Electrophoresis of DNA in agarose gels. II. Effects of loading mass and electroendosmosis on electrophoretic mobilities

We have investigated several experimental factors which affect the accurate determination of electrophoretic mobilities of circular and linear DNAs in agarose gels. We demonstrate that: (1) The mobility of individual DNA species is affected by the total mass in the sample loaded. The increased mobility and band distortion observed become apparent when the DNA mass exceeds approximately 0.2 μg per 0.15 cm² of surface area in the loading well. (2) The migration velocity of a given DNA species depends on the coefficient of electroendosmosis (?m_r) of the agarose preparations used. In the range 0.081 ≤ ?m_r ≤ 0.441, the DNA migration velocity is proportional to (?m_r)^?0.5.     

Rapid separation of DNA molecules by agarose gel electrophoresis: use of a new agarose matrix and a survey of running buffer effects.

This report describes the use of a new type of agarose (FastLane agarose) for faster separation of DNA by agarose gel electrophoresis. DNA molecules separated in this agarose exhibited electrophoretic mobilities up to 30% higher than similar separations in standard analytical grade agarose. DNA molecules of all sizes examined showed higher mobilities in FastLane agarose. The mobility increase was predominantly due to the low electroendosmosis of FastLane agarose and was most pronounced in pulsed field gel electrophoresis separations. The magnitude of mobility increase varied depending on the conditions used for electrophoresis.     

Effect of ribonuclease and neuraminidase on the electrophoretic mobility of tissue culture cells in parasynchronous growth

Cultured mammalian cells (RPMI no. 41) in parasynchronous growth were treated, at different stages of the mitotic cycle, with neuraminidase and ribonuclease, separately and sequentially, and their electrophoretic mobilities determined. Changes in the electrophoretic mobility of these cells are probably mainly due to variations in the density of negatively charged groups susceptible to neuraminidase, although variations in groups susceptible to ribonuclease may occur. It is suggested that the observed variations in electrophoretic mobility of different cells may be due to differences in the relative lengths of different life-cycle phases. Where G₂ phase is relatively long or G₁ relatively short the cell populations will hve higher mean electrophoretic mobilities.     

Physico-chemical characterization of proteins by capillary electrophoresis

The electrophoretic mobility of proteins was successfully determined by means of capillary electrophoresis (CE) with various background electrolytes (BGEs). The objective was focused on the variation in BGE physico-chemical composition and the consequential impact on the observed protein charge. Experimental and calculated mobilities, according to Henry's equation, versus ionic strength have been compared. For positively-charged lysozyme, a good agreement between observed and calculated mobilities was observed using triethanolamine chloride at pH 7.0 as the BGE. Mobility close to zero was shown using borate (pH 8.0) and phosphate (pH 7.0) at a low ionic strength of about 20 mmol l⁻¹, and as a consequence, specific adsorption of oxyanions was evidenced. Lysozyme retention in the case of reversed-phase high-performance liquid chromatography (RP-HPLC) was decreased by the presence of phosphate ions. CE and HPLC are complementary tools for characterizing the behaviour of lysozyme. On the other hand, the mobility of the negatively-charged α-lactalbumin remained constant as regards phosphate at pH 7.0 in the 20–200 mmol l⁻¹ range, contrary to the decrease that had been expected with the increasing ionic strength. β-Lactoglobulin exhibited increasingly lower mobilities than those expected of boric acid/borate at pH 7.0 and 8.0 (I=20 mmol l⁻¹).     

Multiple forms of chlorophyll-protein complexes from a thermophilic cyanobacterium Synechococcus sp

Eight chlorophyll-proteins were resolved from the thylakoid membranes, or digitonin particles, of a thermophilic cyanobacterium Synechococcus sp. by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Six chlorophyll-proteins with slower electrophoretic mobilities were shown to be P700-chlorophyll a-protein complexes (CP1), whereas faster-moving proteins (CP2) were related to photosystem 2. Extraction of CP1 complexes from the membranes with different detergent/chlorophyll ratios and reelectrophoresis of extracted CP1 complexes indicated that the chlorophyll-proteins are closely interrelated with each other; any CP1 complex could be transformed to other CP1 complexes with faster electrophoretic mobilities. This, together with the Ferguson plot and the polypeptide composition, showed that six CP1 complexes are different in terms of polypeptide composition, oligomerization, SDS-binding, or conformation of the proteins but represent, in the order of increasing electrophoretic mobility, increasing degree of modification of the native P700-chlorophyll a-protein.     

