An Efficient, Recyclable, and Stable Immobilized Biocatalyst Based on Bioinspired Microcapsules-in-Hydrogel Scaffolds

Design and preparation of high-performance immobilized biocatalysts with exquisite structures and elucidation of their profound structure-performance relationship are highly desired for green and sustainable biotransformation processes. Learning from nature has been recognized as a shortcut to achieve such an impressive goal. Loose connective tissue, which is composed of hierarchically organized cells by extracellular matrix (ECM) and is recognized as an efficient catalytic system to ensure the ordered proceeding of metabolism, may offer an ideal prototype for preparing immobilized biocatalysts with high catalytic activity, recyclability, and stability. Inspired by the hierarchical structure of loose connective tissue, we prepared an immobilized biocatalyst enabled by microcapsules-in-hydrogel (MCH) scaffolds via biomimetic mineralization in agarose hydrogel. In brief, the in situ synthesized hybrid microcapsules encapsulated with glucose oxidase (GOD) are hierarchically organized by the fibrous framework of agarose hydrogel, where the fibers are intercalated into the capsule wall. The as-prepared immobilized biocatalyst shows structure-dependent catalytic performance. The porous hydrogel permits free diffusion of glucose molecules (diffusion coefficient: ∼6 × 10(-6) cm(2) s(-1), close to that in water) and retains the enzyme activity as much as possible after immobilization (initial reaction rate: 1.5 × 10(-2) mM min(-1)). The monolithic macroscale of agarose hydrogel facilitates the easy recycling of the immobilized biocatalyst (only by using tweezers), which contributes to the nonactivity decline during the recycling test. The fiber-intercalating structure elevates the mechanical stability of the in situ synthesized hybrid microcapsules, which inhibits the leaching and enhances the stability of the encapsulated GOD, achieving immobilization efficiency of ∼95%. This study will, therefore, provide a generic method for the hierarchical organization of (bio)active materials and the rational design of novel (bio)catalysts.

Immersive polymer assembly on immobilized particles for automated capsule preparation

We report a versatile approach for polymer capsule preparation using immobilized particles, which are immersed into polymer solutions either manually or by using an automated robotic dipping machine. This technique produces polyelectrolyte capsules with improved retention over conventionally prepared capsules. Additionally, responsive hydrogel capsules of different diameter can be prepared simultaneously.

Recent advances in electrophoretic techniques for the characterization of protein biomolecules: a poker of aces

The four classical modes of electrophoresis of protein molecules (sodium dodecyl sulphate electrophoresis, SDS-PAGE, isoelectric focusing, IEF, and immobilized pH gradients, IPGs, two-dimensional maps, 2D, and capillary electrophoresis, CE) are here reviewed, with special emphasis on recent innovations. Thus, in the case of SDS-PAGE, a novel method, consisting in focusing SDS-protein micelles against a gradient of cationic charges grafted onto a polyacrylamide gel is presented. In the case of IEF, the recent decoding of the structure, polydispersity, molecular mass distribution and buffering properties of the soluble carrier ampholyte buffers are here discussed. In regard to two dimensional mapping, recent instrumentation for performing 2D maps in horizontal, large gel slabs (up to 30 cm × 40 cm) and in a radial format for the SDS dimension is here evaluated. Finally, in the case of CE, three major applications are presented: a thorough study of capillary IEF and of all experimental variables, a method of importance in screening of rDNA products; the possibility of running proteins and peptide separations in very acidic, amphoteric, isoelectric buffers in absence of any capillary coating; finally, the possibility of producing a facile, user friendly, covalent coating of the wall silanols via bonding of quaternarized piperazines endowed with an iodinated tail. In acidic, volatile buffers, such protein/peptide runs can be directly interfaced with mass spectrometry instrumentation.

