Parametric Finite Element Analysis of Physical Stimuli Resulting From Mechanical Stimulation of Tissue Engineered Cartilage

While mechanical stimulation of cells seeded within scaffolds is widely thought to be beneficial, the amount of benefit observed is highly variable between experimental systems. Although studies have investigated specific experimental loading protocols thought to be advantageous for cartilage growth, less is known about the physical stimuli (e.g., pressures, velocities, and local strains) cells experience during these experiments. This study used results of a literature survey, which looked for patterns in the efficacy of mechanical stimulation of chondrocyte seeded scaffolds, to inform the modeling of spatial patterns of physical stimuli present in mechanically stimulated constructs. The literature survey revealed a large variation in conditions used in mechanical loading studies, with a peak to peak strain of 10% (i.e., the maximum amount of deformation experienced by the scaffold) at 1 Hz on agarose scaffolds being the most frequently studied parameters and scaffold. This loading frequency was then used as the basis for simulation in the finite element analyses. 2D axisymmetric finite element models of 2×4 mm2 scaffolds with 360 modulus/permeability combinations were constructed using COMSOLMULTIPHYSICS software. A time dependent coupled pore pressure/effective stress analysis was used to model fluid/solid interactions in the scaffolds upon loading. Loading was simulated using an impermeable frictionless loader on the top boundary with fluid and solid displacement confined to the radial axis. As expected, all scaffold materials exhibited classic poro-elastic behavior having pressurized cores with low fluid flow and edges with high radial fluid velocities. Under the simulation parameters of this study, PEG scaffolds had the highest pressure and radial fluid velocity but also the lowest shear stress and radial strain. Chitosan and KLD-12 simulated scaffold materials had the lowest radial strains and fluid velocities, with collagen scaffolds having the lowest pressures. Parametric analysis showed maximum peak pressures within the scaffold to be more dependent on scaffold modulus than on permeability and velocities to depend on both scaffold properties similarly. The dependence of radial strain on permeability or modulus was more complex; maximum strains occurred at lower permeabilities and moduli, and the lowest strain occurred at the stiffest most permeable scaffold. Shear stresses within all scaffolds were negligible. These results give insight into the large variations in metabolic response seen in studies involving mechanical stimulation of cell-seeded constructs, where the same loading conditions produce very different results due to the differences in material properties.

Effect of the matrix on DNA electrophoretic mobility

DNA electrophoretic mobilities are highly dependent on the nature of the matrix in which the separation takes place. This review describes the effect of the matrix on DNA separations in agarose gels, polyacrylamide gels and solutions containing entangled linear polymers, correlating the electrophoretic mobilities with information obtained from other types of studies. DNA mobilities in various sieving media are determined by the interplay of three factors: the relative size of the DNA molecule with respect to the effective pore size of the matrix, the effect of the electric field on the matrix, and specific interactions of DNA with the matrix during electrophoresis.

Isolation of novel large and aggregating bacteriophages

Viruses are detected via either biological properties such as plaque formation or physical properties. The physical properties include appearance during microscopy and DNA sequence derived from community sequencing. The assumption is that these procedures will succeed for most, if not all, viruses. However, we have found that some bacteriophages are in a category of viruses that are not detected by any of these classical procedures. Given that the data already indicate viruses to be the "largest reservoir of unknown genetic diversity on earth," the implied expansion of this reservoir confirms the belief that the genome project has hardly begun. The first step is to fill gaps in our knowledge of the biological diversity of viruses, an enterprise that will also help to determine the ways in which (a) viruses have participated in evolution and ecology and (b) viruses can be made to participate in disease control and bioremediation. We present here the details of procedures that can be used to cultivate previously undetectable viruses that are either comparatively large or aggregation-prone.

Computer-assisted 2-D agarose electrophoresis ofHaemophilus influenzae type B meningitis vaccines and analysis of polydisperse particle populations in the size range of viruses: A review

