A protocol for DNA fragment extraction from polyacrylamide gels

A simple and efficient method of purifying linear plasmid DNA from contaminating DNA fragments is described. Both vector and insert containing plasmids may be used without extensive purification, in particular without cesium chloride centrifugation. Careful deproteinization with phenol-chloroform allows efficient restriction enzyme digestion. Fragment separation can be performed immediately after restriction endonuclease digestion in a single 6% polyacrylamide gel. Extraction of DNA fragments from the gel is easy and gives a good yield. The DNA may be used for ligation and transformation without further purification.     

Recovery of proteins on a milligram scale from polyacrylamide electrophoresis gels,exemplified by purification of a retinol-binding protein

An apparatus suitable for the recovery of proteins from polyacrylamide gels on a milligram scale by displacement electrophoresis (isotachophoresis) is described along with a buffer system that is suitable for this purpose with most proteins. The technique is illustrated by the recovery of a protein from a 15% polyacrylamide gel. The recovery was almost quantitative and the eluted protein showed little contamination upon quantitative amino acid analysis and automatic Edman degradation.     

Location and purification of enzymes on polyacrylamide gels using dialyzable fluorescent markers

A method for the location of proteins/enzymes by polyacrylamide gel electrophoresis using dialyzable low-molecular-weight fluorescent peptide markers is described. The markers prepared by treating the peptic digest of casein with fluorescamine showed several bands on gel electrophoresis which helped in locating the proteins. The located desired protein could subsequently be purified by extraction.     

Antigenic alteration of contaminating lipopolysaccharide during extraction of Escherichia coli outer-membrane proteins from polyacrylamide gels

An antiserum raised to the ferric enterobactin receptor protein of Escherichia coli, isolated from SDS-polyacrylamide gels, contained high-titre antibodies to the lipopolysaccharide (LPS) of E. coli O111. This antiserum was used to show that proteins dissected from polyacrylamide gels can be contaminated with comigrating LPS at levels below those detectable by very sensitive silver staining methods. Using this antiserum it was also shown that the procedures used to extract proteins from polyacrylamide gels can alter the molecular structure and, consequently, the antigenic properties of the contaminating LPS.     

Complete extraction in a form suitable for liquid scintillation counting of tritium-labeled proteins from polyacrylamide gels

Large (200 mm3) slices of polyacrylamide gels crosslinked with N,N'-diallyltartardiamide which contain tritium-labeled protein are readily solubilized in periodic acid for liquid scintillation counting of radioactivity, but the apparent recovery of label never exceeds 82%. Extraction of the slices with two commercial solubilizers at 60 degrees C gave recoveries of 82-90% which were not improved by prolonged incubation. Treatment of the slices at ambient temperature with 1.0 ml of 2% sodium periodate for 30 min followed by the addition of 0.7 ml of aqueous tetrabutylammonium hydroxide (40% w/v) gives solutions which can be immediately counted at 35% efficiency with low background and with 100% recovery of tritiated protein     

Protein transfer from fixed, stained, and dried polyacrylamide gels and immunoblot with protein A-gold

The method of electrophoretically transferring proteins from fixed and stained polyacrylamide gels onto nitrocellulose paper has been reevaluated. It is shown that the tedious destaining of gels is not necessary because Coomassie brilliant blue, although it binds tenaciously to nitrocellulose paper, does not reduce the transfer efficiency of proteins. However, its presence impairs the visibility of proteins as detected, for instance, by the immunogold technique. Therefore, a rapid method for the complete removal of the stain from the nitrocellulose paper after completion of the immunogold procedure was developed. Furthermore, it is shown that proteins from dried polyacrylamide gels can still be transferred onto nitrocellulose sheets with an efficiency of approximately 50% compared to proteins transferred from fixed gels.     

Peptide analysis by isoelectric focusing in polyacrylamide gels

We have examined the use of isoelectric focusing in polyacrylamide gels for the analysis of heterogeneous mixtures of cyanogen bromide peptides. High resolution, sensitivity, and reproducibility are obtainable under conditions which are described. Peptides having molecular weights above 1000 or 2000 can be visualized by fixation and staining. The presence of urea in the gels is important to the procedure; formation of carbamylated derivatives from this cause occurs at most in trace amounts in unfavorable cases. No artifactual heterogenelty from any other cause was apparent.     

Isolation of enzymes from polyacrylamide disk gels by a centrifugal homogenization method

A sliced segment of polyacrylamide gel was quickly homogenized without any loss of gel pieces. The gel segment was placed on a disposable pipet tip, which was packed with a small amount of lumped copper wires and held in a microfuge tube. The gel was homogenized by centrifugation for 15 s at 15,000 g at 0 to 4 degrees C. Almost 70% of endodextranase activity could be recovered from homogenized gel within 30 min at 4 degrees C, whereas only 20% of activity was eluted from gel slices. If necessary, copper wire could be replaced by fine stainless-steel wire or by the nylon string used in fishing lines. Proteins could also be recovered from the homogenized gel by charging electric current for 1 h at 4 degrees C.     

Internal sequence analysis of proteins eluted from polyacrylamide gels

We have developed an elution-digestion-sequencing (EDS) method, which yields the internal amino acid sequence of partially purified proteins. The overall yield for the method was greater than 60%. The method yielded peptide peaks that could be sequenced on HPLC for all tested proteins with masses from 45 to 200·10³ and yielded internal amino acid sequence information when as little as 10 pmol of partially purified protein was used as the starting material. The EDS method was extremely reliable and gave sequence information for each of 25 proteins tested, including high-molecular-mass proteins (M_r>100·10³) that were difficult to sequence by other methods.     

Visualization and elution of unstained proteins from polyacrylamide gels

Proteins fractionated by electrophoresis on 18% polyacrylamide gels with low crosslinking can be directly visualized by ultraviolet light-induced fluorescence and can be recovered by electroelution.     

Electrophoretic elution of macromolecules from polyacrylamide or agarose gels

A method for elution of micrograms of macromolecules from polyacrylamide and agarose gels is described. The recoveries were greater than 90% with three different macromolecules tested (28 to 360 kDa). An amount as small as 1 microgram of human serum albumin was eluted from polyacrylamide gel with 90% recovery. The eluted material is collected into a small chamber the size of which can be changed as required. Elution and concentration are achieved simultaneously and in one step under mild conditions. Sterile eluates can be obtained, if the apparatus is constructed under sterile conditions.