Normalization of Western blot data is an analytical step that is performed to compare the relative abundance of a specific protein across the lanes of a blot or gel under diverse experimental treatments, or across tissues or developmental stages. [1] [2] The overall goal of normalization is to minimize effects arising from variations in experimental errors, such as inconsistent sample preparation, unequal sample loading across gel lanes, or uneven protein transfer, which can compromise the conclusions that can be obtained from Western blot data. [1] Currently, there are two methods for normalizing Western blot data: (i) housekeeping protein normalization and (ii) total protein normalization. [1] [2] [3] [4]
Normalization occurs directly on either the gel or the blotting membrane. First, the stained gel or blot is imaged, a rectangle is drawn around the target protein in each lane, and the signal intensity inside the rectangle is measured. [1] The signal intensity obtained can then be normalized with respect to the signal intensity of the loading internal control detected on the same gel or blot. [1] When using protein stains, the membrane may be incubated with the chosen stain before or after immunodetection, depending on the type of stain. [5]
Housekeeping genes and proteins, including β-Actin, GAPDH, HPRT1, and RPLP1, are often used as internal controls in western blots because they are thought to be expressed constitutively, at the same levels, across experiments. [1] [2] [6] [7] However, recent studies have shown that expression of housekeeping proteins (HKPs) can change across different cell types and biological conditions. [1] [8] [9] [10] Therefore, scientific publishers and funding agencies now require that normalization controls be previously validated for each experiment to ensure reproducibility and accuracy of the results. [8] [9] [10]
When using fluorescent antibodies to image proteins in western blots, normalization requires that the user define the upper and lower limits of quantitation and characterize the linear relationship between signal intensity and the sample mass volume for each antigen. [1] Both the target protein and the normalization control need to fluoresce within the dynamic range of detection. [1] Many HKPs are expressed at high levels and are preferred for use with highly-expressed target proteins. [1] Lower expressing proteins are difficult to detect on the same blot. [1]
Fluorescent antibodies are commercially available, and fully characterized antibodies are recommended to ensure consistency of results. [11] [12] [13]
When fluorescent detection is not utilized, the loading control protein and the protein of interest must differ considerably in molecular weight so they are adequately separated by gel electrophoresis for accurate analysis. [1]
Membranes need to be stripped and re-probed using a new set of detection antibodies when detecting multiple protein targets on the same blot. [6] Ineffective stripping could result in a weak signal from the target protein. [6] To prevent loss of the antigen, only three stripping incubations are recommended per membrane. [6] It could be difficult to completely eliminate signal from highly-abundant proteins, so it is recommended that one detects lowly-expressed proteins first. [6]
Since HKP levels can be inconsistent between tissues, scientists can control for the protein of interest by spiking in a pure, exogenous protein of a known concentration within the linear range of the antibody. [8] [9] [10] Compared to HKP, a wider variety of proteins are available for spike-in controls. [14]
In total protein normalization (TPN), the abundance of the target protein is normalized to the total amount of protein in each lane. [3] [4] Because TPN is not dependent on a single loading control, validation of controls and stripping/reprobing of blots for detection of HKPs is not necessary. [6] [15] This can improve precision (down to 0.1 μg of total protein per lane), cost-effectiveness, and data reliability. [16]
Fluorescent stains and stain-free gels require special equipment to visualize the proteins on the gel/blot. [5] Stains may not cover the blot evenly; more stain might collect towards the edges of the blot than in the center. Non-uniformity in the image can result in inaccurate normalization. [1]
Anionic dyes such as Ponceau S and Coomassie brilliant blue, and fluorescent dyes like Sypro Ruby and Deep Purple, are used before antibodies are added because they do not affect downstream immunodetection. [17] [18] [19] [20]
Ponceau S is a negatively charged reversible dye that stains proteins a reddish pink color and is removed easily by washing in water. [21] [22] The intensity of Ponceau S staining decreases quickly over time, so documentation should be conducted rapidly. [5] A linear range of up to 140 μg is reported for Ponceau S with poor reproducibility due to its highly time-dependent staining intensity and low signal-to-noise ratio. [21] [22]
Fluorescent dyes like Sypro Ruby have a broad linear range and are more sensitive than anionic dyes. [22] They are permanent, photostable stains that can be visualized with a standard UV or blue-light transilluminator or a laser scan. [1] [22] Membranes can then be documented either on film or digitally using a charge-coupled device camera. [23] Sypro Ruby blot staining is time-intensive and tends to saturate above 50 μg of protein per lane. [22]
Amido black is a commonly used permanent post-antibody anionic stain that is more sensitive than Ponceau S. [24] This stain is applied after immunodetection. [24]
Stain-free technology employs an in-gel chemistry for imaging. [22] [25] [26] This chemical reaction does not affect protein transfer or downstream antibody binding. [27] Also, it does not involve staining/destaining steps, and the intensity of the bands remain constant over time. [28]
Stain-free technology cannot detect proteins that do not contain tryptophan residues. A minimum of two tryptophans is needed to enable detection. [5] The linear range for stain-free normalization is up to 80 μg of protein per lane for 18-well and up to 100 μg per lane for 12-well Criterion mid-sized gels. This range is compatible with typical protein loads in quantitative western blots and enables loading control calculations over a wide protein-loading range. [29] [4] A more efficient stain-free method has also recently become available. [30] [31] When using high protein loads, stain-free technology has demonstrated greater success than stains. [29]
Molecular biology is a branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including biomolecular synthesis, modification, mechanisms, and interactions.