Quantitative measurement of lipoprotein surface charge by agarose gel electrophoresis.

The electrophoretic mobilities of low density lipoprotein (LDL) and six pure proteins in a 0.5% agarose gel have been compared to literature electrophoretic mobility values determined by the Tiselius moving boundary method. There is a strong correlation (r = 0.99) between the electrophoretic mobilities determined by the two techniques. The electrophoretic behavior of charged particles smaller than very low density lipoproteins (VLDL) is not markedly perturbed by a 0.5% agarose matrix, and variations in mobility primarily reflect differences in particle valence and density of surface charge. Application of electrokinetic theory to derive protein and lipoprotein net charges from the electrophoretic mobilities in agarose yields a quantitative delineation of lipoprotein electrophoretic migration patterns wherein the beta mobility region comprises a surface potential range of -4.5 to -7.0 mV; the pre-beta region a range of -7.0 to -10.5 mV; the alpha mobility region a range of -10.5 to -12.5 mV and the serum albumin region a range of -12.5 to -14.0 mV. Because protein conformation and charge are critical in metabolic regulation, the agarose gel electrophoresis technique provides a valuable analytical tool that should help to elucidate further details of the structure-function relationships of serum lipoprotein particles.     

Separation of DNA by mass-transfer properties in the presence of an electric field

Experimental and theoretical works were performed for the separation of large polyelectrolyte such as DNA in the column packed with gel particles under influence of an electric field. Since DNA quickly orients through the pores in the field direction, this paper presents how intraparticle convection affects the separation of DNAs in the column. Dimensionless transient mass balance equations were derived considering diffusion and electrophoretic convection. The separation criteria are theoretically studied using two different Peclet numbers in the fluid and solid phases and these criteria were verified using two different DNAs by electrophoretic mobilities measured experimentally, showing how the separation position of DNAs varies in the column according to values of Pe_f/Pe_g of individual DNA. Governing equations are solved by an operator theory and the characteristic method to yield the column response.     

Analysis of the electrophoretic properties of double-stranded DNA and RNA in agarose gels at a finite voltage gradient

The electrophoretic mobilities of double-stranded (ds) DNAs and ds RNAs of various lenths, L, were measured in gels of 0.4–1.8% (w/v) agarose at a voltage gradient of 1.0 V/cm. Differences in the electrophoresis of ds DNA and ds RNA are presented and discussed. A general expression is derived that describes the electrophoretic mobility, M, of either type of ds nucleic acid as a function of the gel concentration and the nucleic acid length: M = M′₁(L/L₀)^?x ? M₂, where M′₁ and L₀ are constants, and x and M₂ depend on the agarose gel concentration. The results obtained by fitting our data with this equation are consistent with the mobilities of nucleic acids in a wide range of gel concentrations, including free electrophoresis in solution and electrophoresis in gles of high agarose concentration in which nuleic acids are expected to reptate through the gel matrix. Finally, various methods of plotting agarose gel electrophoresis data are discussed.     

Canine erythrocyte pyruvate kinase. II. Properties of the abnormal enzyme associated with hemolytic anemia in the basenji dog

We have compared the solubility, kinetic, immunological, and electrophoretic properties of erythrocyte pyruvate kinase from normal dogs and Basenji dogs with congenital hemolytic anemia due to pyruvate kinase deficiency. Differences can be detected between the two enzymes by all methods. The enzyme from the affected animals has a greater solubility in ammonium sulfate. It has a lower K _m for phosphoenolpyruvate, while the K _m for ADP is increased. This enzyme is not inhibited by ATP or activated by fructose 1,6-diphosphate. The enzyme from the affected animals has none of the allosteric properties characteristic of the normal canine enzyme. No difference can be detected by enzyme inactivation with rabbit antiserum against the human erythrocyte enzyme, but a slight spur is observed on comparison of the two enzymes by Ouchterlony immunodiffusion. The enzymes also differ in their electrophoretic mobilities on starch gel electrophoresis.     

