New types of separation matrices for electrophoresis

Polyacrylamide Gel Electrophoresis

Cross-linked chains of polyacrylamide can be used as electrically neutral gels to separate double-stranded DNA fragments according to size and single-stranded DNAs according to size and conformation. Polyacrylamide gels have the following three major advantages over agarose gels: (1) Their resolving power is so great that they can separate molecules of DNA whose lengths differ by as little as 0.1% (i.e., 1 bp in 1000 bp). (2) They can accommodate much larger quantities of DNA than agarose gels. Up to 10 µg of DNA can be applied to a single slot (1 cm × 1 mm) of a typical polyacrylamide gel without significant loss of resolution. (3) DNA recovered from polyacrylamide gels is extremely pure and can be used for the most demanding purposes (e.g., microinjection of mouse embryos). However, polyacrylamide gels have the disadvantage of being more difficult to prepare and handle than agarose gels. Methods are presented here for preparing and running nondenaturing polyacrylamide gels and for detection of DNA in these gels by staining.

Cell electrophoresis--a method for cell separation and research into cell surface properties

In this paper, we discuss the application of various methods of cell electrophoresis in research into cell surface properties (analytical methods), and the separation of uniform cell subpopulations from cell mixtures (preparative methods). The emphasis is on the prospects of the development of simplified and versatile methodologies, i.e. microcapillary cell electrophoresis and horizontal cell electrophoresis under near-isopycnic conditions. New perspectives are considered on the use of analytical and preparative cell electrophoresis in research on cell differentiation, neoplastic transformation, cell-cell interactions and the biology of stem cells.

A new method for the preperative and analytical electrophoresis of cells

In this paper, a new method is described for the horizontal electrophoresis of cells on a density cushion under near-isopycnic conditions. When cell sedimentation is minimized, the electrophoresis of red blood cells (RBC) used as model cells within an anti-convective porous matrix (with pores over 300 μm in diameter) was capable of separating a mixture of human and chicken RBC according to their electrophoretic mobilities. Samples taken from the separated RBC bands show over 90% purity for each species. The simultaneous electrophoresis of several RBC samples carried out under identical conditions permitted the use of comparative data based on the electrophoretic mobility of cells which differ in their surface properties. We believe that this relatively simple system, in which cell sedimentation and convection are minimized, has the potential to be modified and adapted for the separation of other cell types/organelles.

Hydrolytically stable, diaminocarboxylic acid-based membranes buffering in the pH range from 6 to 8.5 for isoelectric trapping separations

Diaminocarboxylic acid carrier ampholytes, such as L-histidine, 2,3-diaminopropionic acid, L-ornithine, and L-lysine, were reacted with glycerol-1,3-diglycidyl ether (GDGE) and poly(vinyl alcohol) (PVA) in the presence of sodium hydroxide to produce hydrolytically and mechanically stable hydrogels, supported on a PVA substrate, for use as buffering membranes in isoelectric trapping (IET) separations. The pH values of the DACAPVA membranes were determined with the help of small-molecule pI markers and proteins and were found to be in the 6 < pH < 8.5 range. The membranes were successfully used to isoelectrically trap small ampholytes, desalt ampholyte solutions in IET mode, and effect the binary separation of chicken egg white proteins.

Scaling analysis of polyacrylamide gel surfaces synthesized in the presence of surfactants

Surfaces of polyacrylamide hydrogels synthesized in the presence of surfactants were imaged by atomic force microscopy (AFM), and the surface morphology was studied by numerical scaling analysis. The gels were formed by polymerizing acrylamide plus a cross-linker in the presence of surfactants, which were then removed by soaking in distilled water. Gels formed in the presence of over 20% surfactant (by weight) formed clear, but became opaque upon removal of the surfactants. Other gels formed and remained clear. The surface morphology of the gels was studied by several one- and two-dimensional numerical scaling methods. The surfaces were found to be self-affine on short length scales, with a roughness (Hurst) exponent in the range from 0.85 to 1, crossing over to a constant root-mean-square surface width at long scales. Both the crossover length between these two regimes and the saturation value of the surface width increased significantly with increasing surfactant concentration, coincident with the increase in opacity. We propose that the changes in the surface morphology are due to a percolation transition in the system of voids formed upon removal of the surfactants from the bulk.

