Quantitative electroelution of oligonucleotides and large DNA fragments from gels and purification by electrodialysis

We have designed a new device [Biotrap (Elutrap in the U.S.A. and Canada), available from Schleicher & Schuell] for electroelution, -concentration , and -dialysis of DNA and other charged macromolecules above 5 kDa. In an electric field, the DNA migrates in an open channel out of the gel slice through a microporous membrane, BT2, into the trap section, where it is retained by a very dense, non-adsorbant, and inert membrane BT1. Specifically designed for use in an electric field, the matrix of this new membrane is much denser than that of dialysis membranes. In contrast to dialysis membranes, BT1 will not adsorb large DNA fragments nor allow passage of small DNA fragments when subjected to an electric field. In the absence of an electric field, BT1 and BT2 effectively seal the trap, maintaining the final elution volume of the purified sample. The trap can contain from 200-600 microliter and is collected from above with a pipet. In the experiments described here, 85-95% of oligonucleotides (14-mer) and large (150 kb) DNA fragments were recovered, independent of fragment length. The purity of the eluted DNA was demonstrated by restriction enzyme digestion, nick-translation, primer extension, end-labeling with polynucleotide kinase, and ligation. Electrodialysis was successfully used for the complete removal of common contaminants inhibiting the polynucleotide kinase reaction and for the removal of CsCl from DNA samples.     

Development and optimization of a binding assay for histone deacetylase 4 using surface plasmon resonance

Electroelution is a widely used methodology for protein purification. In this study, a practical and low-cost system for protein electroelution from stained polyacrylamide gels was developed. For this, a horizontal protein electroelution cuve was constructed with glass plates, 1.5-ml capacity microcentrifuge tubes, and dialysis membrane. Analyses of the system efficiency showed high protein recovery from nonfixed and fixed sodium dodecyl sulfate (SDS)-polyacrylamide gels.     

Plasma membrane isolated from Giardia lamblia: identification of membrane proteins

Two methods are introduced for preparing plasma membranes from Giardia lamblia trophozoites. Isolated membranes were purified by centrifugation on either a sucrose step-gradient or a self-generated Percoll gradient, where they band at a density of approximately 1.04 g ml-1. In pure fractions, membranes formed vesicles or extensive sheets. Electron microscope profiles show that they are asymmetric with a thin filamentous coat on one side. Membrane proteins were resolved by SDS/PAGE. They included a major component of apparent Mr 75,000 (75 kDa), and additional bands detectable by gel staining at 58 kDa, 54 kDa, 32 to 38 kDa (5 bands), 22 kDa, and 15 to 20 kDa. To probe the surface location of proteins, gels were also prepared from Giardia cells that were surface radio-iodinated using the immobilised catalyst IODOGEN. The 75 kDa membrane protein was strongly labelled in the corresponding autoradiograph, also the bands at 58 kDa and 54 kDa, the 22 kDa polypeptide, and some faint bands not resolved in the isolated membrane preparations. The set of close-running bands at 32 to 38 kDa were not iodinated. The labelled 58 kDa and 54 kDa proteins comigrated with alpha and beta-tubulins. Controls showed that cytoskeleton and flagellar tubulins were not iodinated in this experiment, indicating that the labelled tubulin is surface-derived. The principal approximately 75 kDa surface protein identified in isolated membranes probably corresponds to an iodinatable and antibody-precipitated "82 kDa" antigen reported previously.     

Efficacy and compatibility with mass spectrometry of methods for elution of proteins from sodium dodecyl sulfate-polyacrylamide gels and polyvinyldifluoride membranes

