Tech Tip #64: Immunoprecipitation (IP) Technical Guide and Protocols
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Supplementary Materials and Method Immunostaining and Western Blot
Supplementary Materials and Method Immunostaining and Western Blot Analysis For immunofluorescence staining, mouse and human cells were fixed with 4% paraformaldehyde- PBS for 15 min. Following Triton-X100 permeabilization and blocking, cells were incubated with primary antibodies overnight at 4°C following with Alexa 594-conjugated secondary antibodies at 4°C for 1 hour (Thermo Fisher Scientific, 1:1000). Samples were mounted using VECTASHIELD Antifade Mounting Medium with DAPI (Vector Laboratories) and immunofluorescence was detected using Olympus confocal microscopy. For western blot analysis, cells were lysed on ice using RIPA buffer supplemented with protease and phosphatase inhibitors (Sigma). Primary Antibodies for Immunostaining and Western Blot Analysis: Yap (14074, Cell Signaling), pYAP (4911, Cell Signaling), Lats1 (3477, Cell Signaling), pLats1( 8654, Cell Signaling), Wnt5a (2530, Cell Signaling), cleaved Caspase-3 (9661, Cell Signaling), Ki-67 (VP-K451, Vector Laboratories), Cyr61 (sc-13100, Santa Cruz Biotechnology), CTGF (sc-14939, Santa Cruz Biotechnology), AXL (8661, Cell Signaling), pErk (4376, Cell Signaling), pMEK (4376, Cell Signaling), Ck-19 (16858-1-AP, Proteintech), Actin (A2228, Sigma Aldrich), Vinculin (V4139, Sigma Aldrich), Kras (sc-30, Santa Cruz Biotechnology). Ectopic expression of YAP1 and WNT5A in mouse and human cells To generate YAP1S127A-expressing stable Pa04C cells, Pa04C cells were transfected with a linearized pcDNA3.1 plasmid with or without YAP1 cDNA containing S127A substitution. Two days post-transfection using Lipofectamine1000, cultures were selected in G418 (Sigma) and single clones were picked and expanded for further analysis. Overexpression of YAPS127A or WNT5A in human or mouse cells other than Pa04C were acheieved with lentivral infection. Briefly, lentivirus infection was performed by transfecting 293T cells with either GFP control, YAP1S127A, or WNT5A cloned in pHAGE lentivirus vector {EF1α promoter-GW-IRES-eGFP (GW: Gateway modified)}. -
Agarose Gel Electrophoresis
Laboratory for Environmental Pathogen Research Department of Environmental Sciences University of Toledo Agarose gel electrophoresis Background information Agarose gel electrophoresis of DNA is used to determine the presence and distinguish the type of nucleic acids obtained after extraction and to analyze restriction digestion products. Desired DNA fragments can be physically isolated for various purposes such as sequencing, probe preparation, or for cloning fragments into other vectors. Both agarose and polyacrylamide gels are used for DNA analysis. Agarose gels are usually run to size larger fragments (greater than 200 bp) and polyacrylamide gels are run to size fragments less than 200 bp. Typically agarose gels are used for most purposes and polyacrylamide gels are used when small fragments, such as digests of 16S rRNA genes, are being distinguished. There are also specialty agaroses made by FMC (e.g., Metaphor) for separating small fragments. Regular agarose gels may range in concentration from 0.6 to 3.0%. Pouring gels at less or greater than these percentages presents handling problems (e.g., 0.4% agarose for genomic DNA partial digests requires a layer of supporting 0.8% gel). For normal samples make agarose gels at 0.7%. The chart below illustrates the optimal concentrations for fragment size separation. The values listed are approximate and can vary depending on the reference that is used. If you do not know your fragment sizes then the best approach is to start with a 0.7% gel and change subsequently if the desired separation is not achieved. Nucleic acids must be stained prior to visualization. Most laboratories use ethidium bromide but other stains (e.g., SYBR green, GelStar) are available. -
Highly Efficient Purification of Protein Complexes from Mammalian Cells
