A rapid and simplified method for protein silver staining in polyacrylamide gels

Silver staining is widely used to detect protein in polyacrylamide gels when high sensitivity is required. A simple and rapid protocol for silver staining of proteins following PAGE was developed in the present study. The number of steps was reduced compared to conventional protocol by combining fixing, rinsing, and soaking into a single impregnating step, thus achieving detection of proteins in 20 min. The present method is as sensitive as current protocols with the advantage of saving time and costs.     

Swelling of polyacrylamide gels in polyacrylamide solutions

Swelling behavior of polyacrylamide (PAAm) and polyacrylamide-co-polyacrylic acid (PAAm-co-PAAc) gels was investigated in aqueous solutions of monodisperse PAAms with molecular weights (M_w) ranging from 1.5 × 10³ to 5 × 10⁶ g/mol. The volume of the gels decreases as the PAAm concentration in the external solution increases. This decrease becomes more pronounced as the molecular weight of PAAm increases. The classical Flory–Huggins (FH) theory correctly predicts the swelling behavior of nonionic PAAm gels in PAAm solutions. The polymer–polymer interaction parameter χ₂₃ was found to decrease as the molecular weight of PAAm increases. The swelling behavior of PAAm-co-PAAc gels in PAAm solutions deviates from the predictions of the FH theory. This is probably due to the change of the ionization degree of AAc units depending on the polymer concentration in the external solution. © 1998 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 36: 1313–1320, 1998     

Stabilizing labile DNA–protein complexes in polyacrylamide gels

The electrophoretic mobility‐shift assay (EMSA) is one of the most popular tools in molecular biology for measuring DNA–protein interactions. EMSA, as standardly practiced today, works well for complexes with association binding constants K_a>10⁹ M^?1 under normal conditions of salt and pH. Many DNA–protein complexes are not stable enough so that they dissociate while moving through the gel matrix giving smeared bands that are difficult to quantitate reliably. In this work we demonstrate that the addition of the osmolyte triethylene glycol to polyacrylamide gels dramatically stabilizes labile restriction endonuclease EcoRI complexes with nonspecific DNA sequences enabling quantitation of binding using EMSA. The significant improvement of the technique resulting from the addition of osmolytes to the gel matrix greatly extends the range of binding constants of protein–DNA complexes that can be investigated using this widely used assay. Extension of this approach to other techniques used for separating bound and free components such as gel chromatography and CE is straightforward.     

'Laterally aggregated' polyacrylamide gels for electrophoresis.

A new method is described for producing highly porous polyacrylamide matrices: polymerization in presence of a preformed hydrophilic polymer. If a standard mixture of monomers (e.g., 5%T, 4%C) is polymerized in presence of, e.g., polyethylene glycol (PEG) 10 kDa, lateral chain aggregation occurs, with formation of large pore sizes. In PEG 10 kDa, the transition from a small- to a large-pore gel is clearly apparent at 0.5% PEG addition and reaches a plateau already at 2.5% PEG. Even with shorter PEG fragments (6.2 and 1 kDa) this transition occurs, but with progressively larger amounts of PEG in solution (up to 25% for the 1 kDa species). Other polymers such as hydroxymethyl cellulose (1000 kDa) and polyvinyl-pyrrolidone (360 kDa and 25 kDa) are also able to elicit this phenomenon. It appears that lateral chain aggregation (before the cross-linking event) is induced via intra-chain hydrogen bonding, since urea and temperature strongly inhibit it, whereas tetramethylurea (an agent quenching hydrophobic interactions) does not hamper it. By scanning electron microscope, it is found that the maximum pore size obtained in a 5%T, 4%C gel in presence of 2.5% PEG 10 kDA is of the order of 0.5 micron, whereas the same 5%T, 4%C control gel would have an average pore diameter of 5 nm. Thus, an increment of pore size of about 2 orders of magnitude is obtained: in these new matrices, a 21000 bp DNA fragment exhibits a much greater migration than in a control gel in which the sample is entrapped at the application site.     

Fluorescent staining of protein in SDS polyacrylamide gels by salicylaldehyde azine

As a noncovalent fluorescence probe, in this study, salicylaldehyde azine (SA) was introduced as a sensitive fluorescence‐based dye for detecting proteins both in 1D and 2D polyacrylamide electrophoresis gels. Down to 0.2 ng of single protein band could be detected within 1 h, which is similar to that of glutaraldehyde‐silver stain, but approximately four times higher than that of SYPRO Ruby fluorescent stain. Furthermore, comparative analysis of the MS compatibility of SA stain with SYPRO Ruby stain indicated that SA stain is compatible with the downstream of protein identification by LC‐MS/MS. Additionally, the probable mechanism of the SA stain was investigated by molecular docking. The results demonstrated that the interaction between SA and protein was mainly contributed by hydrogen bonding and hydrophobic forces.     