The resolving power of sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) combined with isoelectric focusing in two-dimensional gel electrophoresis has made it one of the most important techniques for resolving complex mixtures, and it is of great importance for proteome mapping projects. As a result of this, methods for postelectrophoretic protein characterization are of great interest as exemplified by in situ protease digestion combined with mass spectrometry (MS), which is the method of choice for identification of proteins. In this study we have developed and compared methods for recovering intact proteins from polyacrylamide gels and electroblotting membranes to define efficient methods compatible with MS. These methods complement in situ digestion protocols and allow determination of the molecular mass of whole proteins separated by SDS-PAGE. Passive elution of proteins from SDS-PAGE gels was efficient only in the presence of SDS, whereas electroelution was achieved using buffers without SDS. Surface-enhanced laser desorption/ionization MS (SELDI-MS) analysis of proteins eluted in the presence of SDS was possible using ion exchange ProteinChip arrays for concentration of sample and removal of SDS. Comparison of different electroblotting methods verified that the different membranes and buffers were equally efficient for transfer of proteins in the range 20-100 kDa. Elution from polyvinyldifluoride membranes was most efficient using either concentrated solutions of trifluoroacetic acid (TFA) or combinations of 8M urea and 1% Triton X-100, 1% Tween 20, or 40% isopropanol. The same result was obtained using nitrocellulose membranes, except that these were incompatible with organic solvent and TFA. Elution by TFA was compatible with matrix-assisted laser desorption/ionization MS (MALDI-MS) but was complicated by a high degree of trifluoroacetylation of the proteins. Alternatively, elution by 8M urea+1% Triton X-100, 1% Tween 20, or 40% isopropanol was compatible with both SELDI-MS and MALDI-MS. Eluted proteins were identified in MS experiments by intact mass determination, by peptide mapping, and by MS/MS analysis.     

从琼脂糖电泳凝胶中回收DNA的几种简便方法

介绍两类从普通琼脂糖电泳凝胶中回收ＤＮＡ的简便、快捷、高效且廉价的方法．第一类为电泳洗脱法．方法ａ：利用１．５ｍＬ微量离心管、ｌｍＬ吸头、尼龙网膜和透析膜做成的一个小装置,快速有效回ＤＮＡ,最终回收率为７０％左右．方法ｂ：不用ＤＥＡＥ－纤维素膜,而用透析膜在凝胶中作出横隔挡在ＤＮＡ条带前,最终回收率为５０％左右;第二类为冰冻融解法,最终回收率也在５０％左右．如果联合使用冰冻融解法和电泳洗脱法,回收率可进一步提高至９０％．     

蜘蛛HMW-gDNA的电洗脱纯化提取

该文研究了蜘蛛大分子量基因组DNA（HMW-gDNA）的提取以及一种高效电洗脱纯化装置的构建。以蜘蛛胸部肌肉组织为原料,通过自改良CTAB法提取蜘蛛HMW-gDNA,利用透析膜和2 mL离心管构建一种新的HMW-gDNA快速凝胶回收装置,并对蜘蛛HMW-gDNA进行电洗脱分离回收。结果显示,改良CTAB法可高效提取蜘蛛HMW-gDNA（>48.5 kb）,且通过透析膜的截留作用,对普通琼脂糖凝胶中目的HMW-gDNA进行快速电洗脱分离,其回收率超过75%,OD₂₆₀/OD₂₈₀处于1.8～2.0之间,对HMW-gDNA完整性无影响。综合结果表明, 改良CTAB法可用于蜘蛛HMW-gDNA的提取,此电洗脱纯化装置可从普通琼脂糖中高效回收HMW-gDNA,是一种低成本、简捷、高效且实用性强的凝胶回收方法。     

Recovery of DNA from agarose gels using a modified Elutrap.

We have made a significant improvement in the electroelution device, Elutrap (Schleicher and Schuell) by substituting an agarose gel barrier, which is made from 0.6% agarose (SeaKem GTG; FMC Corporation), into the elution chamber in place of the manufacturer specified BT2 membrane. This modification substantially increases the DNA recovery from agarose gels, even in samples containing less than 1 microgram of DNA, and shortens elution times particularly for large sizes of DNA (greater than 4.4 kbp). Additionally, the gel barrier provides a reproducible quantity and quality of DNA recovery. The high quality of the eluted DNA using the modified Elutrap makes this system suitable for further DNA manipulations.     

