Anisotropic agarose gels

Agarose hydrogels deswell reversibly over a wide range of concentration. Two types of deswelling measurements are considered here, isotropic and uniaxial. We describe some of the properties of the gels observed in the deswollen state. In both the isotropic and uniaxial geometry, the swelling pressure varies approximately as the square of the concentration.     

Oxygen-17 relaxation in aqueous agarose gels

Nuclear magnetic relaxation of oxygen-17 in H₂¹⁷O enriched agarose gels shows that existing explanations of water behaviour are oversimplified. Satisfactory models must include at least three proton phases, two of which involve water molecules.     

Direct chemiluminescent immunodetection of proteins in agarose gels

Chemiluminescent immunodetection of proteins separated by polyacrylamide gel electrophoresis is generally performed only after Western blotting. Agarose gels are adequately permeable to allow immunoprobing directly in the gel. Chemiluminescent substrates had not been applied for direct immunoprobing of agarose gels. In a comparison with direct immunostaining of fibrinogen derivatives with horse radish peroxidase (HRP)-conjugated primary antibody using 3,3'-diaminobenzidene (DAB) yielding a sensitivity in the low nanogram range, a luminol-based chemiluminescent detection extended sensitivity to the mid-picogram range with seemingly no interference from either regular or glyoxyl agarose gels. The high sensitivity of chemiluminescence extends utility of direct immunoprobing of either agarose or glyoxyl agarose composite gels for detection and measurement of both high and low molecular weight proteins/peptides which are not easily detected/measured by Western blotting. However, due to the thickness of the gels, direct immunoprobing can be quite laborious. To eliminate that drawback, we describe a simplified approach, converting the thick gels to thin ones prior to probing, that makes direct immunoprobing as easy as Western blotting.     

Ternary complexes in gels from agarose and from chemically‐modified agarose

Thermodynamic data and mechanical measurements are shown for gels prepared in aqueous binary solvents (water/DMSO, water/DMF, water/methyl formamide and water/formamide). When electrostatic interactions, as opposed to hydrogen bonding, can be established with the cosolvent (DMSO, DMF, methyl formamide) we come to the conclusion that ternary complexes are formed (agarose/water/cosolvent). In the case of chemically‐modified agarose (OH groups replaced by OCH₃ groups) we suggest that these cosolvents are directly involved in the formation of the gel.     

Well-defined star-shaped calcite crystals formed in agarose gels

Single crystals of calcite exhibiting a morphology of well-defined 8-armed stars, which evolved from original rhombohedral calcite crystals with their 8 points extending radially into eight arms, were produced by crystallization of CaCO3 in agarose gels.     

Electrotitration curves of human gastric pepsinogens in agarose gels

Electrotitration curves (ETC) of a marker protein mixture, pH 2.5-5.65, and human pepsinogens were performed in an agarose gel, containing 2% acid carrier ampholytes, forming a pH range of 2.5-5. Although the establishment of the pH gradient by isoelectric focusing was not quite complete and linear, both biochemically and immunochemically different types of pepsinogen C (PGC) and pepsinogen A (PGA) zymogens as well as the acid isoelectric points (pI) marker proteins were separated with good resolution. Three main fractions of PGA (Pg3, Pg4, and Pg5) were detected. To obtain an exact determination of the pepsinogen pIs, a simple and very fast 10 s pressure blot technique was applied. Human pepsinogens were separated alone or mixed with pI marker proteins in the pH range 2.4-5.65. No effect of the markers was observed on the pepsinogen migration. To visualize the different protein samples in the gel and on nitrocellulose membrane, we have used colloidal gold (AuroDye) staining, proteolytic activity, and immunostaining with monoclonal antibodies anti PGA and PGC. The described method shows an ability to separate proteins at acidic conditions with a resolution comparable to isoelectric focusing with immobilized pH gradients, but much faster, easier, and cheaper. In addition, the technique allows us to determine precise and exact pI values, and is suitable for studies of the pepsinogen polymorphism and its role in gastric diseases.     

Diffusion of sodium dodecyl sulfate micelles in agarose gels

The gradient diffusion of ionic sodium dodecyl sulfate micelles in agarose gel was investigated at moderate concentrations above the CMC. Of particular interest were the effects of micelle, gel, and sodium chloride concentration on the micelle diffusivity. Holographic interferometry was used to measure the gradient diffusion coefficient at three sodium chloride concentrations (0, 0.03, 0.10 M), three gel concentrations (0, 1, 2 wt%), and several surfactant concentrations. Time-resolved fluorescence quenching was used to measure aggregation numbers both in solution and gel. The micelle diffusivity increased linearly with surfactant concentration at the two larger sodium chloride concentrations and all gel concentrations. In general, the strength of this effect increased with decreasing sodium chloride concentration and increased with gel concentration. This behavior is evidence of decreasing micelle-micelle electrostatic interactions with increasing sodium chloride concentrations, and increasing excluded volume effects and hydrodynamic screening with increasing gel concentration, respectively. The only exception was at 0.1M sodium chloride and 2 wt% agarose, which showed a slight reduction in the slope compared to 1 wt% agarose. It was found that the concentration effect is quite strong for charged solutes: at a NaCl concentration of 0.03 M in a 2% agarose gel, in a solution with 3% SDS micelles by volume, the micelle diffusion coefficient is doubled relative to its value in the same gel at infinite dilution. The extrapolated, infinite-dilution diffusion coefficients and the rate at which the micelle diffusivity increased with surfactant concentration were compared with predictions of previously published theories in which the micelles are treated as charged, colloidal spheres and the gel as a Brinkman medium. The experimental data and theoretical predictions were in good agreement.     