When protein-polysaccharide conjugated vaccines were first developed for the immunization of small children against meningitis caused by infection with Haemophilus influenzae type b (Hib), the vaccine preparations varied in immunogenicity. Testing for immunogenicity was time-consuming and alternative analytical procedures for determining vaccine quality were unsatisfactory. For example, due to the very high molecular weight of the vaccine particles, immunogens could only be physically characterized as a fraction in the void volume of Sepharose gel filtration. In search of better analytical methods, a computer-assisted electrophoretic technique for analyzing such vaccines was developed in the period from 1983 to 1995. This new approach made it possible to analyze highly negatively charged particles as large as or larger than intact viruses. 2-D gel patterns were generated that varied depending on the conditions of the particular vaccine preparation and were therefore characteristic of each vaccine sample. Thus, vaccine particle populations with a continuous size variation over a wide range (polydisperse) could be characterized according to size and free mobility (related to particle surface net charge density). These advances are reviewed in this article, since the developed methods are still a promising tool for vaccine quality control and for predicting immunogen effectiveness in the production of vaccines. The technique is potentially beneficial for Hib immunogens and other high-molecular-mass vaccines. Additional biomedical applications for this nondenaturing electrophoretic technique are briefly discussed and detailed information about computational and mathematical procedures and theoretical aspects is provided in the Appendices.

Enhanced capacity for electrophoretic capture of plasmid DNA by agarase treatment of agarose gels

Agarase was used investigate the effect of increasing the number of polymer ends on the electrophoretic trapping of circular DNA in agarose gels. The electric field strength required to trap circular DNA was found to be the same in control and treated gels, indicating the treatment did not result in longer traps. Loading experiments indicated that treated gels had a significantly higher capacity for the open circular DNA. Electrophoretic mobility measurements using pulsed fields indicated a higher density of active traps for treated gels compared to controls. Linear dichroism experiments showed that impalement occurred by a fast and a slow process that had characteristic time constants in the one and tens of seconds ranges, respectively. The open circular DNA was more efficiently impaled in the treated gel compared to the control. The considerably higher efficiency of trapping indicated that agarase treatment increased the concentration of traps substantially.

Fluorescence microscopy of single viral capsids

To build a foundation for the single-molecule fluorescence microscopy of protein complexes, the present study achieved fluorescence microscopy of single, nucleic acid-free protein capsids of bacteriophage T7. The capsids were stained with Alexa 488 (green emission). Manipulation of the capsids' thermal motion was achieved in three dimensions. The procedure for manipulation included embedding the capsids in an agarose gel. The data indicate that the thermal motion of capsids is reduced by the sieving of the gel. The thermal motion can be reduced to any desired level. A semilogarithmic plot of an effective diffusion constant as a function of gel concentration is linear. Single, diffusing T7 capsids were also visualized in the presence of single DNA molecules that had been both stretched and immobilized by gel-embedding. The DNA molecules were stained with ethidium (orange emission). This study shows that single-molecule (protein and DNA) analysis is possible for both packaging of DNA in a bacteriophage capsid and other events of DNA metabolism. The major problem is the maintenance of biochemical activity.

Theory of DNA electrophoresis: a look at some current challenges

Although electrophoresis is one of the basic methods of the modern molecular biology laboratory, new ideas are being suggested at an accelerated rate, in large part because of the pressing demands of the biomedical community. Although we now have, at least for some methods, a fairly good theoretical understanding of the physical mechanisms that lead to the observed peak spacings, widths and shapes, this knowledge is often too qualitative to be used to guide further technical developments and improvements. In this article, we review some selected elements of the current state of our theoretical ignorance, focusing mostly on DNA electrophoresis, and we offer several suggestions for further theoretical investigations.

DNA and buffers: the hidden danger of complex formation

The free solution electrophoretic mobility of DNA differs significantly in different buffers, suggesting that DNA-buffer interactions are present in certain buffer systems. Here, capillary and gel electrophoresis data are combined to show that the Tris ions in Tris-acetate-EDTA (TAE) buffers are associated with the DNA helix to approximately the same extent as sodium ions. The borate ions in Tris-borate-EDTA (TBE) buffers interact with DNA to form highly charged DNA-borate complexes, which are stable both in free solution and in polyacrylamide gels. DNA-borate complexes are not observed in agarose gels, because of the competition of the agarose gel fibers for the borate residues. The resulting agarose-borate complexes increase the negative charge of the agarose gel fibers, leading to an increased electroendosmotic flow of the solvent in agarose-TBE gels. The combined results indicate that the buffers in which DNA is studied cannot automatically be assumed to be innocuous.

Free solution mobility of DNA molecules containing variable numbers of cationic phosphoramidate internucleoside linkages

The free solution electrophoretic mobility of an 118-base pair DNA fragment containing zero, three, six or nine cationic phosphoramidate internucleoside linkages has been measured by capillary electrophoresis. The electrophoretic mobility decreases with the increasing number of cationic phosphoramidate linkages, as expected because of the reduced negative charge on the DNA molecules. The decrease in mobility is approximately linear for DNA molecules containing three and six cationic phosphoramidate linkages, but begins to level off when nine cationic phosphoramidate linkages have been added. The mobility also varies somewhat depending on whether the modified phosphoramidate linkages are located at the 5'- or 3'-end of the DNA molecule.