Electrophoretic mobility of lambda phage HIND III and HAE III DNA fragments in agarose gels: a detailed study

The electrophoretic mobility (μ) of DNA fragments from λ phage and ΦX 174, split by restriction enzyme to molecular lengths from 3 × 10² to 2.36 × 10⁴ base pairs, has been investigated in 0.6–4% agarose gels at various field strengths, ionic strengths, and temperatures. As already observed, μ is seen to be very sensitive to the field, increasing with field strength. The sensitivity increases with the molecular length of the DNA and decreases at high gel concentration. Our data are in qualitative agreement with recent theoretical predictions that concern the influence of the electric field on electrophoretic mobility. Mobility data have been extrapolated to zero field. This enables a comparison of our experimental results with theoretical predictions on the dependence of μ on the molecular weight of the DNA fragments. Our data fit, quite closely, a reptation model, where the tube path is described as a semiflexible entity with a persistence length equal to the pore diameter. The influence of the agarose concentration and the ionic strength of the buffer on the two parameters of the model—intrinsic electrophoretic mobility (μ₀) and the number of base pairs per element of the tube (g)—are well described by the model. The temperature dependence of the electrophoretic mobility, together with the influence of the agarose concentration on μ₀, indicate that the hydrodynamic drag is the leading frictional force on the DNA molecules in the gel.     

Factors affecting resolution, band width, number of theoretical plates, and apparent diffusion coefficients in polyacrylamide gel electrophoresis

A systematic study of several variables affecting band width and resolution in polyacrylamide gel electrophoresis (PAGE) has been carried out. This makes it possible to determine resolution, number of theoretical plates, and an apparent diffusion coefficient in PAGE. Measurement of band position yields a linear relationship between logarithm of electrophoretic mobility and gel concentration when other variables are held constant. Similarly, measurement of band width yields a linear relationship between the logarithm of the dispersion coefficient (D′) and gel concentration. This makes it possible to extrapolate to 0 gel concentration and to obtain as estimate of a free dispersion coefficient (D′₀) which is usually one or two orders of magnitude greater than the free diffusion coefficient (D_20,w). D′ depends on protein concentration (which is a function of sample load and time), on ionic strength (I), and on duration of electrophoresis (dependent on field strength which in turn depends on ionic strength and current). Since these several variables introduce nonlinear and interrelated correction factors, extrapolation to “infinite ionic strength,” “zero concentration,” and “infinite time” becomes difficult although it is potentially feasible at both the experimental and the theoretical level, and thus it may be possible to determine diffusion coefficients in PAGE on microgram amounts of material without the need for preliminary purification. Alternatively, PAGE in a nonsieving, anticonvectant gel at high ionic strength and for long duration may be able to provide an estimate of D_20,w. The results also support the validity of previously developed approximations for the relationship between band width and gel concentration, and for the relationship between band dispersion and electrophoretic mobility.     

Some effects of antibiotics on bacterial polyribosomes as studied by gel electrophoresis

Bacterial polyribosomes possess characteristic electrophoretic mobilities in agarose-acrylamide composite gels. In cells whose normal protein synthesis is inhibited by certain antibiotics, the resolution of the gel electrophoresis technique has permitted the detection of specific increases in the mobility of the polyribosomes. Antibiotics producing these changes in polyribosome mobility include inhibitors of the 30 S as well as the 50 S subunit.The in vivo action of streptomycin has been studied in some detail. Streptomycin alters the polyribosomes of sensitive strains, haploid as well as heterodiploid, but does not alter polyribosomes of strains resistant to or dependent upon streptomycin. Streptomycin-altered polyribosomes are stable in vivo for more than one hour and exhibit a considerably prolonged run-off time following rifampicin treatment. They are also significantly more resistant to the in vitro RNase degradation than control ribosomes. The subunit composition ($\text{50}\text{S}\text{30}\text{S}$) of the altered polyribosomes remains unchanged from the control (1:1).Since the electrophoretic mobility of monosomes remains unchanged during the antibiotic treatment, the evidence presented suggests that the alteration of polyribosome mobility involves a stacking of the ribosomes on mRNA.     

