Comparative study of reaction kinetics in membrane and agarose bead affinity systems.

Compared to conventional agarose bead affinity supports, a microporous nylon membrane exhibits greatly improved reaction kinetics as quantified in the reaction between gamma-globulin and immobilised protein A. The improvement is only observed when the solution of gamma-globulin is forced through the membrane pores. In the absence of flow in the pores, it is possible to relate approximately the rate of uptake onto either type of affinity support to independently determined diffusion coefficients. In the presence of flow, the reaction rate is similar for membranes having 0.45 and 3.0 microns diameter pores, and considerably smaller than predicted by the Smoluchowski formula.     

Testing of nonlinear electrofrictiophoresis in agarose gel

It was theoretically predicted earlier that if a periodic force without constant component is applied to a particle, then the particle can produce a directed drift in some direction. The effect is named nonlinear electrofrictiophoresis, because it is crucial for its appearance that the friction force depends on the particle's velocity in a nonlinear manner. We test a possibility to observe this effect when a mixture of fragments of DNA (the DNA ladder) moves in the agarose gel. For this purpose, we study the nonlinear characteristics of a DNA ladder movement in the gel. The gels with the ladder were run under various electric field strengths. It was found that the friction coefficient for each DNA fragment in the ladder depends on the migration velocity, suggesting that energy dissipation during migration is a nonlinear function of velocity. This nonlinearity makes the system under consideration suitable for observing nonlinear electrofrictiophoresis. A possible velocity of directed drift under periodic electric drive without constant component was estimated numerically for experimentally observed dependencies. The velocity appeared to be comparable with that of migration under a constant field of moderate strength. A possible mechanism of energy dissipation during movement of DNA through the gel is discussed.     

Experimental study on moving neutralization reaction boundary created with the strong reactive electrolytes of HCl and NaOH in agarose gel

In this paper, a moving neutralization reaction boundary (MNRB) is created with the strong reactive electrolytes of HCl and NaOH in agarose gel. The motions of the MNRB are investigated and compared with the predictions with the theory of the moving chemical reaction boundary (MCRB). The results show that, under appreciate experimental conditions, the experiments on the MNRB are exactly in coincidence with the predictions with the MCRB theory. Thus, the results excellently demonstrate that the MCRB theory is valid for the MNRB formed with the strong reactive electrolytes of HCl and NaOH. Additionally, it is, as discussed in this paper, imperative to develop a method to obtain ionic mobility at different temperatures and ionic strengths, in order to investigate the movements of the MCRB more efficiently.     

Development of a novel two-dimensional gel electrophoresis protocol with agarose native gel electrophoresis

A new protocol for conducting two-dimensional (2D) electrophoresis was developed by combining the recently developed agarose native gel electrophoresis with either vertical sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis (PAGE) or flat SDS agarose gel electrophoresis. Our innovative technique utilizes His/MES buffer (pH 6.1) during the first-dimensional (1D) agarose native gel electrophoresis, which allows for the simultaneous and clear visualization of basic and acidic proteins in their native states or complex structures. Our agarose gel electrophoresis is a true native electrophoresis, unlike blue native–PAGE, which relies on the intrinsic charged states of the proteins and their complexes without the need for dye binding. In the 2D, the gel strip from the 1D agarose gel electrophoresis is soaked in SDS and placed on top of the vertical SDS–PAGE gels or the edge of the flat SDS–MetaPhor high-resolution agarose gels. This allows for customized operation using a single electrophoresis device at a low cost. This technique has been successfully applied to analyze various proteins, including five model proteins (BSA, factor Xa, ovotransferrin, IgG, and lysozyme), monoclonal antibodies with slightly different isoelectric points, polyclonal antibodies, and antigen–antibody complexes, as well as complex proteins such as IgM pentamer and β-galactosidase tetramer. Our protocol can be completed within a day, taking approximately 5–6 h, and can be expanded further into Western blot analysis, mass spectrometry analysis, and other analytical methods.     

Multiple successive immunoprinting: a fast blotting technique of a single agarose isoelectric focusing gel

Multiple successive pressure blottings of a single agarose isoelectric focusing gel were performed on normal and CNBr-activated nitrocellulose (NC) filters. The results obtained by multiple successive 10s immunoprints were compared to those obtained by a single 10 min immunoprint. To quantify the transfer efficiency of these techniques, a defined amount of radioactive material was separated by isoelectric focusing on agarose gel. After separation and pressure blottings of the gel the NC filters were submitted to autoradiography. The amount of radioactive material bound to the NC filters was determined by scintillation technique. The single 10 min pressure blot was more efficient than each of the multiple successive 10s prints. However, the latter procedure allowed equal resolution and resulted in a higher recovery of total radioactivity than the single immunoprint technique. The aim of this paper is to show how to obtain highly reproducible prints of electrophoretic patterns in an agarose gel of heterogeneous samples when accurate multiple immunodetections are to be performed. This technique was tested to characterize the grass pollen specific immunoglobulin classes and subclasses from an allergic patient.     