Surface scaling analysis of a frustrated spring-network model for surfactant-templated hydrogels

We propose and study a statistical-mechanical model, inspired by recent atomic force microscopy studies of the surface structures of crosslinked polymer gels into which voids are introduced through templating by surfactant micelles [M. Chakrapani et al., e-print cond-mat/0112255]. The gel is represented by a frustrated, triangular network of nodes connected by springs of random equilibrium lengths. The nodes represent crosslinkers, and the springs correspond to polymer chains. The boundaries are fixed at the bottom, free at the top, and periodic in the lateral direction. Voids are introduced by deleting a proportion of the nodes and their associated springs. The model is numerically relaxed to a representative local energy minimum, resulting in an inhomogeneous, "clumpy" bulk structure. The free top surface is defined at evenly spaced points in the lateral (x) direction by the height of the topmost spring, measured from the bottom layer, h(x). Its scaling properties are studied by calculating the root-mean-square surface width and the generalized increment correlation functions C(q)(x)=<|h(x(0)+x)-h(x(0))|(q)>. The surface is found to have a nontrivial scaling behavior on small length scales, with a crossover to scale-independent behavior on large scales. As the vacancy concentration approaches the site-percolation limit, both the crossover length and the saturation value of the surface width diverge in a manner that appears to be proportional to the bulk connectivity length. This suggests that a percolation transition in the bulk also drives a similar divergence observed in surfactant templated polyacrylamide gels at high surfactant concentrations.

Novel cross-linked homogeneous polyacrylamide gels with improved separation properties: investigation of the cross-linker functionality

Polyacrylamide (PAAm) gels were synthesized using cross-linkers with their potential functionality (twice the number of double bonds of a cross-linker) varying from six to sixteen. Improved electrophoretic separation and highly desirable porosity and sieving properties were observed for most of the PAAm gels containing novel cross-linkers. An increase in the potential functionality of cross-linkers used in PAAm gels was an important factor, influencing the pore size and pore size distribution of the network.

Proteome mapping by two-dimensional polyacrylamide gel electrophoresis in combination with mass spectrometric protein sequence analysis

The high resolving power of two-dimensional polyacrylamide gel electrophoresis 2D-PAGE and its full analytical and preparative potential have been described with special emphasis on reproducibility and standardization of protein spot patterns, enhanced protein detection sensitivity, and computer analysis database development. New methodologies for peptide mass fingerprinting, peptide, sequence, and fragmentation tagging have been highlighted. Major challenges associated with 2D-PAGE/mass spectrometric protein sequencing were outlined which need to be addressed in the future, including sample enrichment, use of alternative gel matrices, improvements in separation systems interfaced directly to the mass spectrometer, and design of high-sensitivity instruments with very high mass ranges. It is hoped that comparative studies to identify, quantitate, and characterize proteins differentially expressed in normal versus diseased cells would give insight into mechanisms of pathogenesis and allow the development of a way to control both the etiology and the course of diseases.

Detection of point mutations by capillary electrophoresis with temporal temperature gradients

By combining the advantages of capillary electrophoresis and temperature gradient gel electrophoresis, a method was developed to detect point mutations in polymerase chain reaction (PCR) fragments. Increasing and decreasing temporal temperature gradients were established by means of a computer-controlled Peltier module. Native and denaturing conditions were achieved by cooling to 25 degrees C and heating to 70 degrees C, respectively, a thermostating liquid surrounding the capillary. To separate nucleic acid fragments, a sieving media, containing 4% linear polyacrylamide, 1 x Tris borate EDTA buffer (TBE) and 6 M urea, was found appropriate. Renewal of the sieving matrix before each run significantly improved the reproducibility of fragment separation. The ability of this capillary electrophoresis system to detect point mutations is demonstrated with the human prion-protein gene.