On the sequence determinants and flexibility of the kinetoplast DNA fragment with abnormal gel electrophoretic mobilities

A 410 base-pair (bp) Sau3A restriction fragment derived from a Leishmania tarentolae kinetoplast DNA minicircle, which is known to have slower than expected electrophoretic mobilities in polyacrylamide gels, has been cloned in a plasmid and deletions from one end of the cloned segment have been constructed. Analysis of the gel electrophoretic mobility data of a large number of restriction fragments derived from the kinetoplast DNA clone and its deletion subclones has led to the conclusion that two sequences, one in the region bp 100 to 170 and the other bp 190 to 250, both numbered from one end of the 410 bp kinetoplast DNA segment, are important for the abnormal gel electrophoretic behavior of the kinetoplast DNA fragment. One common feature of these sequences is the periodic presence of short runs of A residues (3 to 6 As in each); auto-correlation analysis of these runs of A residues shows a strong harmonic component with a period around 11 bp. These results support and extend the previous analysis of Wu & Crothers (1984). The abnormal electrophoretic behavior is accentuated at low temperature and by the addition of Mg2+ to the electrophoresis buffer; addition of Na+ has the opposite effect. Insertion of sequences derived from the kinetoplast DNA fragment into nicked circular DNA causes no unexpected change in its electrophoretic mobility in agarose gel, suggesting that the 410 bp sequence, or segments of it, has no significant spatial writhe. Abnormal shifts in agarose gel mobilities are observed, however, when certain segments of the kinetoplast DNA are inserted into positively or negatively supercoiled DNA topoisomers. These results are consistent with a bent structure of the kinetoplast DNA in which the bend has zero writhe in its undistorted form but is easily distorted.     

Hydrophobicities and Electrophoretic Mobilities of Anaerobic Bacterial Isolates from Methanogenic Granular Sludge

The hydrophobicities and electrophoretic mobilities of isolates from methanogenic anaerobic granular sludge were measured and compared with those of strains from culture collections. All new isolates were highly hydrophobic, indicating that the upflow anaerobic sludge blanket reactor concept selects for hydrophobic bacteria. Methanothrix soehngenii, a methanogen often observed in methanogenic granular sludge, was highly hydrophobic and showed low electrophoretic mobility at pH 7. The role of this strain in the formation of methanogenic granular sludge is discussed.     

Analysis of chloroplast ribosomes by polyacrylamide gel electrophoresis and electron microscopy

Ribosomal particles were isolated from chloroplasts and cytoplasm of eukaryotes, Euglena gracilis and Spinacia oleracea, and from prokaryotes, E. coli and Anacystis nidulans. The ribosomes were analyzed by polyacrylamide gel electrophoresis and by negative staining in the electron microscope. The prokaryote ribosomes show a slight difference in their electrophoretic mobilities between the two species: E. coli ribosomes migrate ahead of the Anacystis ribosomes. In comparison to eukaryote cytoplasmic ribosomes, chloroplast ribosomes of both species demonstrate a higher electrophoretic mobility and significantly smaller dimensions (about 230 × 187 Å compared to about 197 × 162 Å). Some differences in form were noted for Euglena cytoplasmic ribosomes which may contribute to their high S value. In comparison to prokaryote ribosomes, the mobility of chloroplast ribosomes is similar to the mobility of the prokaryote group of ribosomes, and it specifically coincides with the migrating band of ribosomes from the blue-green alga, Anacystis. Subunits of chloroplast and prokaryote ribosomes have similar mobilities and cannot be distinguished in gels. The similarities in size and in electrophoretic mobilities of chloroplast and blue-green algal ribosomes support the hypothesis of a common phylogenetic origin for the two.     

