TransAM™ NFkB p65 / NFkB p50 /NFkB p52 Transcription Factor Assay Kits (version G1) Catalog Nos. 40096 & 40596 (p65) Catalog Nos. 41096 & 41596 (p50) Catalog Nos. 48196 & 48696 (p52) Active Motif North America 1914 Palomar Oaks Way, Suite 150 Carlsbad, California 92008, USA Toll free: 877 222 9543 Telephone: 760 431 1263 Fax: 760 431 1351 Active Motif Europe 104 Avenue Franklin Roosevelt B-1330 Rixensart, Belgium UK Free Phone: 0800 169 31 47 France Free Phone: 0800 90 99 79 Germany Free Phone: 0800 181 99 10 Telephone: +32 (0)2 653 0001 Fax: +32 (0)2 653 0050 Active Motif Japan Azuma Bldg, 7th Floor 2-21 Ageba-Cho, Shinjuku-Ku Tokyo, 162-0824, Japan Telephone: +81 3 5225 3638 Fax: +81 3 5261 8733 Copyright 2009 Active Motif, Inc. www.activemotif.com Information in this manual is subject to change without notice and does not constitute a commitment on the part of Active Motif, Inc. It is supplied on an “as is” basis without any warranty of any kind, either explicit or implied. Information may be changed or updated in this manual at any time. This documentation may not be copied, transferred, reproduced, disclosed, or duplicated, in whole or in part, without the prior written consent of Active Motif, Inc. This documentation is proprietary information and protected by the copyright laws of the United States and international treaties. The manufacturer of this documentation is Active Motif, Inc. © 2009 Active Motif, Inc., 1914 Palomar Oaks Way, Suite 150; Carlsbad, CA 92008. All rights reserved. All trademarks, trade names, service marks or logos referenced herein belong to their respective companies. www.activemotif.com TABLE OF CONTENTS Page Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 Flow Chart of Process . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 Introduction NFkB Transcription Factor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 Transcription Factor Assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 TransAM NFkB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 Kit Performance and Benefits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 Kit Components and Storage Additional Materials Required . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 Protocols Buffer Preparation and Recommendations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 Quick Chart for Preparing Buffers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 NFkB Transcription Factor Assay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 Appendix Section A. Preparation of Nuclear Extract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 Section B. Troubleshooting Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 Section C. Related Products . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 Technical Services . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 www.activemotif.com Overview The transcription factor NFκB (nuclear factor κB) is a key component for the inducible expression of a wide variety of cellular and viral genes. Therefore, accurate monitoring of NFκB activation in cells, tissues or animals is crucial for drug development and signal transduction pathway studies. To date, such research projects are time consuming, tedious and lack high-throughput screening systems. With its patented TransAM™ method*, Active Motif introduced the first ELISA-based kits to detect and quantify transcription factor activation. TransAM Kits combine a fast, user-friendly format with a sensitive, specific assay. TransAM NFκB p65, p50 and p52 Kits are designed specifically for the study of NFκB subunits. They contain a 96-well plate to which oligonucleotide containing an NFκB consensus binding site has been immobilized. The activated NFκB homodimers and heterodimers contained in nuclear or whole-cell extracts specifically binds to this oligonucleotide. By using an antibody that is directed against either the NFκB p65, p50 or p52 subunit, the activated NFκB subunit bound to the oligonucleotide is detected. Addition of a secondary antibody conjugated to horseradish peroxidase (HRP) provides sensitive colorimetric readout that is easily quantified by spectrophotometry. The 96-well plate with detachable wells is suitable for manual use or high-throughput screening applications. TransAM NFκB p65, p52 and NFκB p50 Kits are available in two sizes: product format catalog no. TransAM™ NFkB p65 1 x 96 rxns 5 x 96 rxns 40096 40596 TransAM™ NFkB p50 1 x 96 rxns 5 x 96 rxns 41096 41596 TransAM™ NFkB p52 1 x 96 rxns 5 x 96 rxns 48196 48596 The procedure outlined in this manual can be used for TransAM NFκB p65, TransAM NFκB p50 or TransAM NFκB p52 Kits. Active Motif also offers chemiluminescent versions of the TransAM NFκB p65, p50 and p52 Kits that provide increased sensitivity and dynamic range, as well as the TransAM NFκB/Rel Family Kit for the study of NFκB p50, p52, p65, c-Rel and RelB. See these and other Active Motif products related to the NFκB signaling pathway in Appendix, Section C. * Technology covered by AAT-filed patents and licensed to Active Motif. Use of TransAM in NFκB-related drug discovery may be covered under U.S. Patent No. 6,150,090 and require a license from Ariad Pharmaceuticals (Cambridge, MA). www.activemotif.com 1 Flow Chart of Process 2 1 5 4 3 7 6 8 9 10 11 12 A B C D E F Cell extract containing activated transcription factor G H Oligonucleotide coated plate Add cell extract 21 11 01 9 8 7 6 5 4 3 2 1 A B C D E F G H Add primary antibody 1 hr. 2 1 9 8 7 6 