Gelation of amylose

A range of physical techniques, including light-scattering, turbidity measurements, viscometry, dilatometry, rheological measurements, and X-ray diffraction, has been used to study the gelation of amylose. Gels form on cooling entangled amylose solutions and occur as a result of a phase separation which produces a three-dimensional polymer network. Crystallisation, as detected by X-ray diffraction, was observed to be a slower process originating in the polymer-rich phase.     

Recycling agarose

The cost of agarose for DNA gel electrophoresis can be significant in largescale projects. The International Potato Center (CIP) laboratory in Lima-Perú reuses agarose to save money. Due to limited financial resources for research, not uncommon in Latin American laboratories, this practice satisfies a need to control expenses. Recycled agarose can be used for RAPD analysis, or other applications in which no further manipulation of the DNA is necessary. Here we describe an improved CIP method where large amounts of agarose are ultimately equilibrated in water and dried to a powder similar to the original agarose.     

The agarose double helix and its function in agarose gel structure

Agarose and eight different derivatives carrying O-methyl, O-sulphate, O-hydroxyethyl or O-carboxyethylidene substituents in various positions were studied by optical rotation, X-ray diffraction and computerised molecular model building methods. All samples showed essentially the same order-disorder transition during gel-sol interconversion. In addition, all the samples that could be made into oriented films or fibres gave X-ray diffraction diagrams corresponding to a common molecular structure. A double helix model for this structure is proposed that has the 0.95 nm axial periodicity observed and a calculated cylindrically averaged Fourier transform in good agreement with the observed (continuous) layer line intensities. Each chain in the double helix forms a lefthanded 3-fold helix of pitch 1.90 nm and is translated axially relative to its partner by exactly half this distance. This model accounts for the sign and magnitude of the optical rotation shift that accompanies the sol-gel transitions and is sterically accessible to each of the various substituted forms. The relationship between agarose gel properties and the double helix is discussed and the structure compared with i-carrageenan.     

New x-ray diffraction results from agarose: Extended single helix structures and implications for gelation mechanism

A new series of x-ray fiber diffraction patterns is reported from agarose films dried at temperatures close to 100°C from water or dimethylacetamide solutions, cooled to room temperature, stretched above 40°C, and finally x-rayed at room temperature. This procedure gives x-ray patterns showing highly crystalline forms of agarose with projected axial advances (h) per repeating disaccharide in the range of 0.888–0.973 nm, and favoring extended and single agarose chains. Stretching the films below 40°C yields an oriented but fairly diffuse x-ray pattern, similar to that reported previously for agarose, and that has been interpreted in terms of a model with two semicontracted agarose chains, with a value of h = 0.634 nm, draping around each other to form a double helix. The new data requires that double-helix to single-chain transitions be considered in condensed films as well as in solution. Alternatively, two populations of double-helix and single-helix conformations may coexist in the same film, or the original case for the double-helix model may be flawed, perhaps through misinterpretation of the diffuse x-ray pattern. The new results have prompted a critical discussion of evidence for the double-helix model and to indicate that there is potential to improve the data experimentally with a view to gaining a clearer insight into the molecular mechanisms involved in gelation of agarose.     

A further fractionation of agarose

Hydrobiologia - Commercial agarose can be separated into two components by fractional precipitation using alcohols or glycols. The less soluble component has a much higher gel strength and lower...     

Ultrastructure of beaded agarose.

Beaded agarose was dehydrated and embedded in Epon by a procedure that preserves the size, shape and, most likely, the native ultrastructure of the beads. Thin sections of the embedded beads reveal under the electron microscope a network sponge-like structure, uniform throughout the bead. The matrix skeleton is fairly rigid, though it occupies only a small percentage of the bead volume. This skeleton is composed of thin filaments (~20 Å in diameter) bundled in a side-by-side assembly. The pores or channels between the filament bundles vary in shape and diameter (up to 0.3 μm). This structure accounts for some of the known physicochemical properties of beaded agarose.     

Gelation behaviors of schizophyllan-sorbitol aqueous solutions

On addition of D-sorbitol, schizophyllan (SPG) aqueous solution forms a thermoreversible gel upon cooling. The gelation process is characterized by rheology, differential scanning calorimetry (DSC), and optical rotation measurement (ORD). It is found that the Winter-Chambon criterion works well in determining the critical gelation point of the present system, although the criterion has been scarcely applicable to systems that show weak-gel properties even before gelation. Moreover, ORD and DSC results indicate that a disordered to ordered conformational change accompanies the gelation process, which is attributed to the transition from SPG triple helix II to I. The gelation temperature of SPG-sorbitol aqueous solution is almost independent of SPG concentration in the examined concentration range and is slightly decreased by lowering SPG molecular weight, while greatly influenced by sorbitol content. The gelation is considered to be induced by the transition from SPG triple helix II to I, which leads to a three-dimensional network constituted by the extremely entangled and stiff SPG triple helices I. Furthermore, it is proved that neither junction zone nor aggregation of SPG triple helices is involved in the SPG-sorbitol gels. The SPG-sorbitol gel is structurally like a solution that is unable to flow within a timescale of usual observation.     

Purification of DNA from agarose gels

Summary We describe a rapid and easily reproducible modification of the freeze-squeeze method of separating DNA from agarose gels. Our method involves slicing out the agarose gel portion which contains the DNA of interest, freezing this gel slice at –20°C, then centrifuging the frozen slice in a filtration unit which contains a cellulose acetate filter. The agarose is retained on the filter and the filtrate contains the DNA. DNA purified in this manner could be completely digested with restriction endonucleases and completely ligated with DNA ligase, without further purification. The percentages of recovery for various sizes of linear and plasmid double-stranded DNA ranged from 57 to 69%. The procedure takes less than 30 minutes to perform.     