Internal water molecules and magnetic relaxation in agarose gels

Agarose gels have long been known to produce exceptionally large enhancements of the water 1H and 2H magnetic relaxation rates. The molecular basis for this effect has not been clearly established, despite its potential importance for a wide range of applications of agarose gels, including their use as biological tissue models in magnetic resonance imaging. To resolve this issue, we have measured the 2H magnetic relaxation dispersion profile from agarose gels over more than 4 frequency decades. We find a very large dispersion, which, at neutral pH, is produced entirely by internal water molecules, exchanging with bulk water on the time scale 10(-8)-10(-6) s. The most long-lived of these dominate the dispersion and give rise to a temperature maximum in the low-frequency relaxation rate. At acidic pH, there is also a low-frequency contribution from hydroxyl deuterons exchanging on a time scale of 10(-4) s. Our analysis of the dispersion profiles is based on a nonperturbative relaxation theory that remains valid outside the conventional motional-narrowing regime. The results of this analysis suggest that the internal water molecules responsible for the dispersion are located in the central cavity of the agarose double helix, as previously proposed on the basis of fiber diffraction data. The magnetic relaxation mechanism invoked here, where spin relaxation is induced directly by molecular exchange, also provides a molecular basis for understanding the water 1H relaxation behavior that governs the intrinsic magnetic resonance image contrast in biological tissue.     

Ternary complexes in agarose gels prepared from binary solvents

The thermoreversible gelation of agarose has been investigated in four different aqueous binary solvents: Water/dimethyl sulfoxide, water/N,N-dimethylformamide, water/N-methylformamide, and water/formamide. The phase diagrams have been subsequently established as a function of agarose concentration and solvent composition. These diagrams suggest the formation of ternary complexes agarose/water/cosolvent.     

A laser light-scattering study of the structure of agarose gels

Diffusion coefficients of dextran fractions within agarose gels surrounded by dextran solution have been measured by laser light scattering using the autocorrelation method. Plots were made of the diffusion coefficient relative to that in dilute solution, D/D₀, against the logarithm of hydrodynamic diameter logd for each concentration of agarose, and superimposed by displacing horizontally to produce a unified plot. In this way it was shown that D/D₀ is a function of C^bd, where C is agarose concentration, with b = 1/3 and 1/2 for the cases in which the dextrans were mixed in before gelation and allowed to diffuse in afterwards, respectively, the plots being the same for a reference concentration of 0.7%. A value of b = 1/2 is that which would be expected if the molecular weight per unit length of the gel fibers were independent of concentration, and a value of 25 kg mol^?1 nm^?1 is calculated. Mobile concentrations of dextran within the gels relative to those in the surrounding solutions were found by determining the scattered intensity associated with the diffusing dextran molecules from the zero-time value of the autocorrelation function. All results and calculations are discussed in terms of current theories, and compared with earlier work on calcium alginate gels for which a molecular weight per unit length of gel fiber of 0.59 kg mol^?1 nm^?1 was calculated. The nature of the spectral broadening of the light scattered from agarose gels in the absence of dextran is described.     

New hydrogels based on the interpenetration of physical gels of agarose and chemical gels of polyacrylamide

In this paper we report a novel method for preparing interpenetrating polymer hydrogels of agarose and polyacrylamide (PAAm) in three steps. The procedure consists in (i) formation of physical hydrogels of agarose, (ii) diffusion of acrylamide, N,N′-methylene-bis-acrylamide and potassium persulfate (the initiator) from aqueous solutions inside the gel of agarose, and (iii) cross-linking copolymerization reaction of the aforementioned reactants to produce PAAm chemical gels interpenetrated with the agarose physical gels. Viscoelasticity measurements and thermal analysis have been performed in order to follow the kinetics of copolymerization. The viscoelastic, swelling and thermal properties of the resulting hydrogels confirm the formation of an interpenetrated system. Further evidence of interpenetration is obtained from inspection with atomic force microscopy. The improvement of the agarose and PAAm gel properties in the resulting interpenetrated hydrogel is analyzed in view of the results.     

Enhancing the sensitivity of DNA detection and recovery from agarose gels

By inserting nitrocellulose strips into agarose gels alongside the electrophoresed lanes and passing an electric current perpendicularly in the direction of the strips, highly efficient transfer of DNA bands onto the membrane in the form of concentrated dots is achieved. DNA detection limits by this technique are enhanced, at least three times as visualized by ethidium bromide fluorescence and at least twice more by radiolabeling.     