5 4 3 11 10 12 A B C D E F G H Add anti-IgG HRP conjugate 21 11 01 9 8 7 6 5 1 hr. 4 3 2 1 A B C D E F G Add developing and stop solution H 1 hr. 3 2 1 5 4 7 6 A B C D E F G H www.activemotif.com 2 8 9 10 11 12 Introduction NFkB Transcription Factor The transcription factor NFκB is implicated in the regulation of many genes that code for mediators of the immune, acute phase and inflammatory responses1. The DNA-binding protein complex recognizes a discrete nucleotide sequence (5´-GGGACTTTCC-3´) in the upstream region of a variety of cellular and viral response genes2. NFκB is composed of homo- and heterodimeric complexes of members of the Rel (NFκB) family. There are five subunits of the NFκB family in mammals: p50, p65 (RelA), c-Rel, p52 and RelB3. These proteins share a conserved 300 amino acid sequence in the N-terminal region, known as the Rel homology domain, that mediates DNA binding, protein dimerization and nuclear localization. This domain is also a target of the IκB inhibitors, which include IκBα, IκBβ, IκBγ, Bcl-3, p105 and p1004. Various dimer combinations of the NFκB subunits have distinct DNA binding specificities and may serve to activate specific sets of genes such as adhesion molecules, immunoreceptors and cytokines. The p50/p65 (NFκB1/RelA) heterodimers and the p50 homodimers are the most common dimers found in the NFκB signaling pathway. In the majority of cells, NFκB exists in an inactive form in the cytoplasm, bound to the inhibitory IκB proteins5. Treatment of cells with various inducers results in the phosphorylation, ubiquitination and subsequent degradation of IκB proteins6 (For studying the phosphorylation state of IκBα, see Active Motif’s FunctionELISA™ IκBα Kit). Proteolytic cleavage of p105 results in two proteins: p50, which has DNA-binding activity but no transactivation domain, and its antagonist, the inhibitory IκBγ protein. This results in the release of NFκB dimers, which subsequently translocate to the nucleus, where they activate appropriate target genes. NFκB can be activated by a number of stimuli, including components of bacterial cell walls, such as lipopolysaccharide, or inflammatory cytokines, such as TNF-α or IL-1β. Transcription Factor Assays To date, three methods are widely used to measure NFκB activation, either directly or indirectly: 1. NFκB expression or cytoplasmic IκB degradation can be measured by Western blot, using antibodies raised against NFκB subunits or IκB (see Appendix, Section C for related products). This method is time consuming (up to 2 days once the cell extracts are prepared), and is not suitable for processing large numbers of samples. 2. The DNA-binding capacity of NFκB can be assayed by gel retardation, also called electrophoretic mobility shift assay (EMSA). In this method, cell extracts are incubated with a radioactive double-stranded oligonucleotide probe containing the consensus sequence for NFκB binding. If NFκB is active in the cell extract, it will bind to the probe. Samples are then resolved by electrophoresis on a native polyacrylamide gel, followed by autoradiography. This method is sensitive, but like the previous procedure, it is time consuming (multiple days of gel exposure may be required to achieve sufficient sensitivity) and it cannot be applied to high-throughput screening. Gelshift assays also require special precautions and equipment for handling radioactivity. 3. Another method used to assay NFκB activation is based on reporter genes, typically luciferase or β-galactosidase, placed under the control of a promoter containing the NFκB www.activemotif.com 3 consensus sequence. This promoter can be artificial, made of several NFκB cis-elements and a TATA box, or natural, like the HIV long terminal repeat (LTR) sequence. Limitations of this procedure are: (i) reporter gene assays have to be repeated several times to obtain statistically reliable data; and (ii) reporter gene assays are sensitive to confounding factors that may influence the expression level of the reporter gene. Therefore, assays have to be carefully standardized. This method is sensitive and easy to perform with a large number of samples but requires efficient cell transfection with the reporter plasmid. TransAM NFkB NFκB is a key factor in various immune processes and represents an excellent pharmacological target. However, pharmaceutical research in this field has been hampered by the lack of convenient assays suitable for large numbers of samples. To overcome this, Active Motif offers a high-throughput assay to quantify NFκB activation7. The TransAM Kit combines a fast and user-friendly ELISA format with a sensitive and specific assay for transcription factors. TransAM NFκB Kits contain a 96-well plate to which an oligonucleotide containing the NFκB consensus site (5´-GGGACTTTCC-3´) has been immobilized. The active form of NFκB contained in nuclear or whole-cell extract specifically binds to this oligonucleotide. The primary antibodies used to detect NFκB recognize an epitope on p65, p50 or p52 that is accessible only when NFκB is activated and bound to its target DNA. An HRP-conjugated secondary antibody provides a sensitive colorimetric readout that is easily quantified by spectrophotometry. Once the cellular extract is prepared, this assay is completed in less than 3.5 hours. As this assay is performed in a 96-well plate, a large number of samples can be handled simultaneously, allowing for high-throughput automation. This assay is specific