Southern blot is a method used for detection and quantification of a specific DNA sequence in DNA samples. This method is used in molecular biology. Briefly, purified DNA from a biological sample is digested with restriction enzymes, and the resulting DNA fragments are separated by using an electric current to move them through a sieve-like gel or matrix, which allows smaller fragments to move faster than larger fragments. The DNA fragments are transferred out of the gel or matrix onto a solid membrane, which is then exposed to a DNA probe labeled with a radioactive, fluorescent, or chemical tag. The tag allows any DNA fragments containing complementary sequences with the DNA probe sequence to be visualized within the Southern blot.
The western blot, or western blotting, is a widely used analytical technique in molecular biology and immunogenetics to detect specific proteins in a sample of tissue homogenate or extract. Besides detecting the proteins, this technique is also utilized to visualize, distinguish, and quantify the different proteins in a complicated protein combination.
In biochemistry, immunostaining is any use of an antibody-based method to detect a specific protein in a sample. The term "immunostaining" was originally used to refer to the immunohistochemical staining of tissue sections, as first described by Albert Coons in 1941. However, immunostaining now encompasses a broad range of techniques used in histology, cell biology, and molecular biology that use antibody-based staining methods.
Immunofluorescence(IF) is a light microscopy-based technique that allows detection and localization of a wide variety of target biomolecules within a cell or tissue at a quantitative level. The technique utilizes the binding specificity of antibodies and antigens. The specific region an antibody recognizes on an antigen is called an epitope. Several antibodies can recognize the same epitope but differ in their binding affinity. The antibody with the higher affinity for a specific epitope will surpass antibodies with a lower affinity for the same epitope.
In molecular biology and genetics, a blot is a method of transferring large biomolecules onto a carrier, such as a membrane composed of nitrocellulose, polyvinylidene fluoride or nylon. In many instances, this is done after a gel electrophoresis, transferring the molecules from the gel onto the blotting membrane, and other times adding the samples directly onto the membrane. After the blotting, the transferred molecules are then visualized by colorant staining, autoradiographic visualization of radiolabelled molecules, or specific labelling of some proteins or nucleic acids. The latter is done with antibodies or hybridization probes that bind only to some molecules of the blot and have an enzyme joined to them. After proper washing, this enzymatic activity is visualized by incubation with a proper reagent, rendering either a colored deposit on the blot or a chemiluminescent reaction which is registered by photographic film.
Coomassie brilliant blue is the name of two similar triphenylmethane dyes that were developed for use in the textile industry but are now commonly used for staining proteins in analytical biochemistry. Coomassie brilliant blue G-250 differs from Coomassie brilliant blue R-250 by the addition of two methyl groups. The name "Coomassie" is a registered trademark of Imperial Chemical Industries.
In biochemistry, biotinylation is the process of covalently attaching biotin to a protein, nucleic acid or other molecule. Biotinylation is rapid, specific and is unlikely to disturb the natural function of the molecule due to the small size of biotin. Biotin binds to streptavidin and avidin with an extremely high affinity, fast on-rate, and high specificity, and these interactions are exploited in many areas of biotechnology to isolate biotinylated molecules of interest. Biotin-binding to streptavidin and avidin is resistant to extremes of heat, pH and proteolysis, making capture of biotinylated molecules possible in a wide variety of environments. Also, multiple biotin molecules can be conjugated to a protein of interest, which allows binding of multiple streptavidin, avidin or neutravidin protein molecules and increases the sensitivity of detection of the protein of interest. There is a large number of biotinylation reagents available that exploit the wide range of possible labelling methods. Due to the strong affinity between biotin and streptavidin, the purification of biotinylated proteins has been a widely used approach to identify protein-protein interactions and post-translational events such as ubiquitylation in molecular biology.
Immunohistochemistry (IHC) is a form of immunostaining. It involves the process of selectively identifying antigens (proteins) in cells and tissue, by exploiting the principle of antibodies binding specifically to antigens in biological tissues. Albert Hewett Coons, Ernest Berliner, Norman Jones and Hugh J Creech was the first to develop immunofluorescence in 1941. This led to the later development of immunohistochemistry.
A real-time polymerase chain reaction is a laboratory technique of molecular biology based on the polymerase chain reaction (PCR). It monitors the amplification of a targeted DNA molecule during the PCR, not at its end, as in conventional PCR. Real-time PCR can be used quantitatively and semi-quantitatively.