An exactly solvable Ogston model of gel electrophoresis. V. Attractive gel-analyte interactions and their effects on the Ferguson plot

We examine the effect of attractive analyte-gel interactions within the framework of our recently developed lattice model of gel electrophoresis. We show that it is possible to take into account such interactions and still calculate exact mobilities for various analytes and gel structures. Our study then focuses on two main issues: (i) the effect of these interactions on the separation efficiency of the Ogston regime; and (ii) the presence of inflection points (changes of curvature) in Ferguson plots. We establish some general principles, and we describe the results for selected two- and three-dimensional model systems. Numerous practical problems, such as chiral separations and affinity electrophoresis, can be treated using this approach.

Advances in the separation of bacteriophages and related particles

Nondenaturing gel electrophoresis is used to both characterize multimolecular particles and determine the assembly pathways of these particles. Characterization of bacteriophage-related particles has yielded strategies for characterizing multimolecular particles in general. Previous studies have revealed means for using nondenaturing gel electrophoresis to determine both the effective radius and the average electrical surface charge density of any particle. The response of electrophoretic mobility to increasing the magnitude of the electrical field is used to detect rod-shaped particles. To increase the capacity of nondenaturing gel electrophoresis to characterize comparatively large particles, some current research is directed towards either determining the structure of gels used for electrophoresis or inducing steric trapping of particles in dead-end regions within the fibrous network that forms a gel. A trapping-dependent technique of pulsed-field gel electrophoresis is presented with which a DNA-protein complex can be made to electrophoretically migrate in a direction opposite to the direction of migration of protein-free DNA.

Electrophoretic analysis of the ribonucleoproteins of hepatitis delta virus

Replication of hepatitis delta virus (HDV) is dependent on delta antigen (deltaAg), an HDV-encoded protein, which binds to HDV RNA and is capable of multimerization. To characterize HDV-specific ribonucleoprotein complexes (RNP) we used electrophoresis into non-denaturing agarose gels followed by northern analysis, to detect HDV RNA, and immunoblot, to detect deltaAg. We studied RNP from three sources: (i) vRNP, disrupted virions obtained from infected woodchuck serum; (ii) sRNP, disrupted particles secreted from transfected cultured cells; and (iii) cRNP, isolated from cells in which HDV genome replication was occurring. sRNP were approximately 28% smaller than vRNP. Treatment of vRNP with aurin tricarboxylic acid disrupted both deltaAg-deltaAg and deltaAg-RNA interactions while vanadyl ribonucleosides released the RNA without causing detectable disruption of the multimeric deltaAg complex. cRNP were smaller and more heterogeneous than vRNP and sRNP, and probably contained host components. The application of these electrophoretic procedures, and especially the use of prior treatments with vanadyl ribonucleoside complexes have provided valuable information on the RNP of HDV, and we expect they should find applicability in RNP studies of other RNA viruses.

The formation of small-pore gels by an electrically charged agarose derivative

Previous studies have shown that, during the formation of an underivatized agarose gel, agarose molecules laterally aggregate to form thicker fibers called suprafibers; the suprafibers branch to form a gelled network. In the present study, electron microscopy of thin sections is used to investigate both the thickness and the spacing of the fibers of gels formed by agarose chemically derivatized with carboxymethyl (negatively charged) groups. For carboxymethyl agarose, electron microscopy reveals that gels cast in water consist of both fibers narrower and pores smaller than those observed for water-cast underivatized agarose gels at the same concentration. This result is confirmed by using the electrophoretic sieving of spheres to determine the radius (PE) of the effective pore of the gel. At a given concentration of gel less than 1%, the PE for a water-cast carboxymethyl agarose gel is 0.25-0.30x the PE for a water-cast underivatized agarose gel. The value of PE predicts the extent of the electrophoretic sieving that is observed when double-stranded DNA is subjected to electrophoresis through a water-cast carboxymethyl agarose gel; DNA bands formed in a water-cast carboxymethyl agarose gel are comparable in quality to DNA bands formed in a water-cast underivatized agarose gel of equal PE. The following observation supports the hypothesis that electrical charge-charge repulsion among carboxymethyl agarose molecules inhibits the formation of suprafibers in water-cast carboxymethyl agarose gels: Increased content of suprafibers in carboxymethyl agarose gels is observed when the ionic strength is raised by the presence of NaCl, MgCl2, or any of several buffers during gelation of carboxymethyl agarose.