for NFκB activation and has been shown to be 10-fold more sensitive and 40-fold faster than the gel retardation technique. With the 3.5-hour procedure of TransAM, we could detect NFκB activation with 0.5 µg of nuclear extract from Jurkat cells stimulated with TPA and calcium ionophore. A comparable assay using EMSA required 5 µg of extract and a 5-day autoradiography. TransAM has many applications including the study of drug potency, inhibitor or activator proteins, and/or protein structure/function in the NFκB signaling pathway. www.activemotif.com 4 Kit Performance and Benefits Detection limit: < 0.5 µg nuclear extract/well. For whole-cell extract, twice as much input may be needed. Alternatively, < 0.4 ng recombinant p50 or p65 protein/well may be used. TransAM NFκB is 10-fold more sensitive than EMSA. (For increased sensitivity, the TransAM NFκB p50 Chemi, TransAM NFκB p52 Chemi and TransAM NFκB p65 Chemi Kits utilize a chemiluminescent detection method that can detect 5 ng extract/well. See Appendix, Section C, Related Products.) Range of detection: TransAM provides quantitative results from 0.2 to 10 µg of nuclear or wholecell extract per well or 0.1 to 40 ng of recombinant p50 or p65 protein/well. Cross-reactivity: p65 p50 p52 Human + + + Mouse + + + Rat + – – Assay time: 3.5 hours. NFκB p65 activation (OD 450nm) 1.6 1.4 Jurkat Jurkat+TPA+Cl 1.2 1 0.8 0.6 0.4 0.2 0 0.625 1.25 2.5 5 10 Extract (µg/well) Monitoring NFkB activation with the TransAM NFkB Kit: Nuclear extracts from Jurkat cells (Catalog No. 36014) and Jurkat cells stimulated with TPA and calcium ionophore (Catalog No. 36013) were assayed from 0.625-10 µg/well for NFkB p65 activation using the TransAM NFkB p65 Kit. Data shown are the results from wells assayed in duplicate. These results are provided for demonstration only. www.activemotif.com 5 Kit Components and Storage TransAM NFκB Kits are for research use only. Not for use in diagnostic procedures. Except for the nuclear extract that must be kept at -80ºC, kit components can be stored at -20ºC prior to first use. Then, we recommend storing each component at the temperature indicated in the table below. All components are guaranteed stable for 6 months from date of receipt when stored properly. Reagents Quantity 1 plate / 5 plates Storage NFkB p65 or p50 antibody 11 µl / 55 µl -20°C for 6 months NFkB p52 antibody 11 µl / 55 µl 4°C for 6 months Anti-rabbit HRP-conjugated antibody 11 µl / 55 µl 4°C for 6 months Wild-type oligonucleotide AM20 100 µl / 500 µl (10 pmol/µl) -20°C for 6 months Mutated oligonucleotide AM20 100 µl / 500 µl (10 pmol/µl) -20°C for 6 months Positive control nuclear extract 40 µl / 200 µl (2.5 µg/µl) -80°C for 6 months Dithiothreitol (DTT) (1 M) 100 µl / 500 µl -20°C for 6 months Protease Inhibitor Cocktail 100 µl / 500 µl -20°C for 6 months Herring sperm DNA 100 µl / 500 µl (1 µg/µl) -20°C for 6 months Lysis Buffer AM2 10 ml / 50 ml 4°C for 6 months Binding Buffer AM3 10 ml / 50 ml 4°C for 6 months 10X Wash Buffer AM2 22 ml / 110 ml 4°C for 6 months 10X Antibody Binding Buffer AM2 2.2 ml / 11 ml 4°C for 6 months Developing Solution 11 ml / 55 ml 4°C for 6 months Stop Solution 11 ml / 55 ml 4°C for 6 months 96-well NFkB assay plate 1 / 5 4°C for 6 months Plate sealer 1 / 5 Room temperature Additional materials required • Multi-channel pipettor • Multi-channel pipettor reservoirs • Rocking platform • Nuclear or whole-cell extracts • Microplate spectrophotometer capable of reading at 450 nm (655 nm as an optional reference wavelength) www.activemotif.com 6 Protocols Buffer Preparation and Recommendations Preparation of Complete Lysis Buffer We provide an excess of Lysis Buffer AM2 in order to perform the assay AND to prepare customized nuclear extracts. Please refer to the Appendix Section A for a protocol to prepare a nuclear extract. Our Nuclear Extract Kit can also be purchased separately (Cat. Nos. 40010 & 40410). When preparing extracts, it is suggested to perform the final lysis step using the Lysis Buffer AM2 provided in the TransAM Kit. All subsequent dilutions should also be performed using Lysis Buffer AM2 from the TransAM Kit. Prepare the amount of Complete Lysis Buffer required for the assay by adding 5 µl of 1 M DTT and 10 µl Protease Inhibitor Cocktail per ml of Lysis Buffer AM2 (see the Quick Chart for Preparing Buffers in this section). Some of the protease inhibitors lose their activity after a few hours once diluted. Therefore, we recommend adding protease inhibitors immediately prior to use. Any remaining Complete Lysis Buffer should be discarded if not used in the same day. Preparation of Complete Binding Buffer Prepare the amount of Complete Binding Buffer AM3 required for the assay by adding 2 μl of DTT and 10 μl of 1 μg/µl Herring sperm DNA per ml of Binding Buffer AM3 (see the Quick Chart for Preparing Buffers in this section). After use, discard remaining Complete Binding Buffer. Preparation of 1X Wash Buffer Prepare the amount of 1X Wash Buffer required for the assay as follows: For every 100 ml of 1X Wash Buffer required, dilute 10 ml 10X Wash Buffer AM2 with 90 ml distilled water (see the Quick Chart for Preparing Buffers in this section). Mix gently to avoid foaming. The 1X Wash Buffer may be stored at 4°C for one week. The Tween 20 contained in the 10X Wash Buffer AM2 may form clumps, therefore it is necessary to completely resuspend any precipitates by incubating at 50ºC for 2 minutes and mixing prior to use. Preparation