The free solution mobility of DNA

The free solution mobility of DNA has been measured by capillary electrophoresis in the two buffers most commonly used for DNA gel electrophoresis, Tris-borate-EDTA (TBE) and Tris-acetate-EDTA (TAE). The capillaries were coated with polymers of either of two novel acrylamide monomers, N-acryloylaminoethoxyethanol or N-acryloylaminopropanol, both of which are stable at basic pH and effectively eliminate the electroendosmotic mobility due to the capillary walls. The free solution mobility of DNA in TAE buffer was found to be (3.75 +/- 0.04) x 10(-4) cm2 V-1 s-1 at 25 degrees C, independent of DNA concentration, sample size, electric field strength, and capillary coating, and in good agreement with other values in the literature. The free solution mobility was independent of DNA molecular weight from approximately 400 base pairs to 48.5 kilobase pairs, but decreased monotonically with decreasing molecular weight for smaller fragments. Surprisingly, the free solution mobility of DNA in TBE buffer was found to be (4.5 +/- 0.1) x 10(-4) cm2 V-1 s-1, about 20% larger than observed in TAE buffer, presumably because of the formation of nonspecific borate-deoxyribose complexes.

Electrophoresis gel media: the state of the art

Some unique events have occurred in the last few years which might revolutionize the field of polyacrylamide gel electrophoresis. While it was widely recognized that such matrices could normally be cast with a small pore size distribution, typically of the order of a few nanometers diameter (for protein sieving), recent developments suggest that "macroporous" gels could also be produced in the domain of polyacrylamides. If constraints to chain motion are imposed during gel polymerization, large-pore structures can be grown. Such constraints can originate either from low temperatures or from the presence of preformed polymers in the gelling solution; in both cases, the growing chains are forced to "laterally aggregate" via inter-chain hydrogen bond formation. Upon consumption of pendant double bonds, such bundles are frozen in the three-dimensional space by permanent cross-links. As an additional development, a novel photopolymerization system is described, comprising a cationic dye (methylene blue) and a redox couple (sodium toluene sulfinate, a reducer, and diphenyliodonium chloride, a mild oxidizer). Methylene blue catalysis is characterized by a unique efficiency, ensuring >96% conversion of monomers, even in hydro-organic solvents and in the presence of surfactants, which normally quench or completely inhibit the persulphate-driven reaction. In addition, methylene blue-sustained photopolymerization can be operated in the entire pH 3-10 interval, where most other systems fail. Perhaps the most striking novelty in the field is the appearance of a novel monomer (N-acryloylaminopropanol, AAP) coupling a high hydrophilicity with a unique resistance to alkaline hydrolysis. Given the fact that a poly(AAP) matrix is 500 times more stable than a poly(acrylamide) gel, while being twice as hydrophilic, it is anticipated that this novel chemistry will have no difficulties in replacing the old electrophoretic anticonvective media. The review ends with a glimpse at novel sieving media in capillary zone electrophoresis: polymer networks. Such media, by providing an almost infinite range of pore sizes, due to the absence of a rigid support, allow sieving mechanisms to be operative over a wide interval of particle sizes, even up to genomic DNA. Viscous solutions of polymer networks, made with the novel poly(AAP) chemistry, allow repeated use of the same separation column, well above 50 injections. Silica-bound poly(AAP) chains provide effective quenching of electroosmosis and >200 analyses by isoelectric focusing.

Improved electrophoresis and transfer of picogram amounts of protein with hemoglobin

During electrophoresis and electroblotting to transfer membranes, picogram amounts of protein can react irreversibly with the polyacrylamide matrix, preventing complete electrophoresis and efficient electroblotting. Bovine hemoglobin, but not other potential carrier proteins, mitigates this protein loss by migrating with or ahead of other proteins and scavenging reactive groups. Inclusion of 5 micrograms of hemoglobin in sample wells increases by 4-fold the amount of a radiolabeled test protein, myosin I beta, found at its appropriate 120-kDa position in sodium dodecyl sulfate-polyacrylamide gels. For electroblotting, incubating the gel with 0.25 mg/ml hemoglobin prior to transfer improves mobilization of picogram amounts of radiolabeled myosin I beta out of the gel by about 6-fold. For picogram amounts of proteins, therefore, approximately 20-fold more protein transfers to a blotting membrane when hemoglobin is used during both electrophoresis and transfer. This effect is general: transfer of radiolabeled Drosophila embryo proteins is improved dramatically by including hemoglobin in the pretransfer incubation solution. We suggest that electroblot-based detection of small amounts of protein, particularly when in the absence of other potential carrier proteins, can be improved substantially by using hemoglobin.

