric membranes are prepared by the phase inversion process. In this process a thermodynamically stable polymer solution is brought to phase separation by immersing the solution in a surplus of nonsolvent, followed by an exchange of solvent and nonsolvent. The ultimate membrane structure is the result of an interplay of mass transfer and phase separation. Asymmetric membranes as well as symmetrical porous membranes can be obtained. Two types of demixing processes (l-l phase separation and formation of aggregates) can be distinguished by the kinetics of phase separation, as the formation of aggregates is supposed to be a slower process than l-l demixing. Because it is impossible to measure the composition changes during the demixing processes experimentally, a theoretical analysis has to be applied. A suitable formalism to calculate the diffusion induced composition changes in the immersed casting solution, as a function of thermodynamic and hydrodynamic interaction parameters will be described. With this theory it can be shown that two distinctly different mechanisms of membrane formation may occur resulting in two different types of membranes. One type has a relatively thick toplayer and mostly exhibits reverse osmosis, gas separation and pervaporation properties; the other type results in a porous type of membrane, which will exhibit ultra- and microfiltration properties. Model calculations are in agreement with light transmission experiments on membrane forming systems. Therefore, it could be concluded that the elucidation of the diffusion behavior in the immersed polymer film is the key to better understanding of membrane formation by means of immersion precipitation.     

Kinetics of phase separation by spinodal decomposition in a liquid-crystalline polymer solution

Abstract

Time-resolved light scattering studies have been undertaken for elucidating the dynamics of phase separation in aqueous HPC (hydroxypropyl cellulose) liquid-crystalline solutions. The HPC/water system phase separates during heating and returns to a single phase upon cooling. The phase diagram of thermally induced phase separation was subsequently established on the basis of cloud point measurements. For kinetic studies, T (temperature) jump experiments of 10 per cent aqueous HPC solutions were undertaken. Phase separation occurs in accordance with the spinodal decomposition mechanism. At low T jumps or in reverse quenched experiments, the scattering maximum remains invariant as predicted by the linearized Cahn-Hilliard theory. However, at large T jumps, the SD is dominated by non-linear behaviour in which scattering peaks move to low scattering angles. The latter process has been identified to be a coarsening mechanism associated with the coalescence of phase separated domains driven by a surface tension. A reduced plot has been established with dimensionless variables Q and t. It was found that the scaling law is not valid over the entire spinodal process. The time evolution of the scattering profiles of 10 per cent HPC solutions, following a Tjump to 49°C, is tested with the scaling law of Furukawa. It seems that the kinetics of phase separation at 10 per cent solution resemble the behaviour of off-critical mixture.     

Phase separation of a model binary polymer solution in an external field

The phase separation of a simple binary mixture of incompatible linear polymers in solution is investigated using an extension of the sedimentation equilibrium method, whereby the osmotic pressure of the mixture is extracted from the density profiles of the inhomogeneous mixture in a gravitational field. In Monte Carlo simulations the field can be tuned to induce significant inhomogeneity, while keeping the density profiles sufficiently smooth for the macroscopic condition of hydrostatic equilibrium to remain applicable. The method is applied here for a simplified model of ideal but mutually avoiding polymers, which readily phase separate at relatively low densities. The Monte Carlo data are interpreted with the help of an approximate bulk phase diagram calculated from a simple, second-order virial coefficient theory. By derivation of effective potentials between polymer centers of mass, the binary mixture of polymers is coarse-grained to a "soft colloid" picture reminiscent of the Widom-Rowlinson model for incompatible atomic mixtures. This approach significantly speeds up the simulations and accurately reproduces the behavior of the full monomer resolved model.