Gel electrophoresis of gold-DNA nanoconjugates

Gold-DNA conjugates were investigated in detail by a comprehensive gel electrophoresis study based on 1200 gels. A controlled number of single-stranded DNA of different length was attached specifically via thiol-Au bonds to phosphine-stabilized colloidal gold nanoparticles. Alternatively, the surface of the gold particles was saturated with single stranded DNA of different length either specifically via thiol-Au bonds or by nonspecific adsorption. From the experimentally determined electrophoretic mobilities, estimates for the effective diameters of the gold-DNA conjugates were derived by applying two different data treatment approaches. The first method is based on making a calibration curve for the relation between effective diameters and mobilities with gold nanoparticles of known diameter. The second method is based on Ferguson analysis which uses gold nanoparticles of known diameter as reference database. Our study shows that effective diameters derived from gel electrophoresis measurements are affected with a high error bar as the determined values strongly depend on the method of evaluation, though relative changes in size upon binding of molecules can be detected with high precision. Furthermore, in this study, the specific attachment of DNA via gold-thiol bonds to Au nanoparticles is compared to nonspecific adsorption of DNA. Also, the maximum number of DNA molecules that can be bound per particle was determined.

Stacking of unlabeled sodium dodecyl sulfate-proteins within a fluorimetrically detected moving boundary, electroelution and mass spectrometric identification

The previously reported fluorimetric detection of sodium dodecyl sulfate (SDS)-protein in the presence of cascade blue in agarose gel electrophoresis using barbital buffer was found to be equally feasible in the absence of the fluorescent marker and using Tris-Tricinate buffer, provided that SDS was loaded with the sample but not contained in the catholyte. That fluorescent detection is thought to be due to the formation of a moving boundary between leading SDS and trailing barbital, or Tricinate buffer. This hypothesis is supported by the following evidence: (i) The fluorometrically detected band disappears with addition of SDS to the catholyte; (ii) band area is proportional to protein and/or SDS load; (iii) mobility of SDS-proteins differing in mass is the same at agarose concentrations up to 3%; (iv) lowering of protein mobility by increase in gel concentration and/or increase in the size of the SDS-protein leads to band disappearance. Fluorescent detection of the band is like to be nonspecific and due to the light scattering properties of a stack comprising moving boundaries of any analytes with net mobilities intermediate between SDS (or micellar SDS) and the trailing buffer constituent at their regulated very high concentrations. The steady-state stack of SDS-proteins in the size range of 14.4-45.0 kDa, and the transient stack of an SDS-protein of 66.2 kDa have lent themselves to electroelution and characterization by mass of the proteins after removal of SDS and buffer exchange using matrix assisted laser desorption/ionization-time of flight (MALDI-TOF)-mass spectrometry. The possibility to form a stack of protein between leading SDS and trailing buffer anions under conditions of weak molecular sieving (open-pore gel and small-sized protein) contributes to the understanding of moving boundaries in gel electrophoresis, but in view of the narrowly defined conditions, under which this stack forms, is of limited practical significance for the gel electrophoresis of SDS-proteins.

Ultrathin-layer sodium dodecyl sulfate gel electrophoresis of proteins: effects of gel composition and temperature on the separation of sodium dodecyl sulfate-protein complexes

This paper discusses the effects of gel composition and separation temperature on the migration properties of fluorescein-5-isothiocyanate-labeled protein molecular mass markers (ranging from 20 100 to 205 000 Da) in automated ultrathin-layer sodium dodecyl sulfate (SDS) gel electrophoresis. The separation mechanism with the agarose and composite agarose - linear polyacrylamide, agarose - hydroxyethyl cellulose, and agarose - polyethylene oxide matrices were all found to comply with the Ogston sieving model in the molecular mass range of the protein molecules investigated. Our temperature studies revealed that electrophoretic separation of SDS protein complexes is an activated process and, in pure agarose and in composite agarose hydroxyethyl cellulose and agarose - polyethylene oxide matrices that the separation requires increasing activation energy as a function of the molecular mass of the separated proteins. On the other hand, when linear polyacrylamide was used as composite additive, the activation energy demand of the separation decreased with increasing solute molecular mass. The sensitivity of the laser-induced fluorescent detection of the automated ultrathin-layer electrophoresis system was evaluated by injecting a series of dilutions of the markers and was found to be less than 2.5 ng/band for the fluorophore-labeled protein.