Encapsulation of proteins into human erythrocytes: a kinetic investigation

Moderate osmotic shocks of human erythrocytes by hypotonic dialysis (0.06 mosmol/kg) induce cell swelling and formation of pores, without causing apparent lysis. Using 125I-labeled macromolecules of different molecular weight and net charge, we followed the kinetics and efficiency of their encapsulation into erythrocytes. After a 20-30 min period of cell dialysis, macromolecules of up to 50 kDa begin diffusing into the swollen cells by a process which can be described by a first-order two-compartment kinetics. Adsorption to the external cell surface was insignificant, while adsorption to the inner membrane surface was substantial (15-20%) only for positively charged proteins, at physiological pH. After resealing, pores of a 12-14 kDa cut-off might remain open allowing some release of entrapped material (20-30%), depending on the final cytocrit, while the remaining might be associated with inner membrane or cytosolic components. Although the method of hypotonic dialysis is known to affect minimally the biophysical and immunological properties of red blood cell membranes, the interaction of encapsulated material with cell constituents would need to be further assessed when considering red cells as macromolecular carriers.     

Immunoaffinity purification of membrane protein constituents of the IM-9 lymphoblast receptor for substance P

Substance P (SP) is an undecapeptide neuromediator that stimulates human T-lymphocyte function by binding to stereospecific membrane receptors. Human IM-9 cultured B-lymphoblasts express approximately 20,000 receptors per cell for [125I]SP with a Kd of 0.3 nM. [125I]SP was specifically crosslinked by disuccinimidyl suberate to IM-9 cell membrane proteins of 78, 58, and 33 kDa. An indirect immunoaffinity purification procedure has now been developed based on immunoabsorption of detergent-solubilized [125I]SP-labeled IM-9 cell membrane proteins to anti-SP antibody that was bound to an epoxide ultraffinity high-performance liquid chromatography column, followed by elution in acidic 8 M urea. The 58- and 33-kDa SP-receptor complexes were purified to apparent homogeneity by immunoaffinity chromatography and identified by autoradiography and silver staining of sodium dodecyl sulfate-polyacryl-amide gels.     

COST-EFFECTIVE AND EFFICIENT APPARATUS FOR ELECTROELUTION OF MICRO- AND MACROGRAM QUANTITIES OF PROTEINS FROM POLYACRYLAMIDE GELS

Protein recovery from gel electrophoresis plays a significant role in functional genomics and proteomics. To assist in this, a simple, cost-effective, and efficient apparatus for electroelution of proteins has been designed. The performance of the apparatus was demonstrated using the proteins bovine serum albumin (BSA), phosphorylase, ovalbumin, pepsin, and trypsinogen. In all the cases the yield of elution was found to be consistently greater than 85% and the proteins could be eluted without degradation in less than 15 min. The utility of this method can be extended to protein elution from denatured and native polyacrylamide gels, DNA purification from agarose gels, and oligomeric primers purification from polyacrylamide gels. In addition to this, the method offers an effortless purification and characterization of microbial extracellular proteins. The eluted proteins can be directly used in N-terminal amino acid sequencing, and in amino acid and proteomics analyses.     

Fast electrotransfer of human serum proteins in their native state from polyacrylamide thin gradient gels reinforced by textiles to polyvinylidene difluoride membranes. Rapid electrotransfer from thin gradient gels reinforced by textiles.

A fast electroblotting technique of native molecules electrophoretically separated in thin (0.25 to 0.5 mm) gradient gels, onto a high capacity membrane of polyvinylidene difluoride is described. Omitting methanol during transfer, the equilibration step is avoided and the same buffer is used in electrophoresis and transfer. As the gel reinforced by fabric never swells nor shrinks, and as all the bands are blotted, the transfer matrix exactly reflects the protein pattern of the original gel. Autoradiography is enhanced and electroelution is homogeneous in all parts of the gels. Significant improvement is noticed in binding proteins of molecular weight from about 20 kDa to more than 700 kDa, as suggested by complete electroelution of all native serum components.     

Electrophoretic transfer of proteins from sodium dodecyl sulfate-polyacrylamide gels to a positively charged membrane filter

Zeta-bind, a positively charged nylon membrane, was tested as an immobilizing matrix for the electrophoretic transfer of proteins from sodium dodecyl sulfate-polyacrylamide gels. It was found that Zeta-bind has a considerably greater capacity than does nitrocellulose for protein binding. Because of this property, more efficient elution of proteins from gels can be used (by omitting methanol from transfer buffers). The procedure described is more amenable to quantitation than usual nitrocellulose-based transfer. Antibody or lectin overlay techniques are also more sensitive on Zeta-bind than on nitrocellulose.     