Characterisation of histones in the salivary glands of Rhynchosciara americana larvae

The histones from the salivary glands of Rhynchosciara americana larvae were identified. The electrophoretic patterns of the proteins studied resemble that of calf thymus histones, including the H₁ histone, which in Rhynchosciara has a lower electrophoretic mobility in urea/polyacrylamide gels but shows a molecular weight identical to the corresponding histone of calf thymus, as judged by SDS-polyacrylamide gel electrophoresis.     

A new serum component which specifically inhibits thiol proteinases

A serum proteinase inhibitor specific for thiol proteinases was prepared in a functionally pure state by Sephadex G-200 gel filtration, starch block electrophoresis and immunoaffinity chromatography. This component was distinct from the known serum proteinase inhibitors. It was demonstrated by immuno-electrophoresis that the incubated mixture of thiol proteinase and this inhibitor produced a soluble complex possessing both antigenicities. The molecular weight of the inhibitor was found to be 90,000 by gel filtration on Sephadex G-150 column, and the electrophoretic mobility was in the α₂-region. A tentative term, α₂-thiol proteinase inhibitor, was given because of its mobility and inhibition spectrum.     

Studies on the surface of chick blastoderm cells. 3. Calcium binding to ionogenic sites

The effect of increasing calcium concentrations on the electrophoretic mobility of cells obtained from early chick blastoderms at successive developmental stages was studied. Cells had zero mobilities at calcium concentrations in the range of 1 to 2 × 10^?2 M CaCl₂, and became positively charged when calcium concentrations between 2 and 5 × 10^?2 M CaCl₂ were used. Results using trypsin suggest that while some calcium binding sites disappear from the surface ionogenic layer, the majority of them are not removed by this enzyme. The calcium binding capacity did not vary appreciably in the stages studied. Charge reversal induced by calcium is reversible.     

Analysis of polypeptide molecular weights by electrophoresis in urea

Ten proteins of differing disulfide contents and isoionic points were subjected to disc gel electrophoresis in the presence of 8 urea-0.9 acetic acid to evaluate the use of this technique in determining polypeptide molecular weights. Comparison of the electrophoretic mobilities before and after reduction of the proteins' disulfide bonds demonstrated that only after all disulfide bonds were broken, could their molecular weights be estimated with any degree of accuracy. The expression of the electrophoretic mobilities as a function of the proteins' effective hydrodynamic sizes, thereby taking into account the extent of constraint by disulfide bonds, allowed a comparison of disulfide cross-linked and linear forms of the protein polypeptides. The extent to which intrinsic charge affects a protein's electrophoretic mobility was estimated by comparing alpha-lactalbumin and lysozyme, two proteins of identical size but vastly different isoionic points. They exhibited a 20% difference in mobilities. An apparent slow reduction of disulfide bonds was observed to occur when proteins were exposed to reducing agent at low pH in 8 urea.     

Curved DNA molecules migrate anomalously slowly in free solution

The electrophoretic mobility of a curved DNA restriction fragment taken from the VP1 gene in the SV40 minichromosome has been measured in polyacrylamide gels and free solution, using capillary electrophoresis. The 199 bp restriction fragment has an apparent bend angle of 46 ± 2° located at SV40 sequence position 1922 ± 2 bp [Lu Y.J., Weers B.D. and Stellwagen N. C. (2005) Biophys. J., 88, 1191–1206]. The ‘curvature module’ surrounding the apparent bend center contains five unevenly spaced A- and T-tracts, which are responsible for the observed curvature. The parent 199 bp fragment and sequence mutants containing at least one A-tract in the curvature module migrate anomalously slowly in free solution, as well as in polyacrylamide gels. Hence, the anomalously slow mobilities observed for curved DNA molecules in polyacrylamide gels are due in part to their anomalously slow mobilities in free solution. Analysis of the gel and free solution mobility decrements indicates that each A- or T-tract contributes independently, but not equally, to the curvature of the 199 bp fragment and its A-tract mutants. The relative contribution of each A- or T-tract to the observed curvature depends on its spacing with respect to the first A-tract in the curvature module.