Electrophoresis of proteins in semidilute polyethylene glycol solutions: mechanism of retardation

The retardation of proteins in the M(r) range of 15-500 kDa in capillary electrophoresis conducted in semidilute solutions of the polymer polyethylene glycol (M(r) range 0.2-8.0 X 10(6)), was measured. The purpose was to test the predictions of the scaling theory with regard to the relation of retardation to (a) the M(r) of the polymer, (b) the concentration of the polymer, and (c) the radius of the protein particles. These predictions derive from a mechanism that relates retardation to the screening length of the polymer solution, viewed as the average distance between the entanglement points of polymer chains. For the molecular weight range from 60 to 500 kDa of (near) spherical proteins, the retardation was found to be related to polymer concentration c as mu/mu(0) = exp(-Ac0.69) where mu/mu(0) is the retardation expressed as the ratio between the mobility in polymer solution and that in free solution. The value of the exponent of 0.69 is in close agreement with the value of 0.75 predicted by the scaling theory. Parameter A was found (a) to scale as the 0.04th power of M(r) (polymer), approximating the predicted value of 0; and (b) to be proportional to particle radius as predicted. All measured values of retardation were independent of electric field strength in the range of 37-370 V/cm. Thus, experimental findings are consistent with the mechanism relating electrophoretic retardation to the screening length of the polymer network in the specified molecular weight range of proteins. Under the same conditions, log(mu/mu(0)) of proteins with M(r)'s less than 60 kDa (a) scales as the -0.06th power of M(r) (polymer), and (b) is proportional to polymer concentration, suggesting a retardation mechanism that is not related to the screening length.

Reproducibility of mobility in gel electrophoresis

The quantitative exploitation of gel electrophoresis to yield molecular and gel fiber properties rests on the assumption that mobility is characteristic of the macromolecule migrating as a band and is a physical constant for any system defined by pH, ionic strength and temperature. This assumption has not been tested intra-experimentally in previous literature. With the commercial introduction of automated gel electrophoresis apparatus, the collection of multiple mobility data during a single run without additional expense of labor has made it possible to test the assumption. As a start, we undertook that test for three proteins and their sodium dodecyl sulfate (SDS) derivatives, in agarose and polyacrylamide gel electrophoresis, various field strengths, continuous and discontinuous buffers, as well as intra- and interexperimentally. It was found that in agarose gel electrophoresis conducted in a single buffer, the standard deviation of mobility over a wide concentration range ranges intra-experimentally from 0.2 to 1.3% for two globular proteins and 1.4 to 5.3% for the same proteins derivatized with SDS. Interexperimentally, it was 3% in the single case tested to date. The standard deviation in polyacrylamide appears to be higher, varies in inverse relation to the mobility value, i.e. increases with gel concentration in the range of 11 to 19%T, and varies substantially between the two SDS-proteins investigated. Mobility in a discontinuous buffer system decreases continuously due to the decreasing leading phase/trailing phase ratio along the migration path. The decrease is sharpest in the "nonrestrictive" stacking gel.

On the separation mechanism of capillary sodium dodecyl sulfate-gel electrophoresis of proteins

Polyethylene oxide-mediated capillary sodium dodecyl sulfate-electrophoresis is a recently established, high-resolution separation method for fast purity check and molecular mass assessment of protein molecules. The effects of the sieving polymer chain length and concentration on the separation mechanism of sodium dodecyl sulfate-protein complexes were examined. The studies aimed to clarify whether the separation can be described by either the Ogston sieving theory, or the reptation or reptation-with-stretching theory. Polyethylene oxides with molecular masses of 100,000, 300,000 and 900,000 Da were used as separation matrices at various concentrations ranging from 1-4%, 0.5-2% and 0.25-1%, respectively. The separation phenomena was examined using a standard protein test mixture containing six proteins in the molecular mass range of 14,200-97,400 Da. A possible separation mechanism of reptation with stretching is suggested, where separation performance was improved with increasing sieving polymer chain lengths and/or concentration.