Studies on the cationization of agarose

Cationized agaroses with different degrees of substitution (0.04–0.77) were synthesized, employing 3-chloro-2-hydroxypropyltrimethylammonium chloride (CHPTAC). The influence of different reaction parameters on the substitution degree and molecular weight was evaluated. The investigated parameters were concentration of reagents, temperature, time, and addition of NaBH₄. The products were characterized by means of scanning electronic microscopy, infrared spectroscopy, viscosimetry, and NMR spectroscopy. Methanolysis products were studied by electrospray ionization mass spectrometry. The higher the concentration of CHPTAC employed, a higher degree of substitution was obtained, if the optimum concentration of NaOH in each case was employed. Insufficient quantities of NaOH reduced epoxide formation and the reacting alkoxides of the polysaccharide, whereas an excess of NaOH favored degradation of the epoxide and decrease in the molecular weight of the product. A reaction time of 2 h was sufficient to obtain products with the maximum degree of substitution for each case. The addition of NaBH₄ gave products with a slightly higher molecular weight, but the extra cost involved should not justify its use for large-scale application.     

The Mechanism of Gelation of Konjac Mannan

The sol of konjac mannan (KM) was gelatinized with an alkali such as sodium carbonate. The turbidity and the viscosity of sol, the infrared spectra of KM, and the consumption of alkali by KM in the course of gelation were measured. Then, experiments were undertaken in order to elucidate the major role of alkalies in gelation and the mechanism of gel-formation. It was presumed that the alkalies eliminate a moiety containing C=O group (probably an organic acid) from KM, and then the molecules of KM which lost the moiety crystallize in part through a linkage such as hydrogen bonding, and a network structure is formed.     

Electric birefringence of dilute agarose solutions

The technique of transient electric birefringence was used to investigate the orientation of agarose solutions in pulsed electric fields. If the agarose was dissolved in deionized water, the sign of the birefringence was positive when the electric field was small, indicating that the agarose molecules were orienting parallel to the electric field lines. The decay of the birefringence was rapid, consistent with the orientation of individual agarose helices. The amplitude of the birefringence, but not the birefringence decay times, increased as the agarose solution aged, suggesting that the helices formed slowly from the sol state. Increasing the amplitude or duration of the pulsed electric field caused additional negative, and then positive, birefringence signals to appear, characterized by much slower rise and decay times, consistent with the formation of aggregates. The slowest decay times ranged from 7.5-9.0 s, suggesting that the aggregates were several microns in size. When agarose was dissolved in dilute Tris buffer instead of deionized water, the fast positive birefringence signal was not observed, suggesting that individual helices were not present in solutions containing dilute buffer.     

Electron microscopy of beaded agarose gels

Electron microscopy has been carried out on sections of beaded agarose with a wide range of thicknesses, and the results have been analyzed by means of stereological theory using computer graphics. The results agree with a randomly orientated system in which, for 4% gels, the mean molecular weight per unit length of the fiber system is 110 kg mol^?1 nm^?1, and the number average interjunction length is 37 nm, with an asymmetrical distribution resembling a Maxwell-Boltzmann distribution. The spatial distribution of the structure is not uniformly random and there seem to be mi microvoids.     

Preparative isoelectric focusing in agarose

The use of agarose gels as supporting media for flat-bed preparative isoelectric focusing was applied to the fractionation of serum proteins in the pH range 3.5–6, and red cell hemolysates in the pH range 3–8. The agarose gels are easy to prepare, give linear pH gradients, and do not appear to produce molecular sieving effects. Up to 1 g serum proteins can be loaded on the gels, with recoveries between 68 and 82%. Nucleoside phosphorylase from red cell lysates was recovered with 76% yield, indicating that no appreciable denaturation of this enzyme had occurred. Preparative isoelectric focusing in agarose gels provides a useful alternative to existing techniques of preparative isoelectric focusing in sucrose gradients or granulated gels.     

Immobilization of aspartate aminotransferase on agarose

Various methods for immobilization of aspartate aminotransferase (AspAT; from cytosolic fraction of pig heart) on agarose were tested. Aldehyde-, thiol-, and CNBr-activated agaroses were studied in detail. The capacity of the aldehyde support to firmly bind protein was less than 0.2 mg/ml, whereas the apparent remaining specific activity of the bound AspAT was high (50-63% of soluble AspAT). The maximum capacity of SH-agarose to bind enzymatic protein was 3 mg/ml; the apparent remaining activity was 30-40%, and the specific activity determined by Vmax was 51%. Chemical coupling on to thiol-agarose did not denature the enzyme, as 93% of protein and 83% of the activity were recovered after release of the enzyme from the support. Enzyme protein was quantitatively bound to CNBr-activated agarose (up to 10 mg/ml of the gel). The apparent specific activities were 27-35%, while the value calculated from Vmax was 46%. Active site-protecting agents within the CNBr-coupling were tested. Bromphenol blue increased the apparent specific activity to 60% and Vmax to 80% at 3-fold molar concentration at the active sites. Kinetic constants for immobilized preparations were determined.     

Agar and agarose biotechnological applications

Agar, a phycocolloid obtained commercially from species of Gelidium and Gracilaria, has been known for several centuries; its earliest industrial application was in the preparation of solid microbiological media. The numerous techniques available for the purification of agar affect the characteristics of bacterial-grade agar. The availability of agarose, that fraction of agar with the lowest possible charge, has enhanced the utilzation of this phycocolloid. The process of gelation of agarose is discussed and the applications of agarose gels in different types of chromatography are summarized. Agarose has many and diverse important applications in biotechnology. These uses, and newly-developed ones, can be expected to increase the demands for high-quality agarose in the rapidly expanding field of biotechnology.