Highly efficient purification of protein complexes from mammalian cells using a novel streptavidin-binding peptide and hexahistidine tandem tag system: Application to Bruton’s tyrosine kinase Yifeng Li,1 Sarah Franklin,1 Michael J. Zhang,1 and Thomas M. Vondriska1,2,3* 1Department of Anesthesiology, David Geffen School of Medicine, University of California, Los Angeles, CA 2Department of Medicine/Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA 3Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA Received 2 June 2010; Revised 9 September 2010; Accepted 27 October 2010 DOI: 10.1002/pro.546 Published online 15 November 2010 proteinscience.org Abstract: Tandem affinity purification (TAP) is a generic approach for the purification of protein complexes. The key advantage of TAP is the engineering of dual affinity tags that, when attached to the protein of interest, allow purification of the target protein along with its binding partners through two consecutive purification steps. The tandem tag used in the original method consists of two IgG-binding units of protein A from Staphylococcus aureus (ProtA) and the calmodulin- binding peptide (CBP), and it allows for recovery of 20–30% of the bait protein in yeast. When applied to higher eukaryotes, however, this classical TAP tag suffers from low yields. To improve protein recovery in systems other than yeast, we describe herein the development of a three-tag system comprised of CBP, streptavidin-binding peptide (SBP) and hexa-histidine. We illustrate the application of this approach for the purification of human Bruton’s tyrosine kinase (Btk), which results in highly efficient binding and elution of bait protein in both purification steps (>50% recovery). -
"Epitope Mapping: B-Cell Epitopes". In: Encyclopedia of Life Sciences
Epitope Mapping: B-cell Advanced article Epitopes Article Contents . Introduction GE Morris, Wolfson Centre for Inherited Neuromuscular Disease RJAH Orthopaedic Hospital, . What Is a B-cell Epitope? . Epitope Mapping Methods Oswestry, UK and Keele University, Keele, Staffordshire, UK . Applications Immunoglobulin molecules are folded to present a surface structure complementary to doi: 10.1002/9780470015902.a0002624.pub2 a surface feature on the antigen – the epitope is this feature of the antigen. Epitope mapping is the process of locating the antibody-binding site on the antigen, although the term is also applied more broadly to receptor–ligand interactions unrelated to the immune system. Introduction formed of highly convoluted peptide chains, so that resi- dues that lie close together on the protein surface are often Immunoglobulin molecules are folded in a way that as- far apart in the amino acid sequence (Barlow et al., 1986). sembles sequences from the variable regions of both the Consequently, most epitopes on native, globular proteins heavy and light chains into a surface feature (comprised of are conformation-dependent and they disappear if the up to six complementarity-determining regions (CDRs)) protein is denatured or fragmented. Sometimes, by acci- that is complementary in shape to a surface structure on the dent or design, antibodies are produced against linear antigen. These two surface features, the ‘paratope’ on the (sequential) epitopes that survive denaturation, though antibody and the ‘epitope’ on the antigen, may have a cer- such antibodies usually fail to recognize the native protein. tain amount of flexibility to allow an ‘induced fit’ between The simplest way to find out whether an epitope is confor- them. -
Ten Years of Lateral Flow Immunoassay Technique Applications: Trends, Challenges and Future Perspectives
sensors Review Ten Years of Lateral Flow Immunoassay Technique Applications: Trends, Challenges and Future Perspectives Fabio Di Nardo * , Matteo Chiarello , Simone Cavalera , Claudio Baggiani and Laura Anfossi Department of Chemistry, University of Torino, 10125 Torino, Italy; [email protected] (M.C.); [email protected] (S.C.); [email protected] (C.B.); [email protected] (L.A.) * Correspondence: [email protected] Abstract: The Lateral Flow Immunoassay (LFIA) is by far one of the most successful analytical platforms to perform the on-site detection of target substances. LFIA can be considered as a sort of lab-in-a-hand and, together with other point-of-need tests, has represented a paradigm shift from sample-to-lab to lab-to-sample aiming to improve decision making and turnaround time. The features of LFIAs made them a very attractive tool in clinical diagnostic where they can improve patient care by enabling more prompt diagnosis and treatment decisions. The rapidity, simplicity, relative cost-effectiveness, and the possibility to be used by nonskilled personnel contributed to the wide acceptance of LFIAs. As a consequence, from the detection of molecules, organisms, and (bio)markers for clinical purposes, the LFIA application has been rapidly extended to other fields, including food and feed safety, veterinary medicine, environmental control, and many others. This review aims to provide readers with a 10-years overview of applications, outlining the trends for the main application fields and the relative compounded annual growth rates. Moreover, future perspectives and challenges are discussed. Citation: Di Nardo, F.; Chiarello, M.; Cavalera, S.; Baggiani, C.; Anfossi, L. -