Isoelectric focusing of human parotid salivary proteins in hybrid carrier ampholyte-immobilized pH gradient polyacrylamide gels.

Isoelectric focusing of human salivary proteins with carrier ampholyte-isoelectric focusing systems requires prior desalting and concentration of samples, a procedure which is time-consuming and requires relatively large volumes of samples. By contrast, immobilized pH gradient gels are more tolerant to salt loads. Thus pretreatment of samples consists only of centrifugation prior to isoelectric focusing. If larger loads (greater than 50 micrograms) are required, the samples may be concentrated by lyophilization and reconstitution in a smaller volume of water or by dialysis against 30% w/v polyethylene glycol. Immobilized pH gradient polyacrylamide gels (incorporating a hybrid carrier ampholyte system) of two pH ranges (pH 4-9 and pH 3.5-5.0) have been used to separate the proteins in human parotid saliva. The effects of urea on focused patterns were studied; in pH 4-9 gels it gave improved resolution of protein bands, whereas in pH 3.5-5.0 gels it prevented protein precipitation. The salivary proteins were then visualized by staining with Coomassie Brilliant Blue G-250 or a silver procedure. Using the latter, 25-30 well-resolved bands were formed on a pH 4-9 gel loaded with 20 micrograms of proteins. The method offers considerable advantages compared with carrier ampholyte-isoelectric focusing.     

GELANAL, a personal computer-program to compare protein patterns on two-dimensional polyacrylamide gels

Comparing and analyzing a series of two-dimensional gels by hand is troublesome and subjective. So far a number of systems for automatic analysis have been developed on mainly mainframe computers, using complex algorithms. This paper presents an inexpensive system, based on a simple Pascal program, to compare individual spots on two-dimensional gels using an IBM or compatible personal computer in a qualitative way. The accuracy of the method is demonstrated by comparing two patterns of the same extract from different runs.     

Preparative isolation of protein complexes and other bioparticles by elution from polyacrylamide gels

Due to its unmatched resolution, gel electrophoresis is an indispensable tool for the analysis of diverse biomolecules. By adaptation of the electrophoretic conditions, even fragile protein complexes as parts of intracellular networks migrate through the gel matrix under sustainment of their integrity. If the thickness of such native gels is significantly increased compared to the analytical version, also high sample loads can be processed. However, the cage-like network obstructs an in-depth analysis for deciphering structure and function of protein complexes and other species. Consequently, the biomolecules have to be removed from the gel matrix into solution. Several approaches summarized in this review tackle this problem. While passive elution relies on diffusion processes, electroelution employs an electric field to force biomolecules out of the gel. An alternative procedure requires a special electrophoresis setup, the continuous elution device. In this apparatus, molecules migrate in the electric field until they leave the gel and were collected in a buffer stream. Successful isolation of diverse protein complexes like photosystems, ATP-dependent enzymes or active respiratory supercomplexes and some other bioparticles demonstrates the versatility of preparative electrophoresis. After liberating particles out of the gel cage, numerous applications are feasible. They include elucidation of the individual components up to high resolution structures of protein complexes. Therefore, preparative electrophoresis can complement standard purification methods and is in some cases superior to them.     

Fast fluorescent staining of protein in sodium dodecyl sulfate polyacrylamide gels by palmatine

A fast and sensitive protein fluorescent detection method in SDS-PAGE using the natural product palmatine is described. Palmatine is an alkaloid found in various plants exhibiting a broad spectrum of antibiotic activity in humans. The sensitivity of palmatine staining is similar to those of the SYPRO Red, SYPRO Tangerine, and SYPRO Orange protein gel stains - about 4 ng per protein band. This detection sensitivity is comparable to colloidal CBB staining. Since proteins stained with palmatine do not need destaining, the staining procedure can be easily shortened and completed in about 30 min. Stained proteins can be photographed using a UV transilluminator. The results of the present study suggest that the palmatine staining is sensitive, rapid, low cost, and safe for a broad application to the research of protein.     

Electrospray mass spectra from protein electroeluted from sodium dodecylsulfate polyacrylamide gel electrophoresis gels

Electrospray ionization/tandem mass spectrometry of proteins separated on sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE) gels is severely limited by the requirement that the protein be completely separated from the SDS. As shown here, the gaseous noncovalent SDS adducts of protonated proteins thus formed can be dissociated by infrared irradiation. ESI spectra from myoglobin in SDS-containing solutions show molecular ions adducted with up to 15 dodecyl sulfates, but ir irradiation of these ions causes complete dissociation to expel the SDS.     

