Electrophoretic mobility shift assay protocol

A mobility shift assay is electrophoretic separation of a protein—DNA or protein—RNA mixture on a polyacrylamide or agarose gel for a short period about 1. However, assuming that the protein is capable of binding to the fragment, the lane with a protein that binds present will contain another band that represents the larger, less mobile complex of nucleic acid probe bound to protein which is 'shifted' up on the gel since it has moved more slowly.

Under the correct experimental conditions, the interaction between the DNA or RNA and protein is stabilized and the ratio of bound to unbound nucleic acid on the gel reflects the fraction of free and bound probe molecules as the binding reaction enters the gel. This stability is in part due to a "caging effect", in that the protein, surrounded by the gel matrix, is unable to diffuse away from the probe before they recombine.

If the protein concentration is not known but the complex stoichiometry is, the protein concentration can be determined by increasing the concentration of DNA probe until further increments do not increase the fraction of protein bound. By comparison with a set of standard dilutions of free probe run on the same gel, the number of moles of protein can be calculated. An antibody that recognizes the protein can be added to this mixture to create an even larger complex with a greater shift. This method is referred to as a supershift assay , and is used to unambiguously identify a protein present in the protein — nucleic acid complex.

Often, an extra lane is run with a competitor oligonucleotide to determine the most favorable binding sequence for the binding protein. The use of different oligonucleotides of defined sequence allows the identification of the precise binding site by competition not shown in diagram.

Electrophoretic Mobility Shift Assays for RNA–Protein Complexes

Variants of the competition assay are useful for measuring the specificity of binding and for measurement of association and dissociation kinetics. Once DNA-protein binding is determined in vitro , a number of algorithms can narrow the search for identification of the transcription factor.

Consensus sequence oligonucleotides for the transcription factor of interest will be able to compete for the binding, eliminating the shifted band, and must be confirmed by supershift. If the defined DNA elements conform to consensus transcription factor binding sites, and if specific antibodies are available, then EMSA supershifts can be employed to possibly identify the interacting proteins.

Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions.

However, if appropriate supershift antibodies are not available, then EMSA is of limited value in the identification of novel DNA-binding proteins. The traditional route to the identification of cognate trans -acting factors, the biochemical isolation and identification of DNA-binding proteins, is usually a long and labor-intensive process. Purification of transcription factors often involves four or five different chromatographic steps, including ion exchange, gel filtration, and nonspecific and sequence-specific DNA affinity columns 2.

The major impediment to the rapid identification of a transcription factor of interest is the fact that they are generally present in low concentrations, usually less than 0. Additionally they often bind with moderate affinity 3. Recent advents in proteomics and mass spectrometry have created unprecedented power in protein identification. For example, proteins have recently been analyzed directly by matrix-assisted laser desorption ionization time-of-flight mass spectrometry utilizing DNA probes harboring specific sequence motifs 4. Utilizing the power of two-dimensional electrophoresis 2DE and mass spectrometry MS , we have established a novel technique to isolate transcription factors.

General Principle

More importantly, our method obviates the need for laborious and extensive purification of the protein of interest. In this paper, the methodology required and the successful isolation of a functionally relevant transcription factor have been described using our novel proteomics approach. This repeat forms part of a functionally important microsatellite repressor sequence within the CD30 promoter 5. Traditional methods such as sequence-specific DNA affinity chromatography, coupled with chromatographic purification of nuclear proteins, proved unsuccessful because of the high abundance and affinity of nonspecific nuclear proteins.

These candidates were characterized further by excision from a two-dimensional gel at the predetermined pI and MM. Proteins were then eluted, renatured, and tested for original activity in EMSA, and candidate spots were subsequently analyzed by mass spectrometry, and their identity was determined. Finally, we confirmed the identity of the protein isolated via our novel method using EMSA supershift analysis. An overview of the method is shown in Fig. Schematic representation of the novel proteomics approach. The method consists of four phases; first, nuclear proteins are partially purified by S gel filtration.

Next, gel slices are excised from a two-dimensional gel at the predetermined pI and MM coordinate. Identified protein spot candidates are subjected to MS to determine their identity. Nuclear extracts were then subjected to an ammonium sulfate cut 0. Gel slices were crushed into 1. Additionally, molecular mass standards were used to determine the molecular mass intervals of the excised gel slices.

Automatic Translation

Four successive concentration and reconstitution cycles in rehydration solution ensured both buffer exchange and removal of salts for IEF. Strips were rinsed briefly in SDS running buffer 25 m m Tris, m m glycine, 0. Electrophoresis was performed at 20 mA until the dye front reached the anodic end of the gels.


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Monoisotopic peaks were searched against human proteins, 1— kDa, with a maximum of one missed cleavage, unmodified cysteines, and with a mass tolerance of ppm. We were interested in identifying the components of complex E that bound to this repeat sequence. Jurkat nuclear extracts were fractionated using Sephacryl S gel filtration. Fractionation of the extract resulted in partial purification of complex E, as activity was detected mainly in fraction 39 Fig. Fraction 39 F39 contained peak complex E activity and did not contain any of the other complexes. Blank , contains radiolabeled probe only, in binding buffer.

Concentrated crude nuclear extract was analyzed by SDS-PAGE, and fractions of discrete molecular mass intervals were excised and eluted from the gel. Complex E activity was detected in the 55—kDa fraction Fig. This lane also contains two other complexes that are not seen in the crude nuclear extract binding profile.

These complexes may represent multimers of complex E constituents and suggested that complex E is most likely a monomer or homomeric protein complex although it was possible that it consisted of heteromeric subunits that were within the same molecular mass range.

Reagents and Solutions

Complex E contains a monomeric protein of 55—66 kDa. Complex E activity was detected in the 55—kDa fraction see arrow. Protein complexes are indicated with arrows. Unbound radiolabeled oligonucleotide is indicated as Free Probe. Sephacryl fractionation demonstrated that fraction 36 Fig.

Electrophoretic mobility shift assay (EMSA)

Peak complex E activity was detected in two intervals, pI 5. Complex D activity was also reconstituted, and peak activity was seen in the pI 5. Also another complex, which was not seen in the crude nuclear extract binding profile, was seen with peak activity in the pI 4. This complex may represent a nonspecific DNA-binding protein that is normally out competed in the S fractions but is able to bind in the IEF-purified fraction.

Fraction 36 was analyzed by IEF, and pI fractions were isolated in gel pieces. Email Address. Password Forgot Password. Remember me.


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  4. Sign up to our newsletter. Simple interactions Label the RNA of interest. Prepare the labeled RNA with purified protein under suitable binding conditions e. Prerun the gel for 30 min. If the interactions are suspected to be unstable, run the gel in a cold room. Expose the gel to a phosphorimager or X-ray film. Gel-purify the RNA to make sure that the substrate will be a single band on a gel. Incubate the labeled RNA with purified protein under suitable binding conditions.

    Incubate for 10 min at room temperature. Load this sample onto a 1.