of 1X Antibody Binding Buffer Prepare the amount of 1X Antibody Binding Buffer required for the assay as follows: For every 10 ml of 1X Antibody Binding Buffer required, dilute 1 ml 10X Antibody Binding Buffer AM2 with 9 ml distilled water (see the Quick Chart for Preparing Buffers in this section)*. Mix gently to avoid foaming. Discard remaining 1X Antibody Binding Buffer after use. The BSA contained in the 10X Antibody Binding Buffer AM2 may form clumps, therefore it is necessary to completely resuspend the buffer by warming to room temperature and vortexing for 1 minute prior to use. * Volumes listed refer to the preparation of buffer for diluting both the primary & secondary antibodies. www.activemotif.com 7 Developing Solution The Developing Solution should be warmed to room temperature before use. The Developing Solution is light sensitive, therefore, we recommend avoiding direct exposure to intense light during storage. The Developing Solution may develop a yellow hue over time. This does not affect product performance. A blue color present in the Developing Solution indicates that it has been contaminated and must be discarded. Prior to use, place the Developing Solution at room temperature for at least 1 hour. Transfer the amount of Developing Solution required for the assay into a secondary container before aliquoting into the wells (see the Quick Chart for Preparing Buffers in this section). After use, discard remaining Developing Solution. Stop Solution Prior to use, transfer the amount of Stop Solution required for the assay into a secondary container (see the Quick Chart for Preparing Buffers in this section). After use, discard remaining Stop Solution. WARNING: The Stop Solution is corrosive. Wear personal protective equipment when handling, i.e. safety glasses, gloves and labcoat. Nuclear extract The Jurkat (TPA + CI) nuclear extract is provided as a positive control for NFκB p50 and p65 activation. This extract is optimized to give a strong signal when used at 2.5 µg/well. The Raji nuclear extract is provided as a positive control for NFκB p52 activation and should be used at 5 µg/well. We recommend aliquoting the extract in 5 µl fractions and storing at -80ºC. Avoid multiple freeze/thaw cycles of the extract. Various cell extracts are available from Active Motif (see Appendix, Section C. Related Products). Wild-type and mutated consensus oligonucleotides The wild-type consensus oligonucleotide is provided as a competitor for NFκB binding in order to monitor the specificity of the assay. This competition assay will confirm that the protein subunits binding to the plate are specific for the NFκB consensus binding sequence. Used at 20 pmol/well, the oligonucleotide will prevent NFκB binding to the probe immobilized on the plate. Conversely, the mutated consensus oligonucleotide should have no effect on NFκB binding. Prepare the required amount of wild-type and/or mutated consensus oligonucleotide by adding 2 µl of appropriate oligonucleotide to 31.8 µl of Complete Binding Buffer per well being used (see the Quick Chart for Preparing Buffers in this section). To allow for optimum competition, add the oligonucleotide to the well first, then add the cell extract. It is not necessary to perform an incubation step of the oligonucleotide in the well prior to addition of the cell extract. The oligonucleotide competition only needs to be performed as a control. It is suggested to test the oligonucleotide competition each new cell type used. OPTIONAL – Preparation of standard curve For those who wish to quantify the amount of NFκB in their samples, Active Motif offers recombinant NFκB p50 and p65 for use as protein standards (see Appendix, Section C. Related Products). Each protein is supplied with a lot specific Certificate of Analysis. Please refer to this before preparing the standard curve as the concentration of the protein varies from lot to lot. www.activemotif.com 8 1. Begin with a 100 ng/µl working stock of recombinant protein (use the TransAM Complete Lysis Buffer to dilute the protein). Set up a standard curve in duplicate using the following concentrations: 0.5, 0.25, 0.125, 0.0625, 0.0312, 0.0156, 0.008 and 0 ng/µl. Note: The preceding range is provided as guidance, a broader range of values may be used. Refer to the protein’s lot specific data sheet for details. 2. Make up a 0.5 ng/µl solution by adding 1 µl of the 100 ng/µl working stock to 199 µl of Complete Lysis Buffer. Next, pipette 60 µl of Complete Lysis Buffer into the 7 remaining tubes. Use the 0.5 ng/ µl solution to prepare a dilution series as indicated below. Mix tubes thoroughly before each transfer. The 0.5 ng/µl standard is the high standard and Lysis Buffer alone is the 0.0 ng/µl. 60 µl 0.5 ng/µl 60 µl 0.25 ng/µl 60 µl 0.125 ng/µl 60 µl 0.0625 ng/µl 60 µl 0.0312 ng/µl 60 µl 0.0156 ng/µl 0.008 ng/µl 3. 