An exactly solvable Ogston model of gel electrophoresis IV: sieving through periodic three-dimensional gels

In this article, we extend our recently developed lattice model of gel electrophoresis to periodic three-dimensional gels made of either isolated obstacles or infinitely long fibers. Exact mobilities are calculated using a much improved numerical method that allows us to treat very large systems. A comparison of the exact mobilities and free available volumes indicates that the main assumption of the Ogston-Morris-Rodbard-Chrambach model (OMRCM), which postulates that the mobility (mu) of charged particles is directly related to the fractional gel volume available to them, is not valid. However, a study of the gel concentration and analyte size dependence of the zero-field mobility indicates that the OMRCM and the Ferguson plots can indeed be used to obtain useful, semi-quantitative information about the gel properties. A procedure to study more realistic three-dimensional gel systems is discussed.

Polymorphism of bacteriophage T7

For viruses made of nucleic acid and protein, the structure of the protein outer shell has, in the past, been found to be uniquely determined by the viral genome. However, here, non-denaturing agarose gel electrophoresis of bacteriophage T7 reveals two states of the mature T7 capsid; the conditions of growth are found to alter the population by T7 of these two electrophoretically defined states. Both states have been previously observed for a genetically altered T7 and they are observed here for wild-type T7. The average electrical surface charge density of a bacteriophage particle (delta) determines its state; the delta of particles in both states is negative. For a given condition of growth, the population of these two states is influenced by the extent to which the major T7 outer shell protein, p10A, is accompanied by its minor readthrough variant, p10B. Comparison of the two electrophoretic states reveals the following. (1) No difference in radius is present in the outer shell (+/-2%). (2) As the pH of electrophoresis is either increased or decreased from neutrality, the state becomes more highly populated for which delta is greater in magnitude (state 1). By changing the pH, some T7 particles are made to change state. (3) Particles in state 1 adsorb less quickly to host cells than do the particles in the alternative state (state 2). This latter observation suggests the hypothesis that state 1 evolved to reduce the probability of re-initiating an infection when conditions are not favorable for growth. This hypothesis is supported by the observation that, as conditions of growth become apparently more unfavorable, progeny increasingly populate state 1.

Analytical ultracentrifugation and agarose gel electrophoresis as tools for studying chromatin folding in solution

Analytical ultracentrifugation and agarose gel electrophoresis each can be used to accurately quantify changes in structure that accompany chromatin folding in solution. Analytical ultracentrifugation directly measures the extent of compaction of each species present in a chromatin sample under a wide range of solution conditions. Agarose gel electrophoresis yields information about changes in the average surface charge density, size and/or shape, and conformational flexibility during chromatin folding. When used together, these methodologies are particularly powerful. Protocols for the characterization of chromatin folding by analytical ultracentrifugation and agarose gel electrophoresis are described. Discussion focuses on analysis and interpretation of experimental chromatin folding data.

An exactly solvable Ogston model of gel electrophoresis. II. Sieving through periodic gels

Recently, we developed a lattice model to study the dynamics of particles being electrophoresed in gels (G. W. Slater, H. L. Guo, Electrophoresis 1995, 16, 11-15). In Part I of this series (G. W. Slater, H. L. Guo, Electrophoresis 1996, 17,977-988), we showed how to calculate the exact electrophoretic mobility of one-site particles in the limit where the electric field intensity E is vanishingly small. Since we can solve the model for arbitrary gel structures in two or more dimensions, we compared our results with those of the Ogston-Morris-Rodbard-Chrambach model (OMRCM) of gel electrophoresis, which assumes that the mobility (mu) of charged particles is directly proportional to the fractional gel volume (f) that is available to them. Our results and theoretical analysis indicated that the OMRCM is a mean-field approximation that can be useful as a rough guide; however, it generally misses the subtle sieving effects related to the correlations between the position of the obstacles in a given gel structure. In this paper (Part II) we study, for two-dimensional periodic gels, the exact relationships between the zero-field mobility mu and the gel concentration C for larger particle sizes. The fact that mu is a strong function of the particle size suggests that we can separate large particles using two-dimensional periodic gels (similar to those fabricated by W.D. Volkmuth and R.H. Austin, Nature 1992, 358, 600-602). We analyze our data using Ferguson-like plots and we show that one can indeed use a generalized retardation coefficient, K, to estimate the effective pore size aK and effective fiber size rK for these model gels. We conclude that the retardation coefficient is a useful concept to characterize a sieving structure even though it does not permit the inference of the exact gel structure.