A transient entanglement coupling mechanism for DNA separation by capillary electrophoresis in ultradilute polymer solutions

Using capillary electrophoresis, large DNA molecules (2.0-23.1 kbp) may be rapidly separated in ultradilute polymer solutions (< 0.002% w/w) under a high-voltage, steady field (265 V/cm). At this polymer concentration, the separation mechanism appears to be significantly different from that postulated to occur in crosslinked gels. Based on experimental results obtained with DNA restriction fragments and with negatively charged latex microspheres, we conclude that the Ogston and reptation models typically used to describe gel electrophoresis are not appropriate for DNA separations in such dilute polymer solutions. Electrophoresis experiments employing solutions of both small and large hydroxyethyl cellulose polymers highlight the importance of polymer length and concentration for the optimum resolution of DNA fragments varying in size from 72 bp to 23.1 kbp. A transient entanglement coupling mechanism for DNA separation in dilute polymer solutions is developed, which suggests that there is no a priori upper size limit to DNA that can be separated by capillary electrophoresis in a constant field.

How far have we progressed toward automated electrophoresis in sieving media of the twenty-first century?

The automation of electrophoresis in polymeric sieving media requires (i) an objective definition of the conditions (the polymer, its concentration, solvent, buffer, pH, ionic strength, temperature) under which a particular separation proceeds most effectively; (ii) apparatus capable of zone detection, acquisition by computer, evaluation (migration distance, zone width and area) and a print-out of the number of components, their size and net charge, and the polymer conditions under which each component separates most effectively from its two neighboring zones. Both of these prerequisites of automation have been met to a first approximation at this time and, after further maturation, assembly and streamlining should be able to fill the need of the coming century for a more efficient, nonarbitrary and cost-effective mode of macromolecular and cellular particle separation. (i) The realization of the qualitative equivalence of polymer solutions and gels has greatly increased our options in the choice of sieving media. That choice can be made objectively by correlating separation efficiency (S), particle size (R) and intrinsic viscosity (eta o) of the polymer. (S) is a function of the slope, KR(R), of the Ferguson plot [log(mobility) vs. polymer concentration], or with nonlinear plots (DNA, agarose) KR(R,T). KR is at present most easily derived from transverse pore gradient gels or by conducting capillary zone electrophoresis (CZE) at multiple polymer concentrations. Pore gradient CZE appears promising. CZE also defines the free mobility unequivocally. Computer programs exist to generate KR from migration distances (times), and optimal S and polymer concentration for a particular R from KR.(ABSTRACT TRUNCATED AT 250 WORDS)

DNA shape and separation efficiency in polymer media: a computerized method based on electrophoretic mobility data

The computer program ELPHOFIT for evaluation of the nonlinear plots of log-(mobility) vs. polymer concentration (Ferguson plots) in terms of molecular and polymer properties has been extended to yield a measure of the molecular sieving capacity of the polymer medium. The usefulness of the extended program, version 2.2, was exemplified by the evaluation of DNA shape and separation efficiency in solutions and gels of agarose and polyacrylamide, using previous reports in the literature as a data base. That application of the extended program yields the following results:(i) The size of migrating DNA can be compared with an equivalent sphere having the same free mobility for a particular set of experimental conditions. The decrease in size of the equivalent sphere with polymer concentration previously demonstrated for agarose solutions applies to all of these polymer media; it reveals a steep, hyperbolic decline of that radius in uncrosslinked polyacrylamide solutions in contrast to the shallow decline in the other three media. (ii) The separation efficiency of polyacrylamide gels exceeds that of uncrosslinked polyacrylamide solutions; the separation efficiency of agarose solutions for DNA smaller than 1 kb in length is higher than that of polyacrylamide solutions. Program ELPHOFIT 2.2 is available on request from the first author.

Distinction between supercoiled and linear DNA in transverse agarose pore gradient gel electrophoresis

Four species of linear DNA and the first four members of a linking series, generated by treatment of plasmid DNA (PUC19, 2.7 kb) with mitochondrial topoisomerase I, were differentiated by transverse agarose pore gradient gel electrophoresis. The experimental curves of migration distance vs. agarose concentration (Ferguson curves) of supercoiled DNA exhibit a steeper trajectory than those of linear DNA of the same size range. As a consequence, the four supercoiled species exhibit an increase in apparent size (relative to linear DNA standards) with increasing agarose concentration. Both the crossing of the Ferguson curves with those of linear standards as well as the apparent size increase with agarose concentration can serve to detect supercoiled plasmid-sized DNA in mixtures with linear DNA.