20 µl from each tube will be aliquoted to the wells in Step 1, No. 2 of the protocol and will correspond to the following quantities of NFκB: 10, 5, 2.5, 1.25, 0.625, 0.312, 0.156 and 0.0 ng/well. Quick Chart for Preparing Buffers For 1 well For 1 strip (8 wells) For 6 strips (48 wells) For 12 strips (96 wells) DTT Protease Inhibitor Cocktail Lysis Buffer AM2 TOTAL REQUIRED 0.11 µl 0.23 µl 22.2 µl 22.5 µl 0.9 µl 1.8 µl 177.3 µl 180 µl 5.4 µl 10.8 µl 1.064 ml 1.08 ml 10.8 µl 21.6 µl 2.128 ml 2.16 ml Complete Binding Buffer DTT Herring sperm DNA Binding Buffer AM3 TOTAL REQUIRED 0.07 µl 0.34 µl 33.4 µl 33.8 µl 0.54 µl 2.7 µl 267 µl 270 µl 3.2 µl 16.2 µl 1.6 ml 1.62 ml 6.5 µl 32.4 µl 3.2 ml 3.24 ml Complete Binding Buffer with NFκB wild-type or mutated oligonucleotide NFκB wild-type or mutated oligo 2 µl Complete Binding Buffer 31.8 µl TOTAL REQUIRED 33.8 µl 16 µl 254 µl 270 µl 96 µl 1.524 ml 1.62 ml N/A N/A N/A 1X Wash Buffer Distilled water 10X Wash Buffer AM2 TOTAL REQUIRED 2.025 ml 225 µl 2.25 ml 16.2 ml 1.8 ml 18 ml 97.2 ml 10.8 ml 108 ml 194.4 ml 21.6 ml 216 ml 202.5 µl 22.5 µl 225 µl 1.62 ml 180 µl 1.8 ml 9.72 ml 1.08 ml 10.8 ml 19.44 ml 2.16 ml 21.6 ml Reagents to prepare Components Complete Lysis Buffer 1X Antibody Binding Buffer* Distilled water 10X Ab Binding Buffer AM2 TOTAL REQUIRED Developing Solution TOTAL REQUIRED 112.5 µl 900 µl 5.4 ml 10.8 ml Stop Solution TOTAL REQUIRED 112.5 µl 900 µl 5.4 ml 10.8 ml * Volumes listed refer to the preparation of buffer for diluting both the primary & secondary antibodies. www.activemotif.com 9 NFkB Transcription Factor Assay Determine the appropriate number of microwell strips required for testing samples, controls and blanks in duplicate. If less than 8 wells in a strip need to be used, cover the unused wells with a portion of the plate sealer while you perform the assay. The content of these wells is stable at room temperature if kept dry and, therefore, can be used later for a separate assay. Store the unused strips in the aluminum pouch at 4°C. Use the strip holder for the assay. Prepare the Complete Lysis Buffer, Complete Binding Buffer, 1X Wash Buffer and 1X Antibody Binding Buffer as described above in the section Buffer Preparation and Recommendations. Multichannel pipettor reservoirs may be used for dispensing the Complete Binding Buffer, Wash Buffer, Antibody Binding Buffer, Developing Solution and Stop Solution into the wells being used. Step 1: Binding of NFkB to its Consensus Sequence 1. Add 30 µl Complete Binding Buffer to each well to be used. If you wish to perform competitive binding experiments, add 30 µl Complete Binding Buffer that contains 20 pmol (2 µl) of the wild-type or mutated oligonucleotide (see the Buffer Preparation section above for a description of competitive binding). 2. Sample wells: Add 20 µl of sample diluted in Complete Lysis Buffer per well. We recommend using 2-20 µg of nuclear extract diluted in Complete Lysis Buffer per well. A protocol for preparing nuclear extracts is provided on page 13. For whole-cell extracts we recommend using 4-40 µg per well. Positive control wells: For p65 or p50 add 2.5 µg of the provided Jurkat nuclear extract (1 µl of nuclear extract in 19 µl of Complete Lysis Buffer per well). For p52 use 5 µg of the provided Raji nuclear extract diluted in 20 µl of Complete Lysis Buffer per well (2 µl of nuclear extract in 18 µl of Complete Lysis Buffer per well). Blank wells: Add 20 µl Complete Lysis Buffer only per well. OPTIONAL – Protein standard wells for p50 and p65: Add 20 µl of the appropriate protein standard diluted in Complete Lysis Buffer to each well being used (see page 8, for details) (Optional) Blank Positive Control Sample (Optional) (Optional) Recombinant Reagents wells no competition no competition wild-type mutated protein Complete Binding Buffer Wild-type oligonucleotide Mutated oligonucleotide Complete Lysis Buffer Sample in Complete Lysis Buffer Recombinant protein sample 3. 30 µl – – 20 µl – – 30 µl – – – 20 µl – 30 µl – – – 20 µl – 28 µl 2 µl – – 20 µl – 28 µl – 2 µl – 20 µl – 30 µl – – – – 20 µl Use the provided adhesive cover to seal the plate. Incubate for 1 hour at room temperature with mild agitation (100 rpm on a rocking platform). Keep any unused wells covered during the remaining steps in order to preserve those wells for future assays. Any unused strips from the stripwell plate can be placed in the foil bag, sealed with tape and stored at 4°C. www.activemotif.com 10 4. Wash each well 3 times with 200 µl 1X Wash Buffer. For each wash, flick the plate over a sink to empty the wells, then tap the inverted plate 3 times on absorbent paper towels. Step 2: Binding of Primary Antibody 1. Add 100 µl of diluted NFkB antibody (1:1,000 dilution in 1X Antibody Binding Buffer) to each well being used, including blank wells. 2. Cover the plate and incubate for 1 hour at room temperature without agitation. 3. Wash the wells 3 times with 200 µl 1X Wash Buffer (as described in Step 1, No. 4). Step 3: Binding of Secondary Antibody 1. Add 100 µl of diluted HRP-conjugated antibody (1:1,000 dilution in 1X Antibody Binding Buffer) to all wells being used. 2. Cover the plate and incubate for 1 hour at room temperature without agitation. 3. During this incubation, place the Developing Solution at room temperature. 4. Wash the wells 4 times with 200 µl 1X Wash Buffer (as described in Step 1, No. 4). Step 4: Colorimetric Reaction 1. Add 100 µl Developing Solution to all wells being used. 2. Incubate 30 seconds to 5 minutes at room temperature protected from direct light. Please read the Certificate of Analysis supplied with this kit for optimal development time for this specific kit lot. Monitor the blue color development in the sample wells until it turns medium to dark blue. Do not overdevelop. NOTE: Recombinant standards develop quickly. 3. Add 100 µl Stop Solution. In presence of the acid, the blue color turns yellow. 