Cysteine adducts of human haemoglobin measured by isoelectric focusing in polyacrylamide gels with a non-linear pH gradient

The in vitro formation of adducts from human haemoglobin formed by alkylation with methyl-methanesulphonate, dimethyl sulphate and iodoacetamide was determined with isoelectric focusing in ultra-thin polyacrylamide gels with a non-linear pH gradient. The most important adduct seen in the gels was identified as HbA alkylated at the beta-93 cysteine. Influences of the chemical nature of the alkylating agents and of the biological environment are discussed. The method is suggested to be applicable to monitoring the biological effects of low, long-term exposure to mixtures of alkylating agents or of exposure to unknown compounds.     

A motor-driven syringe-type gradient maker for forming immobilized pH gradient gels

A motor driven gradient maker based on the commercial model (Jule Inc., Trumbull, CT) was designed for immobilized pH gradient gels to provide small volumes, rapid stirring and delivery, strict volume and temperature control and air exclusion. The device was constructed and by a convenient procedure yields highly reproducible gradients either in solution or on polyacrylamide gels.     

Laser light scattering study of polyacrylamide gels

Laser light scattering experiments with polyacrylamide gels containing diffusing bovine plasma albumin are described. Complete heterodyne beating has not been assumed, and an account is given of a novel method for finding the degree of spectral broadening by scanning angles of scatter while measuring the temporal autocorrelation function. Results obtained by this method for polyacrylamide gels and un-cross-linked solutions in the absence of diffusing protein, are compared with those of other authors. In the presence of the protein there is a complex interaction between the diffusion coefficient of the protein and the coefficient associated with the diffusing fluctuations in segment density of polyacrylamide. The diffusing protein dominates at low gel concentrations, and the gel density fluctuations dominates at high gel concentrations. It is proposed that the protein preferentially occupies the less dense regions of the gel, so that at low gel concentrations, where it diffuses faster than the gel fluctuations, it tends to cancel them out, whereas at high gel concentrations where the protein is highly impeded by the gel structure, it tends to be carried along by the gel density fluctuations.     

Silver staining of DNA in polyacrylamide gels

Nucleic acids can be detected at the picogram level using a quick and simple silver staining method (2). Using very thin polyesterbacked polyacrylamide gels, a further simplified protocol was compared to other widely used silver staining procedures. The improved protocol described here was the most sensitive, the fastest to perform, and had relatively few steps and reagents. This method also produced the least number of staining artifacts and offered images of high contrast.     

Reinforcement of cellulose nanofibers in polyacrylamide gels

Cellulose nanofibers (CNFs) have emerged as a promising nanofiller for effective reinforcement of nanocomposites due to their excellent mechanical properties. In this study, CNFs were fabricated by a simple grinding method and used to strengthen polyacrylamide (PAM) gels through in situ free radical polymerization. The morphology, compression properties, and chemical structure of the prepared gels were investigated. The results showed that large amounts of nanofibers embedded inside the PAM matrix and formed network structure by increasing the CNF content. Significantly, PAM/CNF gel with 5 wt% CNF exhibited highly improved compression strength by 6.8-fold as compared to that of pure PAM gel. The FTIR analysis indicated that hydrogen bondings between CNF and PAM chains mainly contributed to the superior mechanical properties of the hybrid gels. In summary, this study provides a novel alternative approach for preparing tough composite gels by combing rigid CNF and soft polymer and extending the application of biomedical load-bearing gel materials such as artificial cartilage and other soft tissues.     

Electroosmotically enhanced mass transfer through polyacrylamide gels

We present an internal pumping strategy to enhance solute fluxes in polymer gels. The method is based on electroosmotic flow driven by an electric field applied across a gel that has been doped with charged colloidal inclusions. This work is motivated by the need to enhance the transport in gel-based biosensor devices whose response dynamics are often mass transfer limited. In this case, polyacrylamide gel slabs were doped with immobilized, charged silica colloids, and the flux of a fluorescent tracer was measured as a function of applied field strength, the volume fraction and size of the colloidal silica inclusions, and the bulk electrolyte composition. Significant flux enhancements were achieved with applied electric currents on the order of a few mA. Control experiments indicated that the flux enhancement was not due to any distortion of the gel diffusional properties in response to the presence of the inclusions. At a constant inclusion volume fraction, the electroosmotic solute flux enhancement was strongest for the smallest particle sizes that provide the highest total surface area, consistent with the electroosmotic mechanism whereby fluid flow is generated along the solid/liquid interface.