Concave Ferguson plots of DNA fragments and convex Ferguson plots of bacteriophages: evaluation of molecular and fiber properties, using desktop computers

A desktop computer program evaluating physical properties of DNA and bacteriophages is presented. The analysis is based on data obtained from capillary and submarine-type agarose electrophoresis. Native molecular/particle properties and properties of the gel (or polymer) medium can be derived from electrophoresis at several gel concentrations. This is done conveniently by a computerized evaluation of the semi-logarithmic plot of mobility vs. gel concentration, designated the Ferguson plot. In application to most proteins, this plot is linear and computer programs exist to evaluate it. However, nonlinear Ferguson plots have assumed great importance in view of the fact that the plots are concave for DNA. Similarly, convex plots are important since they prevail in the electrophoresis of large particles in agarose. The computer program reported here is the first to (i) address concave Ferguson plots and (ii) allow for the evaluation of both cases using a desktop computer. Program ELPHOFIT version 2.0, a Macintosh application, is available upon request.

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.

Gel electrophoresis of polystyrene particles in glutaraldehyde crosslinked polyvinyl alcohol

Polystyrene sulfate and carboxylate particles (19-189 nm radius) were subjected to electrophoresis in glutaraldehyde crosslinked polyvinyl alcohol of molecular weight 25.000 and 650.000 Da at various concentrations. The degree of crosslinking is severely limited by the mechanical properties of the gels that deteriorate beyond a glutaraldehyde concentration which decreases with increasing polyvinyl alcohol chain length. The effective fiber radius of the short-chain and long-chain polymer fiber was 45 +/- 25 and 131 +/- 47 nm, respectively. Thus, these media do not significantly exceed the apparent fiber thickness of agarose, are more difficult to prepare--but are well-defined synthetic products rather than natural ones, and have the advantage of carrying no net charge and can therefore be expected to exhibit no electroendosmosis.

Free mobility determination by electrophoresis in polyacrylamide containing agarose at a nonrestrictive concentration

In the determination of the free mobility, related to the surface net charge, by quantitative gel electrophoresis, the previous arbitrary extrapolation of Ferguson plots from the lowest gel concentrations that give a mechanically stable gel to 0% T has recently been replaced by measurement of mobilities across that concentration range, using the addition of 0.5% agarose to polyacrylamide at the various low concentrations in application to a DNA fragment 155 bp in size (Orbán, L. et al., in preparation). The present study applies that approach to several proteins and DNA fragments smaller than 1300 bp, using 0.4% agarose in polyacrylamide gels of varying concentration. The intercepts of the plots with the mobility axis provide experimental data by which the free mobility in polyacrylamide gel electrophoresis can be estimated for molecules not significantly retarded in their migration at the agarose concentration admixed to polyacrylamide. Across the gel concentration range below 3% T, in the presence of agarose, the Ferguson plots of proteins and DNA fragments are convex. It was shown by mass spectrometry that this convex curvature of the plots in the mixed polymer is not significantly due to low polymerization efficiency in the concentration range of liquid polyacrylamide (below 3%T).

Information on DNA conformation derived from the Ferguson plot of DNA fragments of up to 9 kb in size, using polyacrylamide gel electrophoresis in a discontinuous buffer system

The Ferguson plot in polyacrylamide gel electrophoresis (PAGE)(15%CDATD, moving boundary electrophoresis buffer system operative at pH 8.9, 4 degrees C, 8 mA/cm2 of gel) of DNA fragments up to 9.4 kb in size was found to exhibit a linear segment at polyacrylamide concentrations starting at 3% T and undergoing a gradual transition into a concave segment at higher gel concentrations, confirming previous findings by Stellwagen. The larger the DNA, and the higher the gel concentration, the less extended the linear and the more extended the concave segment of the plot. The lowest % T of the linear range for DNA in polyacrylamide remains unknown since mobilities at nongelling concentrations below 3% T have not as yet been measured. As previously suggested, the transition from the linear to the concave segment corresponds to that from the randomly oriented DNA to the anisotropically stretched, "reptating" DNA. For a DNA of 9.4 kb in size, the end of the linear range of the Ferguson plot can be extended from 3.5 to 5% T when 15% DATD rather than 2.5% Bis is used to crosslink the polyacrylamide. Increasing the temperature of PAGE from 4 degrees C to 25 and 50 degrees C widens the linear segment progressively, indicating an increasingly random orientation with rising temperature. When current density is increased from 8 to 40 mA/cm2, the concave curvature of the Ferguson plot of DNA 1 to 9.4 kb in size decreases, suggesting a transition from a "reptating" to a randomly distributed molecule, due to increased Joule heat.(ABSTRACT TRUNCATED AT 250 WORDS)