4. Read absorbance on a spectrophotometer within 5 minutes at 450 nm with an optional reference wavelength of 655 nm. Blank the plate reader according to the manufacturer’s instructions using the blank wells. OPTIONAL – Calculation of results using the standard curve If you have generated a standard curve using Active Motif’s recombinant NFκB p50 or p65 protein, average the duplicate readings for each standard, control, and sample and subtract the optical density (OD) obtained from the zero standard. Plot the OD for the standards against the quantity (ng/well) of the standards and draw the best fit curve. The data can be linearized using log/log paper and regression analysis may also be applied. To quantify the amount of NFκB in the samples, find the absorbance value for the samples on the y-axis and extend a horizontal line to the standard curve. At the intersection point extend a vertical line to the x-axis and read the corresponding standard value. Note: If the samples have been diluted, the value read from the standard curve must be multiplied by the dilution factor. www.activemotif.com 11 Example curve: The following standard curve is provided for demonstration only. A standard curve should be made every time an experiment is performed. NFκB p50 TransAM Assay y = 0.468x - 0.055 r = 0.999 1.5 A450 1 A450 0.5 0 0 0.5 1 1.5 2 2.5 3 p50 Recombinant Protein (ng) References 1. 2. 3. 4. 5. 6. 7. Bauerle P.A. and Baichwal V.R. (1997) Adv. Immunol. 65: 111-137. Parry G.C. and Mackman N. (1994) J. Biol. Chem. 269: 20823-20825. Verma I.M., Stevenson J.K., Schwarz E.M., Van Antwerp D. and Miyamoto S. (1995) Genes & Dev. 9: 2723-2735. Gilmore T.D. and Morin P.J. (1993) Trends Genetics 9: 427-433. Bauerle P.A. and Baltimore D. (1988) Cell 53: 211-217. Chen Z., Hagler J., Palombella V.J., Melandri F., Scherer D., Ballard D. and Maniatis T. (1995) Genes & Dev. 9: 1586-1597. Renard P., Ernest I., Houbion A., Art M., Le Calvez H., Raes M. and Remacle J. (2001) Nucleic Acids Res. 29:(4), e21. www.activemotif.com 12 Appendix Section A. Preparation of Nuclear Extract For your convenience, Active Motif offers a Nuclear Extract Kit (Cat. Nos. 40010 & 40410). This kit contains buffers optimized for use in TransAM Kits, which serves to reduce inconsistencies in the assay that may arise from using homemade or other buffers. If you prefer to make your own buffers, please refer to the following protocol. This procedure can be used for a confluent cell layer of 75 cm2 (100-mm dish). The yield is approximately 0.15 mg of nuclear proteins for 9 x 106 cells. 1. Wash cells with 10 ml ice-cold PBS/PIB. Discard PBS/PIB. 2. Add 10 ml ice-cold PBS/PIB and scrape the cells off the dish with a cell lifter. Transfer cells into a pre-chilled 15 ml tube and spin at 300 x g for 5 minutes at 4°C. Do not use Trypsin to remove cells as it may alter transcription factor activation states. 3. Resuspend the pellet in 1 ml ice-cold HB buffer by gentle pipetting and transfer the cells into a pre-chilled 1.5 ml tube. 4. Allow the cells to swell on ice for 15 minutes. 5. Add 50 µl 10% Nonidet P-40 (0.5 % final) and vortex the tube vigorously for 10 seconds. Check the cells under a microscope to monitor the cell lysis. The cell membrane should be completely lysed, while the nuclear membrane remains intact. 6. Centrifuge the homogenate for 30 seconds at 4°C in a microcentrifuge. Remove the supernatant (cytoplasmic fraction) and, if you wish to save this for other uses, transfer it into a pre-chilled microcentrifuge tube. (Store the cytoplasmic fraction at –80°C.) 7. Resuspend the nuclear pellet in 50 µl Complete Lysis Buffer and rock the tube gently on ice for 30 minutes on a shaking platform. 8. Centrifuge for 10 minutes at 14,000 x g at 4°C and save the supernatant (nuclear extract). Aliquot and store at –80°C. Avoid freeze/thaw cycles. Discard the debris pellet. 9. Determine the protein concentration of the extract by using a Bradford-based assay. It is recommended to perform a 1:50 dilution of your samples for protein determination. A blank sample consisting of Complete Lysis Buffer diluted 1:50 should be run as control. Standard controls should also be generated in Complete Lysis Buffer diluted 1:50. www.activemotif.com 13 Preparation of Buffers for Nuclear Extract 10X PBS 0.1 M phosphate buffer, pH 7.5 For 250 ml, mix: 3.55 g Na2HPO4 + 0.61 g KH2PO4 1.5 M NaCl 21.9 g 27 mM KCl 0.5 g Adjust to 250 ml with distilled water. Prepare a 1X PBS solution by adding 10 ml 10X PBS to 90 ml distilled water. Sterilize the 1X PBS by filtering through a 0.2 µm filter. The 1X PBS is at pH 7.5. Store the filter-sterilized 1X PBS solution at 4°C. PIB (Phosphatase Inhibitor Buffer) 125 mM NaF For 10 ml, mix: 52 mg 250 mM β-glycerophosphate 0.55 g 250 mM p-nitrophenyl phosphate (PNPP) 1.15 g 25 mM NaVO3 31 mg Adjust to 10 ml with distilled water. Mix the chemicals by vortexing. Incubate the solution at 50ºC for 5 minutes. Mix again. Store at –20°C. PBS/PIB Prior to use, add 0.5 ml PIB to 10 ml 1X PBS. HB (Hypotonic Buffer) For 50 ml, mix: 20 mM Hepes, pH 7.5 0.24 g 5 mM NaF 12 mg 10 µM Na2MoO4 5 µl of a 0.1 M solution 0.1 mM EDTA 10 µl of a 0.5 M solution Adjust pH to 7.5 with 1 N NaOH. Adjust volume to 50 ml with distilled water. Sterilize by filtering through a 0.2 µm filter. Store the filter-sterilized solution at 4°C. www.activemotif.com 14 Section B: Troubleshooting Guide Problem/question Possible cause Recommendation No signal or weak signal Omission of key reagent Check that all reagents have been added in all wells in the correct order Substrate or conjugate is no longer active Test conjugate and substrate for activity