Assocation of the 33 kDa extrinsic polypeptide (water-splitting) with PS II particles: immunochemical quantification of residual polypeptide after membrane extraction

Various washing procedures were tested on Triton-prepared PS II particles for their ability to remove the 33 kDa extrinsic polypeptide (33 kDa EP) associated with the water-splitting complex. Residual 33 kDa EP was evaluated by Coomassie blue staining of SDS gels of washed particles and by Western blotting with an antibody specific for the 33 kDa EP. A wash with 16 mM Tris buffer, pH 8.3, inhibited water-splitting activity but did not remove all the 33 kDa EP. Sequential washes with 30 mM octyl glucoside (pH 8.0 and 6.8), and a single wash with 0.8 M Tris were also ineffective in removing all the 33 kDa EP. Washing with 1 M CaCl₂ was more effective in removing 33 kDa EP; while only a faint trace of protein was detectable by Coomassie-staining, immunoblotting revealed a considerable remainder. The treated particles retained some water-splitting activity. The two step procedure of Miyao and Murata (1984) involving 1 M NaCl and 2.3 M urea was most effective, removing all but a trace of antibody positive protein. Our finding suggests that (1) the degree of depletion of the 33 kDa EP cannot be judged on the basis of Coomassie stain alone, and (2) this extrinsic protein is very tightly associated with the membrane, perhaps via a hydrophilic portion of this otherwise hydrophilic protein. The results also suggest that the presence or absence of the 33 kDa protein per se is not the primary determinant of residual water splitting activity.Abbreviations Chl chlorophyll - DCPIP dichlorophenolindophenol - DPC diphenolcarbazide - DTT dithiothreitol - HEPES N-2-hydroxyethylpiperazine-N-2-ethanesulfonic acid - MES 2(N-morpholino)ethanesulfonic acid - SDS sodium dodecyl sulfate - Tris Tris(hydroxymethyl)aminomethane     

The plasma membrane proteome of germinating barley embryos

Cereal seed germination involves a complex coordination between different seed tissues. Plasma membranes must play crucial roles in coordination and execution of germination; however, very little is known about seed plasma membrane proteomes due to limited tissue amounts combined with amphiphilicity and low abundance of membrane proteins. A fraction enriched in plasma membranes was prepared from embryos dissected from 18 h germinated barley seeds using aqueous two‐phase partitioning. Reversed‐phase chromatography on C₄ resin performed in micro‐spin columns with stepwise elution by 2‐propanol was used to reduce soluble protein contamination and enrich for hydrophobic proteins. Sixty‐one proteins in 14 SDS‐PAGE bands were identified by LC‐MS/MS and database searches. The identifications provide new insight into the plasma membrane functions in seed germination.     

Transfer in SDS of biotinylated proteins from acrylamide gels to an avidin-coated membrane filter

Avidin was covalently linked to aldehyde-derivatized polyethersulfone membrane filters. These filters were used in Western blot analysis of proteins reacted with biotinylation reagents and electrophoresed in sodium dodecyl sulfate (SDS) on polyacrylamide gels. Electrophoretic transfer from the gels to these filters was in 0.1% SDS, in which the covalently bound avidin retained its biotin-binding capacity. We compared Western blots on avidin-coated membrane filters of biotinylated and nonbiotinylated forms of mouse immunoglobulin G (IgG), mouse IgG heavy chain, muscle-type acetylcholine receptor alpha subunit, and fused alpha and beta subunits of receptor. Biotinylated proteins were captured with high specificity compared to their nonbiotinylated counterparts and sensitively detected on the avidin-coated membranes.     

Efficient transfer of proteins from acetic acid-urea and isoelectric-focusing gels to nitrocellulose membrane filters with retention of protein antigenicity

A method which facilitates the rapid and quantitative electrophoretic transfer of proteins from gels not containing sodium dodecyl sulfate (SDS) to nitrocellulose membranes is described. The equilibration of non-SDS-polyacrylamide gel electrophoretic gels in a buffer containing SDS confers a net negative charge to the proteins present, presumably as a result of the formation of SDS-protein complexes. Proteins from gels equilibrated in the SDS buffer and then electroblotted in a Tris-glycine buffer at pH 8.3 are transferred with much greater efficiency than are proteins from untreated gels. The method has been shown to significantly enhance the electrophoretic transfer of polyoma viral proteins resolved in either acetic acid-urea or isoelectric-focusing gels to nitrocellulose membranes, and it is suggested that the method should have universal applicability to all gel electrophoresis systems currently employed. The proteins from isoelectric-focusing gels treated with SDS and transferred to nitrocellulose membranes were found to retain antigenicity to antisera prepared against either denatured or native viral proteins.     