Analysis of one-dimensional gels and two-dimensional Serwer-type gels on the basis of the extended Ogston model using personal computers

This report presents the stand-alone computer application ELPHOFIT, a software package for the analysis of gel electrophoretic data based on Ferguson plots. Either conventional one-dimensional gels or two-dimensional agarose gels (Serwer-type) can be evaluated. Special emphasis is on the latter gel type, which has been applied previously for the separation of DNA, intact viruses and polydisperse meningitis vaccines. ELPHOFIT is designed for Macintosh PCs and for the IBM XT, AT, PS/2 and compatibles. The program operates interactively with the user, who determines the course of evaluation. Data input is in the format of files providing values of gel electrophoretic migration distances or particle mobility (absolute or relative). Data processing involves a simultaneous least-square curve fitting algorithm (Newton-Gauss, Marquardt-Levenberg) which uses equations derived from the extended Ogston model. Functions are fit to the database by adjusting their variables, representing physical parameters of the gel and the electrophoresed particle. The program output consists of tables and graphics accompanied by an explanatory text providing the following information: (i) radius and free mobility of the electrophoresed particle, (ii) fiber radius, length and volume, mean or median pore radius of the gel, (iii) linear Ferguson plots, (iv) iso-free-mobility/iso-size nomogram for two-dimensional gels, (v) confidence ellipses, (vi) required parameters for image processing program GELFIT and (vii) goodness-of-fit and other statistical parameters, such as standard errors, dependency values, root-mean-square (RMS) error and determination coefficient. Other features of the program are (i) simulation of Serwer-type two-dimensional electrophoresis, (ii) standardization according to size, or size and free mobility, (iii) the conversion of particle radii to molecular (or particle) weight and vice versa, (iv) interconversion of DNA size specifications, i.e. the number of base pairs and the geometric mean radii, (v) computation of gel concentration for optimal resolution of two components, (vi) option to obtain a session record, (viii) option to establish a data output file containing the information of generated graphics (IBM only) and (ix) a text editing facility, e.g., for creating data files. Graphics (Macintosh version, PICT format) and text output files (both IBM and Macintosh versions, standard ASCII format) generated by ELPHOFIT are compatible with commercially available software.

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.

Computer-assisted evaluation of polydisperse two-dimensional gel patterns of polysaccharide-protein conjugate preparations with regard to size and net charge

Native Hemophilus influenzae polysaccharide-protein conjugate particles were analyzed by a two-dimensional agarose electrophoresis procedure. In view of their preparation by random chemical crosslinking, the conjugates necessarily exhibit a polydisperse two-dimensional gel pattern which varies depending on the conditions of the particular preparation. The polydisperse patterns were interpreted with regard to the size and surface net charge density of the conjugate on the basis of the extended Ogston model. Data processing was performed by a new program, designated ZWEIDI.DO, written in the language of M-LAB (modeling laboratory). The program computes particle and gel fiber specific parameters from the positions of standards and unknown(s) on the two-dimensional gel using a simultaneous linear least-square curve fitting routine. Based on these calculations, the program serves to compute a nomogram of iso-size and iso-free-mobility profiles. Superimposing these profiles on the gel patterns, the size and free mobility range of the polydisperse conjugate mixtures is obtained. Potentially, the procedure could serve as a tool for quality control in the production of conjugates as vaccines and for the physical characterization of polydisperse subcellular particles and vesicles.