Topology evolution and gelation mechanism of agarose gel

Kinetics as well as the evolution of the agarose gel topology is discussed, and the agarose gelation mechanism is identified. Aqueous high melting (HM) agarose solution (0.5% w/v) is used as the model system. It is found that the gelation process can be clearly divided into three stages: induction stage, gelation stage, and pseudoequilibrium stage. The induction stage of the gelation mechanism is identified using an advanced rheological expansion system (ARES, Rheometric Scientific). When a quench rate as large as 30 deg C/min is applied, gelation seems to occur through a nucleation and growth mechanism with a well-defined induction time (time required for the formation of the critical nuclei which enable further growth). The relationship between the induction time and the driving force which is determined by the final setting temperature follows the 3D nucleation model. A schematic representation of the three stages of the gelation mechanism is given based on turbidity and rheological measurements. Aggregation of agarose chains is promoted in the polymer-rich phase and this effect is evident from the increasing mass/length ratio of the fiber bundles upon gelation. Continuously increasing pore size during gelation may be attributed to the coagulation of the local polymer-rich phase in order to achieve the global minimum of the free energy of the gelling system. The gel pore size determined using turbidity measurements has been verified by electrophoretic mobility measurements.     

Boronate-containing copolymers: polyelectrolyte properties and sugar-specific interaction with agarose gel

Copolymers of N-acryloyl-m-aminophenylboronic acid (NAAPBA) with acryamide (AA), N,N-dimethylacrylamide (DMAA), and N-isopropylacrylamide (NIPAM) were found to adsorb on cross-linked agarose gel (Sepharose CL-6B) in the pH range from 7.5-9.2, due to specific boronate-sugar interactions. The molar percentages of phenylboronic acid (PBA) groups in the boronate-containing copolymers (BCCs), as estimated by 1H NMR spectroscopy, were 13, 10, and 16%, respectively, whereas the apparent ionization constants, the pKa values, of the copolymers were similar and equal to 9.0 +/- 0.2 at 20 degrees C. The copolymers adsorption capacities were in the range of 15-30 mg x ml(-1) gel (14-36 micromol pendant PBA ml(-1) gel) at pH 9.2 and decreased with decreasing pH value. The interaction of monomeric NAAPBA with Sepharose CL-6B was characterized by an equilibrium association constant of 53 +/- 17 M(-1), the chromatographic capacity factor k' = 1.8, and a total content of binding sites of 27 +/- 10 micromol x ml(-1) gel at pH 9.2. The weak reversible binding of monomeric NAAPBA and almost irreversible binding of NAAPBA copolymers to the gel at pH 9.2 suggested a multivalent character of the copolymer adsorption. At pH 7.5, the maximal adsorption capacity was displayed by the AA-NAAPBA copolymer (15 mg x ml(-1) gel). All the BCCs could be completely desorbed from the gel by 0.1 M fructose in aqueous buffered media with pH values from 7.5-9.2. The strong adsorption of AA-NAAPBA on agarose gel probably relates to the conformation of the copolymer in aqueous solution and provides opportunities for biomedical applications of the copolymer under physiological conditions. Multivalent, weak-affinity adsorption of BCCs to the agarose gel seems to be a tentative model for the copolymers' binding to oligo- and polysaccharides of cell membranes and mucosal surfaces.     

Method for immobilization of liposomes in capillary electrophoresis by electrostatic interaction with derivatized agarose

A novel procedure for immobilization of liposomes inside fused-silica capillaries is demonstrated. First, the inner wall of the capillaries was coated with a positively charged polymer, composed of derivatized agarose. Subsequently, negatively charged liposomes were immobilized by electrostatic interaction on the polymer coating. The developed liposome coated capillaries were used as a nanoseparation tool for studying interactions between small drug compounds and liposomes. Part of this work was presented at the 15th International Symposium on Microscale Separations and Analysis, HPCE 2002, Stockholm, Sweden, April 2002.     