An exactly solvable Ogston model of gel electrophoresis: I. The role of the symmetry and randomness of the gel structure

The Ogston-Morris-Rodbard-Chrambach model (OMRCM) of gel electrophoresis assumes that the mobility (mu) of charged particles is directly proportional to the fractional volume (f) of the gel that is available to them. Many authors have studied the fractional volume f in detail for various particle shapes, but the original assumption, that mu sf, has not been scrutinized seriously. In fact, this geometrical model of electrophoresis does not take into account the connectivity of the gel pores or the precise gel architecture. Recently (G. W. Slater and H. L. Guo, Electrophoresis 1995, 16, 11-15) we developed a Monte Carlo computer simulation algorithm to study the electrophoretic motion of simple particles in gels in the presence of fields of arbitrary strength. Our preliminary results indicated that the mobility and the fractional volume were not generally proportional to one another. In this article, we show how to calculate, in the limit where the field intensity is vanishingly small, the exact electrophoretic mobility of particles in any type of gel in two or more dimensions. Our results, presented here for some simple two-dimensional systems, indicate that a particle can have different electrophoretic mobilities in gels in which it has access to the same fractional available volume f. The curvature of the Ferguson plot is shown to be related to the symmetry and the degree of randomness that characterize the gel. We also demonstrate that the OMRCM is, in fact, a mean field approximation that corresponds to a uniform, annealed gel. We thus conclude that the relation between the electrophoretic mobility and the gel concentration (C) is a delicate function of the gel architecture, and that one needs more than the fractional volume f to fully characterize the transport properties of migrating particles in separation media. Exact relationships between the mobility mu and the gel concentration C are given for our model gels.

Cyclic migration of DNA in gels: DNA stretching and electrophoretic mobility

Available data from spectroscopic and microscopy studies of electrophoretic orientation of long DNA (above 40 kbp) in agarose gels is analyzed on the basis of the fact that the migration in constant fields is cyclic in nature. Defining a cycle period as the time between two consecutive compact states, a simple model is used to obtain data on the average time period (< T >) and the step length (< L >) of the migration cycle from spectroscopic measurements of the dynamics of helix orientation and center-of-mass velocity. Furthermore, the degree of orientation is used to analyze tube-orientation and DNA stretching contributions to < L > and < T >. Finally, the average electrophoretic velocity v = < L >/< T > is analyzed in terms of < L > and < T > for different DNA sizes (Lc), field strengths (E), and gel concentrations (A). The main results of the analysis are: (i) the increase and saturation of the electrophoretic mobility with increasing E is mainly governed by < L > via the degree of DNA stretching, (ii) DNA molecules of different sizes migrate with the same velocity because < L > and < T > both increase approximately linearly with Lc, and (iii) migration in a denser gel is slower mainly because < T > increases, while the step length is approximately constant. Assuming the charge Q of DNA is the same as in free solution, these results suggest that the reason the fundamental reptation equation for the electrophoretic mobility mu = (Q/zeta) < (hx/Lt)2 > also applies in the presence of strong fluctuations in the tube length Lt, and end-to-end distance hx, is that the friction coefficient zeta for motion along the tube is lower the more stretched the DNA is.

Electrophoretic separation of biopolymers in a matrix of polyacrylamide covalently linked to agarose

A new type of agarose polyacrylamide mixed-bed gel, obtained by simultaneous gelation of a novel type of allyl-activated agarose and its copolymerization with acrylamide, has pore sizes intermediate between those of polyacrylamide and agarose. The process used to activate the agarose chains enables the substitution to be controlled. As indicated by nuclear magnetic resonance (NMR), only one allyl group was inserted per agarose basic unit. Several formulations of mixed-bed gels, containing different percentages of acrylamide, were compared with conventional polyacrylamide or agarose gels. Resolution, migration distance and band sharpness of different molecular mass fragments were evaluated, with two types of gel run side-by-side in a vertical or horizontal system. The faster electrophoretic mobility of DNA in dilute mix-bed gels and the improved separation of the component of high molecular mass (1 to 6 kbp) of the 1 kbp ladder indicate that these matrices have larger porosity than any dilute polyacrylamide formulations. Sodium dodecyl sulfate (SDS)-protein complexes migrate in the mixed gels faster than in polyacrylamide gels of the same %T.