Comparison of Immunohistochemistry with Immunoassay (ELISA
British Journal of Cancer (1999) 79(9/10), 1534–1541 © 1999 Cancer Research Campaign Article no. bjoc.1998.0245 Comparison of immunohistochemistry with immunoassay (ELISA) for the detection of components of the plasminogen activation system in human tumour tissue CM Ferrier1, HH de Witte2, H Straatman3, DH van Tienoven2, WL van Geloof1, FJR Rietveld1, CGJ Sweep2, DJ Ruiter1 and GNP van Muijen1 Departments of 1Pathology, 2Chemical Endocrinology and 3Epidemiology, University Hospital Nijmegen, PO Box 9101, 6500 HB Nijmegen, The Netherlands Summary Enzyme-linked immunosorbent assay (ELISA) methods and immunohistochemistry (IHC) are techniques that provide information on protein expression in tissue samples. Both methods have been used to investigate the impact of the plasminogen activation (PA) system in cancer. In the present paper we first compared the expression levels of uPA, tPA, PAI-1 and uPAR in a compound group consisting of 33 cancer lesions of various origin (breast, lung, colon, cervix and melanoma) as quantitated by ELISA and semi-quantitated by IHC. Secondly, the same kind of comparison was performed on a group of 23 melanoma lesions and a group of 28 breast carcinoma lesions. The two techniques were applied to adjacent parts of the same frozen tissue sample, enabling the comparison of results obtained on material of almost identical composition. Spearman correlation coefficients between IHC results and ELISA results for uPA, tPA, PAI-1 and uPAR varied between 0.41 and 0.78, and were higher for the compound group and the breast cancer group than for the melanoma group. Although a higher IHC score category was always associated with an increased median ELISA value, there was an overlap of ELISA values from different scoring classes. -
Immunoassay - Elisa
IMMUNOASSAY - ELISA PHUBETH YA-UMPHAN National Institute of Health, Department of Medical Sciences 0bjective After this presentation, participants will be able to Explain how an ELISA test determines if a person has certain antigens or antibodies . Explain the process of conducting an ELISA test. Explain interactions that take place at the molecular level (inside the microtiter well) during an ELISA test. Outline - Principal of immunoassay - Classification of immunoassay Type of ELISA - ELISA ELISA Reagents General - Applications Principal of ELISA ELISA workflow What is immunoassay? Immunoassays are bioanalytical methods that use the specificity of an antigen-antibody reaction to detect and quantify target molecules in biological samples. Specific antigen-antibody recognition Principal of immunoassay • Immunoassays rely on the inherent ability of an antibody to bind to the specific structure of a molecule. • In addition to the binding of an antibody to its antigen, the other key feature of all immunoassays is a means to produce a measurable signal in response to the binding. Classification of Immunoassays Immunoassays can be classified in various ways. Unlabeled Labeled Competitive Homogeneous Noncompetitive Competitive Heterogeneous Noncompetitive https://www.sciencedirect.com/science/article/pii/S0075753508705618 Classification of Immunoassays • Unlabeled - Immunoprecipitation • Labeled Precipitation of large cross-linked Ag-Ab complexes can be visible to the naked eyes. - Fluoroimmnoassay (FIA) - Radioimmunoassay (RIA) - Enzyme Immunoassays (EIA) - Chemiluminescenceimmunoassay(CLIA) - Colloidal Gold Immunochromatographic Assay (ICA) https://www.creative-diagnostics.com/Immunoassay.htm Classification of Immunoassays • Homogeneous immunoassays Immunoassays that do not require separation of the bound Ag-Ab complex. (Does not require wash steps to separate reactants.) Example: Home pregnancy test. • Heterogeneous immunoassays Immunoassays that require separation of the bound Ag-Ab complex. -
Analysis of Proteins by Immunoprecipitation