Vertical agarose gel electrophoresis and electroblotting of high-molecular-weight proteins

The electrophoretic separation of high-molecular-weight proteins (> 500 kDa) using polyacrylamide is difficult because gels with a large enough pore size for adequate protein mobility are mechanically unstable. A 1% vertical sodium dodecyl sulfate (SDS)-agarose gel electrophoresis (VAGE) system has been developed that allows titin (a protein with the largest known SDS subunit size of 3000-4000 kDa) to migrate over 10 cm in a approximately 13 cm resolving gel. Such migration gives clear and reproducible separation of titin isoforms. Proteins ranging in size from myosin heavy chain ( approximately 220 kDa) up to titin can be resolved on this gel system. Electroblotting of these very large proteins was nearly 100% efficient. This VAGE system has revealed two titin size variants in rabbit psoas muscle, two N2BA bands in rabbit cardiac muscle, and species differences between titins from rat and rabbit muscle. Agarose electrophoresis should be the method of choice for separation and blotting of proteins with very large subunit sizes.     

Enhanced detection of gold nanoparticles in agarose gel electrophoresis

Gel electrophoresis is a powerful tool in gold nanoparticle (AuNP) research. While the technique is sensitive to the size, charge, and shape of particles, its optimal performance requires a relatively large amount of AuNP in the loading wells for visible detection of bands. We here describe a novel and more sensitive method for detecting AuNPs in agarose gels that involves staining the gel with the common organic fluorophore fluorescein, to produce AuNP band intensities that are linear with nanoparticle concentration and almost an order of magnitude larger than those obtained without staining the gel.     

Monitoring of single nicks in duplex DNA by gel electrophoretic mobility-shift assay

We demonstrate that the gel electrophoretic mobility-shift assay (EMSA) can be used for site-selective and quantitative monitoring of nicks in linear double-stranded DNA (dsDNA) thus allowing to expediently follow the nicking activity of enzymes or other agents targeted to a designated dsDNA site. At elevated temperature and/or in the presence of urea, DNA fragments carrying a single nick produced by the nicking enzyme N.BstNBI exhibit a well-detectable gel retardation effect. On the basis of permutation analysis, the decreased electrophoretic mobility of nicked dsDNA fragments is attributed to a bend (or hinge) in the DNA double helix sequence-specifically generated by a nick. Since nick-induced DNA bending depends on interaction between base pairs adjacent to a nick, the change in mobility is different for nicked DNA sites with different sequences. Therefore, EMSA monitoring of differential mobility change caused by nicks within various DNA sequences could be useful for studying the differential base stacking and nearest-neighbor energetics.     

Separation and purification of puerarin using beta-cyclodextrin-coupled agarose gel media

The isoflavonoid puerarin, a well-known traditional Chinese drug, has been purified in one step from an extract of Radix puerariae (root of the plant Pueralria lobata) by adsorption chromatography on an epichlorohydrin polymerized beta-cyclodextrin ligand coupled to brominated allyl-group substituted Sepharose HP. Acetic acid (10%) was used as the mobile phase and the optimum loading capacity was around 1.2 mg crude extract/ml packed gel. The purity of the collected puerarin was about 98% with a recovery of about 62%.     

Water structure in nanopores of agarose gel by Raman spectroscopy

The evolution of water structure during the gelation process is examined in aqueous solution of agarose using Raman spectroscopy of the O-H stretching band. The measurements have been performed at room temperature for different concentrations of agarose, which yields different dimensions of nanopores in the network of the created gel. Our results show that water confined in the gel pores exhibits evident changes in the local order of molecules in comparison with bulk water and water in the sol state. During the sol-gel transition the number of molecules that participate in the regular tetrahedral H-bond structure increases, and the effect is stronger for higher concentration of the biopolymer.     

pH-Sensitive liposomes with embedded ampholytic derivatives of cholan-24-oic acid

Stimulus-sensitive liposomes have been prepared from zwitterionic dioleoylphosphocholine and ampholytic molecular switches with carboxylic anionic groups and the triazole or isobutylamino cationic ones attached to the opposite ends of the steroid core. When the pH of outer solution was altered from slightly alkaline to slightly acidic, the switches changed their orientation in the liposomal membrane, which induced temporal defects formation and the release of a drug model load. The low-toxic pH-sensitive isobutylamino derivative–dioleoylphosphocholine liposomes demonstrated fast cargo release.     

Interaction of cationic liposomes with cell membrane models

The colloidal dispersion stability of nano-sized graphene sheets in supercritical fluid (SCF) media is very important for developing SCF-based exfoliation and dispersion technologies for stabilization and solubilization of graphenes. We carried out molecular dynamics simulations to elucidate the stability mechanism of graphene in supercritical CO(2) (scCO(2)). The potential of mean force (PMF) between two graphene nanosheets in scCO(2) was simulated, and the effect of scCO(2) density and temperature on the PMF behavior has been investigated. The simulation results demonstrate that there exists a free energy barrier between graphenes in the scCO(2) fluid, possibly obstructing the aggregation of graphenes. The single-layer confined CO(2) molecules between the graphene sheets can induce a dominating repulsion interaction between graphene sheets. At higher scCO(2) fluid density, there are more confined CO(2) molecules within the interplate regions, resulting in a stronger repulsive free energy barrier. The effect of temperature on the PMF is relatively minor. The scCO(2) solvent structure shows layered confined arrangement in the interfacial region near the graphene nanosheets, which is correlated well with the PMF profile curve.     