by mixing HRP and Developing Solution together Enzyme inhibitor present Sodium azide will inhibit the peroxidase reaction. Follow our recommendations to prepare buffers Plate reader settings not optimal Verify the wavelength and filter settings Incorrect assay temperature Bring Developing Solution and Stop Solution to room temperature before using Inadequate volume of Developing Solution Check to make sure that correct volume is delivered by pipette Measurement time too long Stop enzymatic reactions as soon as the positive wells turn medium-dark blue Concentration of antibodies is too high Increase antibody dilutions Inadequate washing Ensure all wells are filled with Wash Buffer and follow washing recommendations Incomplete washing of wells Ensure all wells are filled with Wash Buffer and follow washing recommendations Well cross-contamination Follow washing recommendations Too much nuclear extract per well Decrease amount of nuclear extract down to 1-2 µg/well Concentration of antibodies is too high Perform antibody titration to determine optimal working concentration. Start using 1:2,000 for primary antibody and 1:5,000 for the secondary antibody. The sensitivity of the assay will be decreased Not enough nuclear extract per well Increase amount of nuclear extract. Not to exceed 50 µg/well Too many freeze/thaw cycles of extract Aliquot extract into 5 µl aliquots and store at -80°C to avoid multiple freeze/thaws NFkB is poorly activated or inactivated in nuclear fractions Perform a time course for NFkB activation in the studied cell line Nuclear extracts are not from correct species The p65, p50 and p52 antibodies work in human and mouse samples. The p65 antibody also cross-reacts with rat. Salt concentration too high in binding reaction Reduce amount of extract per well or dialyze extract before use High background in all wells Uneven color development High background in sample wells No signal or weak signal in sample wells www.activemotif.com 15 Section C. Related Products Transcription Factor ELISAs Format Catalog No. TransAM™ AML-1/Runx1 1 x 96-well plate 47396 1 x 96-well plate 44496 TransAM™ AML-3/Runx2 2 x 96-well plates 44296 TransAM™ AP-1 Family 1 x 96-well plate 44096 TransAM™ AP-1 c-Fos 1 x 96-well plate 46096 TransAM™ AP-1 c-Jun 1 x 96-well plate 45096 TransAM™ AP-1 FosB 1 x 96-well plate 43496 TransAM™ AP-1 JunD 1 x 96-well plate 42396 TransAM™ ATF-2 1 x 96-well plate 43396 TransAM™ c-Myc 1 x 96-well plate 44196 TransAM™ C/EBP a/b 1 x 96-well plate 42096 TransAM™ CREB 1 x 96-well plate 43096 TransAM™ pCREB 1 x 96-well plate 44396 TransAM™ Elk-1 1 x 96-well plate 41396 TransAM™ ER 1 x 96-well plate 46396 TransAM™ FKHR (FOXO1/4) 2 x 96-well plates 48296 TransAM™ GATA Family 1 x 96-well plate 46496 TransAM™ GATA-4 1 x 96-well plate 45496 TransAM™ GR 1 x 96-well plate 47096 TransAM™ HIF-1 2 x 96-well plates 46296 TransAM™ HNF Family 1 x 96-well plate 46196 TransAM™ HNF-1 1 x 96-well plate 48396 TransAM™ IRF-3 (Human) 1 x 96-well plate 48496 TransAM™ IRF-3 (Mouse) 1 x 96-well plate 50196 TransAM™ IRF-7 2 x 96-well plates 47296 TransAM™ MAPK Family 1 x 96-well plate 43196 TransAM™ MEF2 1 x 96-well plate 47196 TransAM™ MyoD 1 x 96-well plate 40396 TransAM™ NF-YA 1 x 96-well plate 40296 TransAM™ NFATc1 2 x 96-well plates 43296 TransAM™ NFkB Family 2 x 96-well plates 43298 TransAM™ Flexi NFkB Family 1 x 96-well plate 41096 TransAM™ NFkB p50 1 x 96-well plate 41097 TransAM™ NFkB p50 Chemi 1 x 96-well plate 41098 TransAM™ Flexi NFkB p50 1 x 96-well plate 48196 TransAM™ NFkB p52 1 x 96-well plate 48197 TransAM™ NFkB p52 Chemi 1 x 96-well plate 40096 TransAM™ NFkB p65 1 x 96-well plate 40097 TransAM™ NFkB p65 Chemi 1 x 96-well plate 40098 TransAM™ Flexi NFkB p65 1 x 96-well plate 50296 TransAM™ Nrf2 1 x 96-well plate 42496 TransAM™ Oct-4 1 x 96-well plate 41196 TransAM™ p53 1 x 96-well plate 40196 TransAM™ PPARg 1 x 96-well plate 41296 TransAM™ Sp1 1 x 96-well plate 40496 TransAM™ Sp1/Sp3 2 x 96-well plates 42296 TransAM™ STAT Family 1 x 96-well plate 45196 TransAM™ STAT3 1 x 96-well plate 51396 TransAM™ T-bet For a complete, up-to-date list of available TransAM™ Kits, please visit www.activemotif.com/transam Function ELISA FunctionELISA IkBa www.activemotif.com 16 Format Catalog No. 1 x 96-well plate 48005 Recombinant Proteins Format Catalog No. Recombinant c-Fos protein Recombinant c-Jun protein Recombinant c-Myc protein Recombinant CREB protein Recombinant elF2a protein Recombinant NFkB p50 protein Recombinant NFkB p65 protein Recombinant p53 protein Recombinant p300 protein Purified Sp1 protein Recombinant STAT3 protein 5 µg 5 µg 5 µg 25 µg 25 µg 5 µg 5 µg 5 µg 4 µg 2 µg 10 µg 31115 31116 31117 31107 31108 31101 31102 31103 31124 31137 31140 Histone ELISAs Format Catalog No. Histone H3 monomethyl Lys4 ELISA Histone H3 dimethyl Lys4 ELISA Histone H3 trimethyl Lys4 ELISA Histone H3 dimethyl Lys9 ELISA Histone H3 trimethyl Lys9 ELISA Histone H3 monomethyl Lys27 ELISA Histone H3 trimethyl Lys27 ELISA Histone H3 phospho Ser10 ELISA Histone H3 phospho Ser28 ELISA Total Histone H3 ELISA 1 x 96 rxns 1 x 96 rxns 1 x 96 rxns 1 x 96 rxns 1 x 96 rxns 1 x 96 rxns 1 x 96 rxns 1 x 96 rxns 1 x 96 rxns 1 x 96 rxns 53101 53112 53113 53108 53109 53104 53106 53111 53100 53110 Histone Purification & Chromatin Assembly Format Catalog No. Histone Purification Kit Histone Purification Mini Kit Chromatin Assembly Kit HeLa Core Histones 10 rxns 10 rxns 10 rxns 36 µg 40025 40026 53500 53501 Co-Immunoprecipitation