Laboratory Procedures, PJ Hansen Laboratory - University of Florida Analysis of Proteins by Immunoprecipitation P.J. Hansen1 1Dept. of Animal Sciences, University of Florida Introduction Immunoprecipitation is a procedure by which peptides or proteins that react specifically with an antibody are removed from solution and examined for quantity or physical characteristics (molecular weight, isoelectric point, etc.). As usually practiced, the name of the procedure is a misnomer since removal of the antigen from solution does not depend upon the formation of an insoluble antibody-antigen complex. Rather, antibody-antigen complexes are removed from solution by addition of an insoluble form of an antibody binding protein such as Protein A, Protein G or second antibody (Figure 1). Thus, unlike other techniques based on immunoprecipitation, it is not necessary to determine the optimal antibody dilution that favors spontaneously-occurring immunoprecipitates. Figure 1. Schematic representation of the principle of immunoprecipitation. An antibody added to a mixture of radiolabeled (*) and unlabeled proteins binds specifically to its antigen (A) (left tube). Antibody- antigen complex is absorbed from solution through the addition of an immobilized antibody binding protein such as Protein A-Sepharose beads (middle panel). Upon centrifugation, the antibody-antigen complex is brought down in the pellet (right panel). Subsequent liberation of the antigen can be achieved by boiling the sample in the presence of SDS. Typically, the antigen is made radioactive before the immunoprecipitation procedure, either by culturing cells with radioactive precursor or by labeling the molecule after synthesis has been completed (e.g., by radioiodination to iodinate tyrosine residues or by sodium [3H]borohydride reduction to label carbohydrate). -
Blotting Techniques Blotting Is the Technique in Which Nucleic Acids Or
Blotting techniques Blotting is the technique in which nucleic acids or proteins are immobilized onto a solid support generally nylon or nitrocellulose membranes. Blotting of nucleic acid is the central technique for hybridization studies. Nucleic acid labeling and hybridization on membranes have formed the basis for a range of experimental techniques involving understanding of gene expression, organization, etc. Identifying and measuring specific proteins in complex biological mixtures, such as blood, have long been important goals in scientific and diagnostic practice. More recently the identification of abnormal genes in genomic DNA has become increasingly important in clinical research and genetic counseling. Blotting techniques are used to identify unique proteins and nucleic acid sequences. They have been developed to be highly specific and sensitive and have become important tools in both molecular biology and clinical research. General principle The blotting methods are fairly simple and usually consist of four separate steps: electrophoretic separation of protein or of nucleic acid fragments in the sample; transfer to and immobilization on paper support; binding of analytical probe to target molecule on paper; and visualization of bound probe. Molecules in a sample are first separated by electrophoresis and then transferred on to an easily handled support medium or membrane. This immobilizes the protein or DNA fragments, provides a faithful replica of the original separation, and facilitates subsequent biochemical analysis. After being transferred to the support medium the immobilized protein or nucleic acid fragment is localized by the use of probes, such as antibodies or DNA, that specifically bind to the molecule of interest. Finally, the position of the probe that is bound to the immobilized target molecule is visualized usually by autoradiography. -
Microchip Electrophoresis
Entry Microchip Electrophoresis Sammer-ul Hassan Mechanical Engineering, University of Southampton, Southampton SO17 1BJ, UK; [email protected] Definition: Microchip electrophoresis (MCE) is a miniaturized form of capillary electrophoresis. Electrophoresis is a common technique to separate macromolecules such as nucleic acids (DNA, RNA) and proteins. This technique has become a routine method for DNA size fragmenting and separating protein mixtures in most laboratories around the world. The application of higher voltages in MCE achieves faster and efficient electrophoretic separations. Keywords: electrophoresis; microchip electrophoresis; microfluidics; microfabrications 1. Introduction Electrophoresis is an analytical technique that has been applied to resolve complex mixtures containing DNA, proteins, and other chemical or biological species. Since its discovery in the 1930s by Arne [1], traditional slab gel electrophoresis (SGE) has been widely used until today. Meanwhile, new separation techniques based on electrophoresis continue to be developed in the 21st century, especially in life sciences. Capillary electrophoresis (CE) provides a higher resolution of the separated analytes and allows the automation of the operation. Thus, it has been widely used to characterize proteins and peptides [2], biopharmaceutical drugs [3], nucleic acids [4], and the genome [5]. The development of microfabrication techniques has led to the further miniaturization of electrophoresis known Citation: Hassan, S.