The sieving of spheres during agarose gel electrophoresis: quantitation and modeling

By use of agarose gel electrophoresis, the sieving of spherical particles in agarose gels has been quantitated and modeled for spheres with a radius (R) between 13.3 and 149 nm. For quantitation, the electrophoretic mobility has been determined as a function of agarose percentage (A). Because a previously used model of sieving [D. Rodbard and A. Chrambach (1970) Proc. Natl. Acad. Sci. USA 65, 970-977] was found incompatible with some of these data, alternative models have been tested. By use of an underivatized agarose, two models, both based on the assumption of a single effective pore radius (PE) for each A, were found to yield PE values that were independent of R and that were in agreement with values of PE obtained independently (PE = 118 nm X A-0.74): sieving by altered hydrodynamics in a cylindrical tube of radius, PE, and sieving by steric exclusion from a circular hole of radius, PE. The same analysis applied to a 6.5% hydroxyethylated commercial agarose yielded a steeper PE vs A plot and also agreement of the above two models with the data. The PE vs A plot was significantly altered by both further hydroxyethylation and factors that cause variation in the electro-osmosis found in commercial agarose.

Program in BASIC for Ferguson plot analysis, using a personal computer: application to gel electrophoresis in a continuous buffer

A program in BASIC suitable for personal computers is described which is applicable to gel electrophoresis conducted in a single (continuous) buffer. The curve fitting is to a polynomial function, allowing for an objective selection of the most appropriate curve type and order--linear, convex or concave--in the particular application. Results do not differ significantly from previous programs for evaluation of linear Ferguson plots or of curve fitting to an exponential function for evaluating convex plots, executed on mainframe computers such as the DEC-10 (Digital) and IBM 370 computers. Thus, the program combines original versatility with, for the first time, the possibility for widespread application of Ferguson plot analysis on personal computers.

Ferguson plots based on absolute mobilities in polyacrylamide gel electrophoresis: dependence of linearity of polymerization conditions and application to the determination of free mobility

In contrast to Ferguson plots based on relative mobilities, Ferguson plots of proteins in polyacrylamide gel electrophoresis based on their absolute mobilities were found to be linear under unusual polymerization conditions which yield relatively wide gel fibers and a low total fiber length per unit weight, but not under previously and commonly used conditions. These linear Ferguson plots in gels of 1, 3 and 5% crosslinking intersect at a single gel concentration between 1 and 2% T (M-point). It is postulated that the measure of free mobility of the proteins is the M-point, and not the intercept of their Ferguson plots with the mobility axis as assumed previously. This postulate abolishes the well-known paradoxical interpretation of the increase with %C of the linearly extrapolated intercept of the Ferguson plot with the log(mobility) axis (designated Yo) in terms of free mobility. The postulate is also compatible with the interpretation of the points of intersection of the Ferguson plots of oligomeric series of proteins at finite gel concentrations (designated mu-points) as their common free mobilities.

Linear Ferguson plots of polystyrene sulfate size standards for the quantitative agarose gel electrophoresis of subcellular particles

Accurately standardized commercial polystyrene sulfate particles in agarose gel electrophoresis yield linear Ferguson plots at pH 7.4 over a gel concentration range up to 0.9% agarose which do not exhibit any significant sigmoidal curve elements, using either a discontinuous buffer system or a continuous buffer. Ferguson plots of these standard-sized particles were evaluated using alternatively a linear or convex model, by means of a newly developed set of programs (to be used in conjunction with program M-LAB) which (i) is sufficiently user-friendly to allow for quantitative agarose gel electrophoresis of subcellular-sized spherical particles based on their convex Ferguson plots with the same operational simplicity previously available for linear Ferguson plots only; (ii) simultaneously and interactively analyzes the Ferguson plots of all particles under consideration on the basis of an extended Ogston model.

Discontinuous buffer systems optimized for the agarose gel electrophoresis of subcellular particles

Discontinuous buffer systems operative between pH 5.7 and 7.4, 0 degrees C, were generated, which are characterized by more rapidly displaced moving boundaries than applied previously. These allow one to resolve subcellular particles relatively rapidly and at relatively low agarose gel concentrations. A commercial mixture of DNA restriction fragments pre-stained with ethidium bromide was found to be a suitable tracking dye for these boundaries.