Eliciting macroporosity in polyacrylamide and agarose gels with polyethylene glycol

Preparation of highly porous polyacrylamide has recently been described (Righetti et al., Electrophoresis, 1992, 13, 587-595). In this report we add new observations on the conditions of promoting macroporosity in polyacrylamide gels and extend the possibility of eliciting this phenomenon to agarose matrices by the combined use of polyethylene glycol and glycerol. The process of cluster formation in hot agarose solutions was studied and gel structures were examined by scanning electron microscopy. A definition of macroporosity in gel, related to controlled microsyneresis during gelation, is tentatively proposed. The unexpected influence of acrylamide and agarose concentrations upon the size of macroporous structures in the corresponding gels is revealed.

Electrophoretic size separation of proteins treated with sodium dodecyl sulfate in 1% agarose gels

Separation of proteins treated with sodium dodecyl sulfate (SDS) according to molecular size was achieved by discontinuous electrophoresis in vertical low-concentration agarose gels. A linear relationship was found between the migration distance and the square root of the molecular weight. This holds for proteins in the range of 7-200 kDa separated in 1.25% w/v agarose gel slabs (7 x 7 x 0.15 cm) with 0.1% w/v SDS and sulfate as leading ion. The linear regression coefficient was 0.998. The molecular weight and charge of coions influenced the separation. Small ions with low pKa values were found suitable as coions. The migration distance of proteins treated with SDS varied linearly with the agarose concentration of the gel. The agarose type and quality affected the resolution of the SDS-protein bands. We conclude that agarose gels can substitute polyacrylamide gels for the separation of proteins treated with SDS. A homogeneous agarose gel at a concentration of about 1% is a nonsieving support for electrophoresis. Therefore, the separation described here cannot be explained by the pore size of the gel. The results suggest that the separation is mainly due to the relative migration velocities of the coion and the proteins treated with SDS.

Non-denaturing gel electrophoresis of biological nanoparticles: viruses

Although gel electrophoresis is usually used for the fractionation of monomolecular particles, it is also applicable to the fractionation of the multimolecular complexes produced during both cellular metabolism and assembly of viruses in virus-infected cells. Gel electrophoretic procedures have been developed for determining both the size of a spherical particle and some aspects of the shape of a non-spherical particle. Capsids bound to DNA outside of the capsid can also be both fractionated and characterized. The procedures developed will be used for screening viral mutants; they also can potentially be used for diagnostic virology. Sensitivity of detection, the major current limitation, is being improved by use of both improved stains and scanning fluorimetry. The gels used for fractionation sometimes approximate random straight fiber gels, but become increasingly biphasic as the gel concentration is decreased.

Electrophoretic isolation of extrachromosomal DNA from tumor cells

Gene amplification allows transformed cells to overexpress specific genes and gain a survival advantage. For this reason, cloning and characterization of amplified genes can improve our understanding of the biology of transformed cells. The techniques of in-gel renaturation and chromosome microdissection can enrich for amplified DNA sequences, but both are labor intensive and have other drawbacks. We have developed an alternative strategy of enriching for amplified DNA sequences that involves two-directional agarose gel electrophoresis of extrachromosomal circular DNA. Extrachromosomal circles can be detected with repetitive DNA probes and can be used to produce DNA probes suitable for fluorescence in situ hybridization for location of genomic origin. The ability to enrich for amplified DNA without specialized equipment or transformed cell metaphases should prove useful in the search for new genes which are important in tumor cell progression.

The use of coated and uncoated capillaries for the electrophoretic separation of DNA in dilute polymer solutions

We show that both uncoated and polyacrylamide-coated capillaries provide separation of large DNA restriction fragments (2.0-23.1 kbp) by capillary electrophoresis in dilute cellulosic polymer solutions. Uncoated capillaries, however, provide significantly better resolution of DNA fragments, particularly when ultra-dilute polymer solutions are used. This is because electroosmotic flow in uncoated capillaries increases the residence time of DNA in the capillary, without significantly contributing to band-broadening. At a given field strength and polymer concentration in the buffer, the electrophoretic mobilities of DNA restriction fragments in coated capillaries are virtually identical to those previously measured in uncoated capillaries. It is concluded that the fused silica surface of the capillary does not play a significant role in the mechanism of DNA separation by capillary electrophoresis in uncrosslinked polymer solutions. Thus, the separation of large DNA which has been observed to occur in ultra-dilute polymer solutions arises primarily from entanglement interactions between the cellulosic polymers and DNA restriction fragments which occur within the bulk of the polymer solution.