-u. Microchip as microchip electrophoresis (MCE). MCE offers many advantages over conventional Electrophoresis. Encyclopedia 2021, 1, capillary electrophoresis techniques such as the integration of different separation functions 30–41. https://dx.doi.org/10.3390/ onto the chip, the consumption of small amounts of sample and reagents, faster analyses encyclopedia1010006 and efficient separations [6,7]. -
Western Blotting Guidebook
Western Blotting Guidebook Substrate Substrate Secondary Secondary Antibody Antibody Primary Primary Antibody Antibody Protein A Protein B 1 About Azure Biosystems At Azure Biosystems, we develop easy-to-use, high-performance imaging systems and high-quality reagents for life science research. By bringing a fresh approach to instrument design, technology, and user interface, we move past incremental improvements and go straight to innovations that substantially advance what a scientist can do. And in focusing on getting the highest quality data from these instruments—low backgrounds, sensitive detection, robust quantitation—we’ve created a line of reagents that consistently delivers reproducible results and streamlines workflows. Providing scientists around the globe with high-caliber products for life science research, Azure Biosystems’ innovations open the door to boundless scientific insights. Learn more at azurebiosystems.com. cSeries Imagers Sapphire Ao Absorbance Reagents & Biomolecular Imager Microplate Reader Blotting Accessories Corporate Headquarters 6747 Sierra Court Phone: (925) 307-7127 Please send purchase orders to: Suite A-B (9am–4pm Pacific time) [email protected] Dublin, CA 94568 To dial from outside of the US: For product inquiries, please email USA +1 925 307 7127 [email protected] FAX: (925) 905-1816 www.azurebiosystems.com • [email protected] Copyright © 2018 Azure Biosystems. All rights reserved. The Azure Biosystems logo, Azure Biosystems™, cSeries™, Sapphire™ and Radiance™ are trademarks of Azure Biosystems, Inc. More information about Azure Biosystems intellectual property assets, including patents, trademarks and copyrights, is available at www.azurebiosystems.com or by contacting us by phone or email. All other trademarks are property of their respective owners. -
Magresyn ® Protein G
MagReSyn® Protein G Immobilized Protein G magnetic 1.4. Additional Equipment and Materials microparticles Magnetic separator, Vortex mixer, Buffers and solutions, end-over-end mixer (optional) Ordering Information Cat. No. Quantity 2. Immunoglobulin Purification Factors that may affect the attachment of antibodies include the isotype of the MR-PRG002 2 ml immunoglobulin, buffer composition and pH, and the presence of MR-PRG005 5 ml contaminants/interfering compounds. The quantity of microparticles needs to be optimized for each individual application. We recommend the application of excess MR-PRG010 2 x 5 ml ligand to ensure saturation of the Protein G microparticles. The binding efficiency can be determined by comparing the ligand concentration before and after coupling. This product is for research use only MagReSyn® Protein G is compatible with various commonly used buffers, including Tris and Phosphate. Recommended buffers include: Binding/wash buffer - TBS (50 mM Tris pH 7.5, 150 mM NaCl, 0.025% Tween® 20) or PBS (50 mM Phosphate pH 7.5, 150 mM Table of Contents: NaCl, 0.025% Tween® 20); Elution Buffer (Native): 0.1 M glycine pH 2.5 or 2.5% acetic 1. Product Description acid; Elution Buffer (Denaturing): SDS-PAGE electrophoresis buffer. 2. Immunoglobulin Purification 3. Immunoprecipitation NOTE: All reagents should be freshly prepared and of analytical grade to ensure 4. Recommended Storage optimal performance. The procedures, methods and buffer solutions described below serve as an example and are not intended to be limiting. MagReSyn® Protein G is 5. Antibody Binding Guide compatible with a range of different buffers for binding of antibodies.