Physical identification of a virus in a crude leaf extract by its Ferguson plot in agarose gel electrophoresis

Crude extracts of turnip crinkle virus upon agarose gel electrophoresis yield (i) virus patterns unperturbed by contaminants; (ii) plots of mobility vs. gel concentration (Ferguson plots) parallel with those of the purified virus. The parallelism suggests similarity in size and shape but a lower net charge for the crude virus. This result is obtained when gel electrophoresis is carried out either in a continuous buffer or in a discontinuous (moving boundary electrophoresis) buffer system. The latter mode has the substantial benefit of electrophoretic (auto-)concentration of dilute virus sample prior to resolution. Thus, the Ferguson plot analysis in a discontinuous buffer system of turnip crinkle virus can be viewed as a model procedure for the physical identification of other viruses contained in dilute extracts, feasible even in the absence of a prior knowledge as to the nature of, or isolation of, the virus.

Gel electrophoresis of intact subcellular particles

The review describes the application of gel electrophoresis to the characterization and separation of viruses, ribosomes, vesicles and other subcellular particles. The preparation of the sample, the choice of the buffer, the gel medium, the apparatus and the detection of the particle (staining and scanning) as well as the necessary theory are discussed. This includes the mathematical evaluation of experimental data on the basis of Ferguson plots using the extended Ogston theory. Simple methods and sophisticated computer simulation techniques are described and exemplified in application to the determination of particle size and charge, the pore size of the gel (unpublished data) and the two-dimensional agarose electrophoresis (unpublished). It is shown that the nature of the particle (e.g. spherical or rod-shaped, pliable or rigid texture) determines the shape of the non-linear Ferguson plot. In addition, the review gives a number of practical applications of gel electrophoresis, isoelectric focusing, titration curves and immuno-electrophoresis to subcellular particles. Pros and cons are evaluated. A comparison with other analytical procedures is made. The review is concluded by a futuristic outlook.

Agarose gel electrophoresis of bacteriophages and related particles

Viruses and related particles have been fractionated by electrophoresis through gels. For agarose gels, the radius at the exclusion limit for spheres varies from 1500 nm in a 0.04% gel to 3.6 nm in a 4.0% gel. Thus, the size of the gel's pores can be adjusted to sieve all known viruses. By measurement of electrophoretic mobility (mu) as a function of agarose concentration, the mu in the absence of a solid support (mu 0) can be determined for any particle. From the shape of a semilogarithmic plot of mu as a function of agarose percentage, a rod-shaped particle can be discriminated from a spherical particle. The sphere's radius can be determined from this plot with an accuracy of +/- 8%. Accuracy of +/- 1% has been more recently achieved using two-dimensional agarose gel electrophoresis. Though bacteriophages have been the primary object of study, the above techniques of agarose gel electrophoresis have also been applied to plant viruses and should be applicable to animal viruses. The mu 0 values measured for bacteriophages with and without their tail fibers suggest a mechanism of controlling attachment to a host. A related mechanism is proposed for the control of the virulence of animal viruses. Measurement of outer radius for different forms of the capsid of bacteriophage P22 reveals variability in outer radius too small to be detected by electron microscopy.

Computer simulation of the variable agarose fiber dimensions on the basis of mobility data derived from gel electrophoresis and using the Ogston theory

Agarose gel electrophoresis of viruses and proteins was evaluated for estimating fiber dynamics of agarose by computer simulation based on the extended Ogston theory. By introducing functions, in place of previously used constant parameters, into the equations derived from the Ogston theory it was demonstrated that the effective fiber properties are variable as a function of both gel concentration and the size of the particle passing through the gel. This variability accounts for the curvature of plots of log(mobility) vs gel concentration in agarose gel electrophoresis as well as for the apparent dichotomy between fiber properties obtained from the electrophoresis of either viruses or proteins. Specifically, computer simulation based on the electrophoretic mobility values of five viruses and seven proteins by use of an eight (gel-specific) parameter model yielded functions relating gel concentration and/or particle size with electrophoretic mobility of particles, the retardation coefficient, K'R, and effective fiber radius, length, and volume. The simulations give further insights into, as well as mathematical basis for, a number of previously made assumptions (such as variation of agarose fiber structure with gel concentration, variation of fiber volume with particle size, continuity of the K'R vs radius plot from 0 to 45 nm), thus demonstrating the continued usefulness of the Ogston model. The mathematical model provides the elements for an improved method for the determination of particle size, charge, and potentially shape by agarose gel electrophoresis, and can be regarded as the basis for future elaboration of a computer program for the routine determination of these parameters.