Diffusion of sucrose and dextran through agar gel membranes

Mass transfer limitations severely impede the performance of bioreactions involving large molecules by gel-entrapped microorganisms. This paper describes a quantitative investigation of such diffusional limitations in agar gel membranes. Sucrose and commercial dextran fractions with (weight-average) molecular weights ranging from 10,000 to 2,000,000 Da were used as standard diffusants. For all tested solutes but sucrose, the values of the agar/water partition coefficients highlighted steric hindrance at the entrance of the membrane pores. The effective diffusivity of sucrose in agar was similar to that in water. All dextran fractions, however, displayed restricted diffusion in the agar membranes. Their effective diffusivities were a decreasing function of the agar content of the gel membrane (0.5, 1.0, or 1.5% w/v). The effective diffusivity in a given membrane decreased as the molecular weight of the diffusing molecule increased. T500 (Mw = 470,000 Da) and T2000 (Mw = 1,950,000 Da) fractions were unable to diffuse through 1.0 or 1.5% agar membranes. The diffusion data did not agree with the classical (Renkin) model for a hard sphere diffusing through a cylindrical pore. These results are discussed in terms of gel and diffusant characteristics.

Comparison of properties of agarose for electrophoresis of DNA

Agarose as a medium for separation of DNA was first introduced in 1962 and since the early 1970s agarose submarine gel electrophoresis has been synonymous with separations of DNA molecules larger than 1 kilobase pair (kb). The large pore size, low electroendosmosis and strength of the matrix have advantages over other media such as polyacrylamide for many applications. The variety of grades of agarose, developed by chemical manipulation of the substitutions on the agarose polymer, provides a range of matrices for separation of DNA molecules from a few base pairs (bp) to over 5 megabase pairs (Mb) in length. The introduction of low-melting-temperature agarose has revolutionised the extraction and manipulation of chromosome-sized molecules. On the other hand, the demand for analysis of very small quantities of DNA will most likely lead to the increasing importance of capillary electrophoresis. Many theories have been propounded to explain the electrophoretic migration of DNA in agarose. The most popular of these has been reptation theory but none can account for all of the reported anomalies in migration. However, anomalous migration has been exploited to study DNA structure, topology and catenation. An example of the use of two-dimensional electrophoresis to demonstrate the complexity of DNA migration through agarose is given. Generally, for molecules smaller than 50 kb, electrophoretic separation is a function of length. By alternately electrophoresing DNA in two different directions, molecules as large as 5.7 Mb have been effectively separated, although with such large molecules DNA structure as well as size may determine migration. In the case of separations of chromosomes from the intestinal protozoan, Giardia duodenalis, for example, a discrepancy of 1 Mb in the size of one chromosome, with an apparent size of 0.7-2.0 Mb, depended on the boundary conditions of separation. Major challenges for the molecular biologist are separation of larger chromosomal sized molecules, greater number of samples and smaller formats. Towards this challenge computer-aided technology is a key component in the control of electrophoresis parameters and analysis.

Conventional isoelectric focusing and immobilized pH gradients in 'macroporous' polyacrylamide gels

Lateral aggregation in presence of a hydrophilic polymer (e.g. 10 kDa polyethylene glycol) in the gelling solution (Righetti et al., Electrophoresis 1992, 13, 587-595) is not inhibited by high ionic strength nor in the pH 4-10 interval. However, the bundles are disaggregated by glycerol (Tm at 20%) and by ethylene glycol (Tm at 24.5%) as well as by pH extremes (pH 3 and pH 11). Supercoiling is also strongly inhibited in a copolymer, formed by acrylamide an N,N-dimethylacrylamide or N-methylacrylamide. A level of 50% uncoiling is obtained well before a 1:1 ratio, already at a level of 18% N,N-dimethylacrylamide. All the above data strongly suggest that the nascent chains are held together in bundles by hydrogen bonds prior to the cross-linking event, instead of having a random orientation and distribution in the solvent. However, it is not possible to distinguish between H-bonds oriented perpendicular to the chain axis vs. H-bonds occurring within a single polymer filament, and the two types of H-bonds probably coexist. Macroporous gels perform well in steady-state electrophoretic techniques, such as conventional isoelectric focusing and immobilized pH gradients, where a large-pore structure is necessary for fast protein migration and for attainment of equilibrium conditions.