A dot blot is a technique in molecular biology used to detect proteins. It represents a simplification of the western blot method, with the exception that the proteins to be detected are not first separated by electrophoresis. Instead, the sample is applied directly on a membrane in a single spot, and the blotting procedure is performed.
Immunoproteomics is the study of large sets of proteins (proteomics) involved in the immune response.
Tetrasodium tris(bathophenanthroline disulfonate)ruthenium(II) (Na4Ru(bps)3) is a sodium salt of coordination compound. In this form, it is the salt of a sulfonic acid. This compound is an extension of the phenanthroline series of coordination compounds. Ruthenium(II) tris(bathophenanthroline disulfonate), referring to the anionic fragment, is used as a protein dye in biochemistry for differentiating and detecting different proteins in laboratory settings.
A reverse phase protein lysate microarray (RPMA) is a protein microarray designed as a dot-blot platform that allows measurement of protein expression levels in a large number of biological samples simultaneously in a quantitative manner when high-quality antibodies are available.
The eastern blot, or eastern blotting, is a biochemical technique used to analyze protein post-translational modifications including the addition of lipids, phosphates, and glycoconjugates. It is most often used to detect carbohydrate epitopes. Thus, eastern blot can be considered an extension of the biochemical technique of western blot. Multiple techniques have been described by the term "eastern blot(ting)", most use phosphoprotein blotted from sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE) gel on to a polyvinylidene fluoride or nitrocellulose membrane. Transferred proteins are analyzed for post-translational modifications using probes that may detect lipids, carbohydrate, phosphorylation or any other protein modification. Eastern blotting should be used to refer to methods that detect their targets through specific interaction of the post-translational modifications and the probe, distinguishing them from a standard far-western blot. In principle, eastern blotting is similar to lectin blotting.
A gel doc, also known as a gel documentation system, gel image system or gel imager, refers to equipment widely used in molecular biology laboratories for the imaging and documentation of nucleic acid and protein suspended within polyacrylamide or agarose gels. Genetic information is stored in DNA. Polyacrylamide or agarose gel electrophoresis procedures are carried out to examine nucleic acids or proteins in order to analyze the genetic data. For protein analysis, two-dimensional gel electrophoresis is employed (2-DGE) which is one of the methods most frequently used in comparative proteomic investigations that can distinguish thousands of proteins in a single run. Proteins are separated using 2-DGE first, based on their isoelectric points (pIs) in one dimension and then based on their molecular mass in the other. After that, a thorough qualitative and quantitative analysis of the proteomes is performed using gel documentation with software image assessment methods on the 2-DGE gels stained for protein visibility. Gels are typically stained with Ethidium bromide or other nucleic acid stains such as GelGreen.
A thermal shift assay (TSA) measures changes in the thermal denaturation temperature and hence stability of a protein under varying conditions such as variations in drug concentration, buffer pH or ionic strength, redox potential, or sequence mutation. The most common method for measuring protein thermal shifts is differential scanning fluorimetry (DSF) or thermofluor, which utilizes specialized fluorogenic dyes.
Epicocconone is a long Stokes' shift fluorogenic natural product found in the fungus Epicoccum nigrum. Though weakly fluorescent in water it reacts covalently yet reversibly with primary amines such as those in proteins to yield a product with a strong orange-red emission (610 nm). Epicoconone is notable because it the first covalent/reversible/turn-on fluorophore to be discovered and is a natural product with a new fluorescent scaffold. It is also cell membrane permeable, unlike many other fluorophores, and subsequently can be used in in vivo applications. Additionally, this dye can be used as a sensitive total protein stain for 1D and 2D electrophoresis, quantitative determination of protein concentration, making it a powerful loading control for Western blots.
SDS-PAGE is a discontinuous electrophoretic system developed by Ulrich K. Laemmli which is commonly used as a method to separate proteins with molecular masses between 5 and 250 kDa. The combined use of sodium dodecyl sulfate and polyacrylamide gel eliminates the influence of structure and charge, and proteins are separated by differences in their size. At least up to 2012, the publication describing it was the most frequently cited paper by a single author, and the second most cited overall.
A collagen hybridizing peptide (CHP) is a synthetic peptide sequence with typically 6 to 10 repeating units of the Gly-Xaa-Yaa amino acid triplet, which mimics the hallmark sequence of natural collagens. A CHP peptide usually possesses a high content of proline and hydroxyproline in the Xaa and Yaa positions, which confers it a strong propensity to form the collagen's unique triple helix conformation. In the single-stranded (monomeric) status, the peptide can recognize denatured collagen strands in tissues by forming a hybridized triple helix with the collagen strands. This occurs via the triple helical chain assembly and inter-chain hydrogen bonding, in a manner similar to primers binding to melted DNA strands during PCR. The binding does not depend on a specific sequence or epitope on collagen, enabling CHPs to target denatured collagen chains of different types.
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