Replaceable polymers in DNA sequencing by capillary electrophoresis

Much progress has been made in the development of replaceable sieving polymers and capillary coatings for high-performance DNA sequencing by capillary electrophoresis. Several studies of parameters that affect resolution, read length and reproducibility have begun to reveal the physical mechanisms acting on single-stranded DNA during electrophoresis through semidilute polymer solutions. Recently developed electro-osmosis-inhibiting matrix polymers have simplified the process of coating capillaries, facilitating the automation of high-throughput parallel systems for large-scale sequencing.

Oligonucleotide analysis by capillary polymer sieving electrophoresis using acryloylaminoethoxyethanol-coated capillaries

Capillary polymer sieving electrophoresis using dynamic sieving polymer solutions provides size-based separations of oligonucleotides. The polymer sieving system described here resolves single-stranded oligonucleotides with single-base resolution up to lengths of 30 bases within 10 min. The effect of temperature on the separation of synthetic oligonucleotide standards was examined between 20 degrees C and 40 degrees C, with optimal performance at 35-40 degrees C. By adding urea to the sieving buffer single-base resolution could be extended to 60 bases in about 40 min. Best performance was achieved with capillaries coated with a new monomer, acryloylaminoethoxyethanol. This coating provides the necessary stability to ensure long lifetimes.

Electrophoresis of DNA in novel thermoreversible matrices

We demonstrate the feasibility of temperature-sensitive polymers as novel matrices for capillary and slab electrophoresis of DNA. These matrices combine the case-of-use of agarose with resolution properties of polyacrylamide. Two classes of matrices are used: (i) aqueous suspensions of gel microspheres and (ii) solutions containing uncross-linked temperature-sensitive polymers. When heated, the viscosity of these solutions drops dramatically because of the phase transition behavior of these polymers, and therefore these formulations are easy to pour or load. Results are presented for separation of double-stranded DNA fragments (< 2000 bp) in capillary, tube, and slab electrophoresis. Preliminary results are also presented for separation of single-stranded sequencing fragments by capillary electrophoresis. In the tube format, good resolution was obtained for phi X174/HaeIII fragments. In the slab format, excellent resolution of double-stranded DNA was obtained, including simultaneous separation of a 10 bp ladder up to 150 base pairs. In the capillary format, pBR322/MspI fragments were completely resolved, and single-base resolution of sequencing fragments was obtained up to 150 bases. We believe that temperature-sensitive polymers represent a new and promising class of electrophoretic media.

Probing soft polymeric coatings of a capillary by atomic force microscopy

Atomic force microscopy (AFM) has been used to probe the surface of a capillary after coating with "soft" polymers, notably polyacrylamides. The aim was the investigation of the efficiency of coverage of the silica surface, so as to reduce or eliminate the electroosmotic flow (EOF), particularly noxious in the separation of macromolecules. The quality of such coating is strongly dependent on two variables: temperature and pH. In the first case, progressively higher temperatures produce open silica patches, where no polymer seems to be bound. The transition from coated to largely uncoated surfaces occurs at 50 degrees C. Also the pH of the polymerizing solution strongly affects the coating efficiency. Since in all coating procedures the monomer solution is not buffered, addition of accelerator (TEMED, N,N,N'N'-tetramethylethylendiamine) induces polymer growth at pH 10-11. These pH values generate hydrolysis of the siloxane bridge anchoring the bifunctional agent (Bind Silane, onto which the polymer chain should grow) to the wall. Thus, coating and de-coating occur simultaneously. Low temperatures during polymer growth (typically 10 degrees C) and buffered solutions (pH 7, titrated after TEMED addition) ensure a most efficient and thorough coating, with virtual elimination of EOF: well coated capillaries exhibit residual EOF values, at pH 10, of the order of 10(-7) cm2 V-1 s-1 vs. a standard value for uncoated capillaries of the order of 10(-4) cm2 V-1 s-1. The AFM data have been fully confirmed by direct measurement of EOF in coated and uncoated capillaries under an electric field.