Influence of the agarose matrix in pulsed-field electrophoresis

Properties of agarose potentially relevant to PFGE (pulsed-field gel electrophoresis) are reviewed, and some new information is presented. Agarose polymers appear to have molecular weights in the range of 100,000 to 200,000 Da, but this is not tightly related to the effective gel strength. Agarose has some residual charge, and hence exhibits electroendosmosis (EEO). It is possible to markedly increase the speed of separation of DNA molecules by using agarose of low EEO, especially in low ionic strength, non-borate buffers. This increase is especially noticeable in the relatively long experiments required for separation of large DNAs. It is also possible to increase the range of separation in a single run by use of step gradients of agarose concentration, which allows visualization of yeast chromosomes and lambda-phage restriction fragments in the same lane. Because of the strong influence of concentration on separation, it may be useful for investigators to control water content and related variables. Our lack of knowledge of the detailed microstructure of gels may be barrier to complete understanding of PFGE.

Agarose gel pore radii are not dependent on the casting buffer

Previous studies have shown that the apparent pore size of agarose gels is dependent on the buffer in which the gel is cast and run (D.L. Holmes and N.C. Stellwagen, Electrophoresis 1990, 11, 5-15; N.C. Stellwagen and D.L. Holmes, Electrophoresis 1990, 11, 649-652). However, these studies, based on the mobility of DNA restriction fragments, neglected the effect of electroendosmosis. By measuring the mobility of vitamin B12 under various experimental conditions, it is shown here that electroendosmosis is highly buffer-dependent. When the observed mobilities of DNA are corrected for electroendomosis, the apparent pore radii of agarose gels are found to be independent of the casting buffer.

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.

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).

The distribution of particles characterized by size and free mobility within polydisperse populations of protein-polysaccharide conjugates, determined from two-dimensional agarose electropherograms

New approaches for the characterization of polydisperse particle populations are presented*. The investigated samples contain virus-sized protein-polysaccharide conjugates which had previously been prepared as immunogens against bacterial meningitis (Hib). The analysis is based on two-dimensional agarose electrophoresis (Serwer-type). This method, like the one of O'Farrell, achieves a separation according to size and charge. It relies on a different principle, however, and is applicable to nondenatured particles which are 100 to more than 1000 times larger in mass than regular uncrosslinked proteins. Data from stained gel patterns are evaluated by the computer program ELPHOFIT, which makes it possible to standardize the gel and to construct a nomogram which defines every position on the gel in terms of particle size and free mobility (related to surface net charge density). The output of ELPHOFIT, consisting of nomogram parameters, is transferred to the image processing program GELFIT. This software is used to evaluate the computer images obtained by digitizing the stained gel patterns: (i) The nomogram is electronically superimposed on the computer image. (ii) The gel pattern is transformed from a curvilinear to a rectangular coordinate system of particle size and free mobility. The center of gravity as well as density maxima are given in coordinates of particle size and free mobility. Ranges of grey levels can be accentuated by adding 16 pseudocolors. (iii) Using surface-stripping techniques, GELFIT provides an estimate for the number of major subpopulations within each preparation. (iv) Numerical values for the distribution of particle size and free mobility are determined. Using program IMAGE, the quantitative physical assessment of a given conjugate preparation is presented in the form of a computer-generated three-dimensional plot, the shape of which serves to identify and characterize the preparation visually. The data analysis based on digitized two-dimensional gel patterns is automated to an extent that a technician can perform routine evaluations. It uses the Macintosh II personal computer.

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.

Calibration of polyacrylamide gel columns for the separation of oligonucleotides by capillary electrophoresis

Polyacrylamide-filled gel columns are used to separate oligonucleotide samples. For homopolymeric standard samples, plots of migration time versus molecular size are presented over a range of 30-160 bases. With 2.5-4% T and 3.3% C gels, good resolution over the examined mass range, with peak width at half height of 3 to 6 s, is obtained by applying electrical fields of 200-400 V/cm. The separation of heteropolymeric nucleotides by slab gel electrophoresis under routine conditions was compared with capillary gel electrophoresis. Using the same column and the same separation conditions, the plot of migration time versus base number is linear with an identical slope for three oligonucleotide samples which were examined, allowing a calibration of a gel-filled capillary for molecular mass determination.