Format Catalog No. Nuclear Complex Co-IP Kit Universal Magnetic Co-IP Kit 50 rxns 25 rxns 54001 54002 DNA Methylation Format Catalog No. MethylDetector™ MethylCollector™ MethylCollector™ Ultra UnMethylCollector™ Fully Methylated Jurkat DNA 50 rxns 25 rxns 30 rxns 30 rxns 10 µg 55001 55002 55005 55004 55003 SUMOylation Format Catalog No. SUMOlink™ SUMO-1 Kit SUMOlink™ SUMO-2/3 Kit 20 rxns 20 rxns 40120 40220 www.activemotif.com 17 ChIP-validated Antibodies Application AP-2 pAb ChIP, EMSA ChIP, EMSA, IF c-Jun pAb ChIP, EMSA, IF, WB C/EBPa pAb ChIP, WB CTCF mAb ChIP, IHC, IP, WB DNMT1 mAb ChIP, IF, IHC, WB DNMT3A mAb ChIP, IF, IP, WB DNMT3B mAb ChIP, EMSA E2F-1 pAb ChIP, WB E2F-6 mAb ChIP, WB EZH2 pAb ChIP, IF, WB HBP-1 mAb ChIP, IF, IHC, IP, WB HDAC1 mAb (Clone 10E2) ChIP, IF, IHC, IP, WB HDAC2 mAb (Clone 3F3) ChIP, WB HDAC3 pAb ChIP, WB HDAC4 pAb ChIP, WB HDAC5 pAb ChIP, WB HDAC6 pAb ChIP, WB Histone H2A pAb ChIP, IF, IP, WB Histone H2A phospho Ser129 pAb ChIP, WB Histone H2A.Z pAb ChIP, WB Histone H2B pAb ChIP, WB Histone H2B acetyl Lys5 pAb ChIP, WB Histone H2B acetyl Lys16 pAb ChIP, WB Histone H2B acetyl Lys46 pAb ChIP, WB Histone H3, C-terminal pAb ChIP, IF, WB Histone H3 acetyl Lys4 pAb ChIP, WB Histone H3 monomethyl Lys4 mAb ChIP, WB Histone H3 dimethyl Lys4 pAb ChIP, WB Histone H3 trimethyl Lys4 pAb ChIP, IF, WB Histone H3 dimethyl Lys9 pAb ChIP, WB Histone H3 trimethyl Lys9 pAb ChIP, IF, WB Histone H3 acetyl Lys18 pAb ChIP, IF, WB Histone H3 acetyl Lys27 pAb ChIP, WB Histone H3 acetyl Lys27 pAb ChIP, IF, WB Histone H3 dimethyl Lys27 pAb ChIP, WB Histone H3 trimethyl Lys27 mAb ChIP, IF, WB Histone H3 trimethyl Lys27 pAb ChIP, WB Histone H3 trimethyl Lys27 pAb ChIP, IF, WB Histone H3 acetyl Lys36 pAb ChIP, WB Histone H3 acetyl Lys56 pAb ChIP, IF, WB Histone H3 acetyl Lys64 pAb ChIP, WB Histone H3 acetyl Lys79 pAb ChIP, IF, WB Histone H4 pan-acetyl pAb ChIP, WB Histone H4 tetra-acetyl pAb ChIP, IF, WB Histone H4 acetyl Lys5 pAb ChIP, IF, WB Histone H4 acetyl Lys5 pAb ChIP, IF, WB Histone H4 acetyl Lys12 pAb ChIP, WB Histone H4 acetyl Lys16 pAb ChIP, IF, WB Histone H4 monomethyl Lys20 pAb ChIP, IF, WB Histone H4 trimethyl Lys20 pAb ChIP, WB IRF-3 pAb ChIP, EMSA JunB pAb ChIP, EMSA JunD pAb ChIP, IP, WB L3MBTL1 pAb ChIP, EMSA p53 pAb www.activemotif.com 18 Format Catalog No. 17 rxns 100 µg 100 µg 200 µg 100 µg 100 µg 100 µg 17 rxns 100 µl 100 µg 100 µl 200 µl 200 µl 100 µg 100 µg 100 µg 100 µg 200 µl 200 µl 200 µl 200 µl 200 µl 200 µl 200 µl 200 µl 200 µl 100 µg 200 µl 200 µl 200 µl 200 µl 200 µl 200 µg 200 µl 200 µl 200 µl 200 µg 200 µl 200 µl 200 µl 200 µl 200 µl 200 µl 50 µl 200 µl 200 µl 200 µl 200 µl 200 µl 200 µl 100 µl 17 rxns 100 µl 200 µl 17 rxns 39304 39309 39306 39621 39204 39206 39207 39313 39509 39639 39511 39531 39533 40968 40969 40970 40971 39235 39271 39113 39237 39123 39121 39571 39163 39381 39635 39141 39159 39239 39161 39587 39133 39135 39245 39535 39155 39156 39379 39281 39545 39565 39243 39179 39169 39583 39165 39167 39175 39180 39033 39326 39328 39182 39334 PP2A pAb ChIP, IP, WB 200 µl 39192 ChIP, WB 200 µl 39198 RbAp46/48 pAb ChIP, ELISA, IF, IP, WB 200 µl 39097 RNA pol II mAb ChIP, IF, IP, WB 200 µl 39543 SNF2h mAb ChIP, WB 100 µl 39058 Sp1 pAb ChIP, IP, WB 100 µg 39223 TRF2 Goat pAb For an up-to-date list of ChIP-validated antibodies, please visit www.activemotif.com/chipabs Application Key: ChIP = Chromatin Immunoprecipitation; EMSA = Electrophoretic Mobility Shift Assay; IF = Immunofluorescence; IHC = Immunohistochemistry; IP = Immunoprecipitation; WB = Western blot ChIP-IT™ Kits Format Catalog No. ChIP-IT™ Express ChIP-IT™ Express Enzymatic ChIP-IT™ Express HT Re-ChIP-IT™ ChIP-IT™ ChIP-IT™ Enzymatic ChIP-IT™ Shearing Kit Enzymatic Shearing Kit ChIP-IT™ Protein G Magnetic Beads Salmon Sperm DNA/Protein G agarose ChIP-IT™ Control Kit – Human ChIP-IT™ Control Kit – Mouse ChIP-IT™ Control Kit – Rat Ready-to-ChIP HeLa Chromatin Ready-to-ChIP Hep G2 Chromatin Ready-to-ChIP K-562 Chromatin Ready-to-ChIP NIH/3T3 Chromatin 25 rxns 25 rxns 96 rxns 25 rxns 25 rxns 25 rxns 10 rxns 10 rxns 25 rxns 25 rxns 5 rxns 5 rxns 5 rxns 10 rxns 10 rxns 10 rxns 10 rxns 53008 53009 53018 53016 53001 53006 53002 53005 53014 53003 53010 53011 53012 53015 53019 53020 53021 www.activemotif.com 19 Technical Services If you need assistance at any time, please call Active Motif Technical Service at one of the numbers listed below. Active Motif North America 1914 Palomar Oaks Way, Suite 150 Carlsbad, CA 92008 USA Toll Free: 877 222 9543 Telephone: 760 431 1263 Fax: 760 431 1351 E-mail: [email protected] Active Motif Europe 104 Avenue Franklin Roosevelt B-1330 Rixensart, Belgium UK Free Phone: 0800 169 31 47 France Free Phone: 0800 90 99 79 Germany Free Phone: 0800 181 99 10 Telephone: +32 (0)2 653 0001 Fax: +32 (0)2 653 0050 E-mail: [email protected] Active Motif Japan Azuma Bldg, 7th Floor 2-21 Ageba-Cho, Shinjuku-Ku Tokyo, 162-0824, Japan Telephone: +81 3 5225 3638 Fax: +81 3 5261 8733 E-mail: [email protected] Visit Active Motif on the worldwide web at http://www.activemotif.com At this site: • Read about who we are, where we are, and what we do • Review data supporting our products and the latest updates • Enter your name into our mailing list to receive our catalog, MotifVations newsletter and notification of our upcoming products • Share your ideas and results with us • View our job opportunities Don’t forget to bookmark our site for easy reference! www.activemotif.com 20
© Copyright 2026 Paperzz