Purification of daptomycin binding proteins (DBPs) from the membrane of Enterococcus hirae

Daptomycin binding proteins (DBPs) are membrane proteins which act as daptomycin targets. Daptomycin is a cyclic lipopeptide antibiotic which is active against Gram-positive bacteria and was shown to be the first inhibitor of lipoteichoic acid (LTA) synthesis. It was found that the antibiotic did not penetrate the bacterial cytoplasm but bound membranes with a non-covalent bond and in particular some proteins which were called DBPs. DBPs were indicated as enzymes involved in LTA synthesis whose binding and inhibition by daptomycin is responsible for the observed effect on bacterial LTA synthesis. The purification of DBPs will make it possible not only to shed light on the biosynthesis of the cell wall polymer but will also provide innovative targets for selection of new antibacterial compounds. In this study, the purification of DBPs is described. Affinity chromatography was used with daptomycin as the ligand. Final elution of DBPs from daptomycin-coupled resin was performed using either 0.1% SDS or 3 M NaCl. Polyacrylamide gel electrophoresis of the eluted protein fractions consistently showed four protein bands (ranging from 55 to 66 kDa) in denaturating conditions and two protein bands (60 and 66 kDa) in non-denaturating conditions. Isoelectrofocusing analysis of the same sample consistently revealed two bands with pIs around 5. That these purified proteins were really the desired DBPs is demonstrated by the retention of daptomycin-binding capability they displayed.     

A microdialysis method for the in situ investigation of the action of large peptide molecules in human skeletal muscle: detection of local metabolic effects of insulin

The possibility of using microdialysis catheters with a large pore size dialysis membrane (100 kDa) to investigate the action of macromolecules perfused into the interstitial space of peripheral tissues was explored. This was made possible by increasing the colloid osmotic pressure of the perfusate with 40 g/l of dextran-70 to prevent perfusate loss across the dialysis membranes. Microdialysis catheters were inserted into the quadriceps femoris muscle of 13 human subjects. With different perfusion flow rates (1. 33, 0.66, 0.33 and 0.16 microl/min) the recorded concentrations of glucose, lactate, and urea were in agreement with values previously obtained using a conventional membrane with a smaller pore size (20 kDa) [Rosdahl H, Hamrin K, Ungerstedt U, Henriksson. J Am J Physiol 1998;274:E936-45.]. When insulin was added to the perfusate, the concentration of glucose was significantly reduced, indicating that insulin diffuses across the dialysis membrane and has cellular effects that can be simultaneously recorded. The present findings are the first documentation on the use of microdialysis to study the local metabolic action of large peptide molecules in human tissues and may open new avenues for in-vivo metabolic research.     

Preparative elution of proteins blotted to Immobilon membranes

Conditions for the preparative elution of proteins from Immobilon membranes after transfer of proteins to this matrix from sodium dodecyl sulfate-polyacrylamide gels have been established. Proteins were completely eluted from the membrane at room temperature by short incubation in 50 mM Tris-HCl, pH 9.0, containing 2% SDS and 1% Triton X-100. Good protein recoveries were also obtained in the same buffer containing 1% Triton X-100 only. The efficiency of elution was practically independent of the molecular weight of proteins, the method allowed for the precise excision of protein bands, and the proteins eluted from the matrix were not degraded. In some cases it was possible to recover enzymatic activity of the eluted proteins.     

简便实用的琼脂糖凝胶回收DNA片段方法

介绍一种简便实用的DNA片段回收方法,与以前所报道的DEAE-纤维素膜电泳法、透析袋电洗脱法、低融点琼脂糖凝胶法、凝胶冻融法等相比,所需器材简单、操作简便、回收率高、成本低。回收的DNA片段在进一步克隆和测序中表现出较好的效果,是一种适合于科研和教学的实验方法。