Procedures and computer program for deriving the Ferguson plot from electrophoresis in a single pore gradient gel: application to agarose gel and a polystyrene particle.

This study presents a computerized evaluation of pore gradient gel electrophoretograms to arrive at estimates for both the particle-free mobility and retardation coefficient, which is related to particle size. Agarose pore gradient gels ranging from 0.2 to 1.1% agarose were formed. Gel gradients were stabilized during their formation by a density gradient of 0-20% 5-(N-2,3-dihydroxypropylacetamido)- 2,4,6-triiodo-N,N'bis-(2,3-dihydroxypropyl)-isophthalamide (Nycodenz). Densitometry of gelled-in Bromophenol Blue showed that these pore gradients exhibited a linear central segment and were reproducible. Migration distances of polystyrene sulfate microspheres (36.5 nm radius) in agarose pore gradient gel electrophoresis were determined by time-lapse photography at several durations of electrophoresis. These migration distances were evaluated as a function of migration time as previously reported (D. Tietz, Adv. Electrophoresis 1988, 2, 109-169). Although this is not necessarily required, the mathematical approach used in this study assumed linearity of both the pore gradient and the Ferguson plot for reasons of simplicity. The data evaluation on the basis of the extended Ogston model is incorporated in a user-friendly program, GRADFIT, which is designed for personal computers (Macintosh). The results obtained are compared with (1) conventional electrophoresis using several gels of single concentration with and without Nycodenz, and (ii) a different mathematical approach for the analysis of gradient gels (Rodbard et al., Anal. Biochem. 1971, 40, 135-157). Moreover, a simple procedure for evaluating linear pore gradient gels using linear regression analysis is presented. It is concluded that the values of particle-free mobility and retardation coefficient derived from pore gradient gel electrophoresis using the different mathematical methods are statistically indistinguishable from each other. However, these values are different, albeit close, to those obtained from conventional Ferguson plots. One of the possible reasons for this relatively minor discrepancy is that the particle-free mobility changed slightly during electrophoresis, which has a different effect on electrophoresis in homogeneous gels (single time measurement) and pore gradient gels (multiple time measurements). The characterization of particles according to size and charge by pore gradient electrophoresis provides a significant operational simplification and sample economy compared to that requiring the use of several gel concentrations, although at the price of increased requirements of instrumentation.     

Orientation of DNA and the agarose gel matrix in pulsed electric fields

Transient electric birefringence has been used as an analytical tool to study the orientation of DNA in agarose gels, and to study the orientation of the matrix alone. The sign of the birefringence of DNA oriented in an agarose gel is negative, as observed in free solution, indicating that the DNA molecules orient parallel to the direction of the electric field. If the median pore diameter of the gel is larger than the contour length of the DNA molecule, the DNA effectively does not see the matrix and the birefringence relaxation time is the same as observed in free solution. However, if the median pore diameter of the gel is smaller than the contour length of the DNA, the DNA molecule becomes stretched as well as oriented. For DNA molecules of moderate size (less than or equal to 4 kb), stretching in the gel causes the birefringence relaxation times to increase to the values expected for fully stretched molecules. Complete stretching is not observed for larger DNA molecules. The orientation and stretching of DNA molecules in the gel matrix indicates that end-on migration, or reptation, is a likely mechanism for DNA electrophoresis in agarose gels. When the electric field is rapidly reversed in polarity, very little change in the orientation of the DNA is observed if the DNA molecules were completely stretched and had reached their equilibrium orientation before the field was reversed in direction. Hence completely stretched, oriented DNA molecules are able to reverse their direction of migration in the electric field with little or no loss of orientation. However, if the DNA molecules were not completely stretched or if the equilibrium orientation had not been reached, substantial disorientation of the DNA molecules is observed at field reversal. The forced rate of disorientation in the reversing field is faster than the field-free rate of disorientation. Complicated patterns of reorientation can be observed after field reversal, depending on the degree of orientation in the original field direction. The effect of pulsed electric fields on the orientation of the agarose gel matrix itself was also investigated.(ABSTRACT TRUNCATED AT 400 WORDS)