Tuning the size of silver deposits by templated electrodeposition using agarose gels

Tuning the size of electrochemically deposited silver crystals is possible by using template layers of agarose gels of certain concentrations on platinum electrodes. The size of the silver crystals can be controlled in the range of 100 to 400 nm by choosing the appropriate agarose concentration. The obtained crystal sizes match very well with the size of the pores that have been reported in literature for the used agarose concentrations. This is also a good proof of the correctness of the earlier pore-size estimations applying other techniques.     

A method for recovery of native, clonally-restricted immunoglobulins from agarose gels

Multiple low level, clonally-restricted, immunoglobulins (Ig) are commonly encountered on routine serum protein electrophoresis by clinical laboratories using high resolution zone electrophoresis on agarose. We sought a method for recovering the clonally-restricted Ig, in native configuration, from clinical laboratory gels as a first step in the investigation of its clinical significance. We found that a two-stage electrophoretic procedure gave consistently good recoveries. After routine agarose gel electrophoresis, portions of the electropherogram, containing clonally-restricted Ig, were excised and subjected to flatbed isoelectric focusing in agarose to enhance separation of the individual antibody clonotypes. Multiple slabs, containing the same clonally-restricted Ig, could be cut from adjacent tracks (i.e., tracks loaded with the same specimen) on the zone electropherogram and applied to a single track on the focusing gel to improve separation and increase yields. The focused gels were cut to isolate slabs containing individual clonotypes. These slabs were washed to remove carrier ampholytes and held at -20 degrees C overnight. Ig was extracted from the thawed gels, with 61-68% recovery, by ultracentrifugation following physical disruption of the gel. Antigen binding activity of the recovered Ig was verified by rate nephelometry. Clonally-restricted antibodies were successfully isolated from an immune animal serum by this procedure and biotinylated for use as probes on Western blots.     

Resolution of a paradox in the electrophoresis of DNA in agarose gels

A paradox was observed in a previous study of the electrophoresis of linear DNA fragments in agarose gels (D. L. Holmes and N. C. Stellwagen, Electrophoresis 1990, 11, 5-15). The pore size of the agarose matrix was more accurately determined if the root-mean-square radius of gyration was used to measure DNA macromolecular size. However, the Ogston equations were obeyed and other gel parameters such as the apparent fiber radius and fiber volume appeared to be better described if the geometric mean radius was used to measure DNA size. This paradox can be resolved if relative mobilities (with respect to the smallest DNA molecule in the data set) are used to construct the Ferguson plots, instead of absolute mobilities. Using relative mobilities and the root-mean-square radius of gyration, the Ogston equations are obeyed and the pore size of the matrix is consistent with values determined by other methods.     

Effects of concentration on the partitioning of macromolecule mixtures in agarose gels

To test the effects of solute concentration on the equilibrium partitioning of single macromolecules and macromolecule mixtures between bulk solutions and gels, the partition coefficient in agarose was measured for BSA and for four narrow fractions of Ficoll with Stokes radii of 30-59 A. Solutions of each test macromolecule were equilibrated with a known volume of gel, final liquid concentrations measured, and partition coefficients (gel concentration divided by bulk concentration) calculated by applying a material balance. The partition coefficient of each macromolecule was measured in 4 and 6% gels under dilute conditions and with BSA present at initial concentrations up to 13.5 g/dl. As expected, the partition coefficients decreased with increasing agarose concentration and with increasing macromolecular size. Moreover, increasing the BSA concentration increased the partition coefficient of BSA itself and that of all four Ficolls. This effect was most pronounced for the largest test solutes. Measurements at two ionic strengths confirmed that electrostatic interactions were negligible under the conditions used. The experimental results were compared with predictions from a previously developed excluded volume theory for the partitioning of mixtures of rigid, spheroidal macromolecules in fibrous media. Agarose was represented as a randomly oriented array of cylindrical fibers, BSA as a prolate spheroid, and Ficoll as a sphere. The quantitative agreement between the model predictions and the data was generally quite good, indicating that steric interactions among solute molecules and between solute molecules and gel fibers could explain the partitioning results. The theory is simple enough computationally to be applied to a variety of processes that are influenced by the equilibrium partitioning of macromolecules.     

New hydrogels from interpenetrated physical gels of agarose and chemical gels of polyacrylamide: Effect of relative concentration and crosslinking degree on the viscoelastic and thermal properties

In this article, we report on the viscoelastic and thermal properties of agarose–polyacrylamide (PAAm) interpenetrating polymer hydrogels (IPHs) and semi‐IPHs as a function of agarose concentration and PAAm crosslinking degree. The results demonstrated that the agarose is able to gel in the presence of crosslinked and linear IPHs. In addition, the reticulation of PAAm in the presence of agarose is confirmed for the case of IPHs giving rise to systems with dimensional stability at high temperatures. The formation of a fully IPH was ascertained at low agarose concentrations. A study of the morphology and nanoscale elasticity of the different systems has been carried out with atomic force microscopy/ultrasonic force microscopy (UFM). UFM data provide further evidence of interpenetration, allowing us to visualize—if present—phase‐separated domains with nanoscale resolution for the various crosslinking degrees and PAAm and agarose concentrations used during the formation of the IPHs. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2010