Introduction to Antibodies

100 Pages·2013·4.25 MB·English

by  Merck Millipore

3rd Edition
An Introduction to Antibodies
and Their Applications
Merck Millipore is a division of
By:
Manpreet Mutneja, Ph.D.
Chandra Mohan, Ph.D.
Kevin D. Long, Ph.D.
Chandreyee Das, Ph.D.
In collaboration with:
John L. Hermesman
Robin T. Clark, Ph.D.
Robert Brockett, HTL (ASCP)CM
Acknowledgements:
Mary Ann Ford, Marketing
Communications, and
Liza Benson, Design for their
contributions and dedication
to make this guide possible.
EMD Millipore
An Introduction to Antibodies
and Their Applications
Merck Millipore – your partner in Life Science research.
At Merck Millipore, our commitment to advancing scientific research defines us.
We understand the challenges faced by today’s researcher and know the importance of research tools (antibodies,
proteins, enzymes, inhibitors, and other reagents) for research, drug discovery, and publications. This technical
guide on the theory and practical use of antibodies in biological research is a part of our continuing commitment
to provide useful information and exceptional service to researchers.
The 3rd edition of An Introduction to Antibodies and Their Applications provides a concise overview of some
of the key features for the use of antibodies and immunochemical techniques in biological research. This handy
reference guide supplements the techniques described in literature, recorded in general laboratory procedures,
and described on individual product data sheets. Antibody design, development, and production are our expertise.
Stringent validation of our antibodies is only one component of a comprehensive process we undertake to provide
the antibodies most cited by the research community (see section Antibody Quality on page 2 for an in-depth look
at our expertise).
As every antibody and experimental design is unique, these general principles and suggestions should not be
interpreted as applicable to all situations, but rather as an additional source of information. As always, individual
assays must be optimized empirically and antibody titers must be established for every unique batch of antibody.
Whether you are a veteran researcher or just beginning your research career, we hope that you will find this guide
to be useful in your research. Your suggestions and comments for further improvements are always welcome.
Merck Millipore products are among the best in the industry, and include the expertise of Chemicon®, Upstate®,
Calbiochem®, and Novagen®. For more information about using any of our research products, including more than
10,000 antibodies and kits, or simply to get scientific advice for a variety of immunological applications, please
contact us. In addition, you can find extensive general information and technical specifications on our website
www.merckmillipore.com. Rest assured that our highly trained, exceptional customer and technical service
support specialists are always available to support you in your research.
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A Note on Antibody Quality
It is often assumed that because specificity defines certain, uncommon immunization protocols are robust
their function, antibodies must have some intrinsic enough to use the less immunogenic, but more specific
high quality, which implies reliability and ease of use. peptides critical for generating a quality antibody.
Surprisingly, this is most often not the case. Although
it is true that antibody binding to a specific amino acid Based on the combined strengths of Chemicon®,
sequence or conformational form can be theoretically Upstate®, Millipore®, Calbiochem® and Novagen®,
modeled and is predictable in theory, decades of at Merck Millipore, we have decades of experience in
user experience has demonstrated that factors such innovative immunogen design, immunization, selection,
as antigenicity and uniqueness of the immunogen screening, and validation to create many of our highly
sequence, antibody concentration, buffers, immunization cited antibodies. Our commitment to produce high
and sample preparation techniques, contribute quality antibodies is based not only on innovation, but is
significantly to issues of cross-reactivity and nonspecific also tempered with customer beta testing and feedback
binding. to the design/engineering team, prior to release. These
efforts and collaborations have lead to the development
Since the early 1970s, when researchers began to use of new validation techniques and novel antibody-based
antibodies as protein probes, the problem of inconsistent technologies, such as improved multiplexing and high
antibody performance has plagued researchers. The resolution imaging flow cytometry. This cycle, from
pioneer developers and users of antibodies had fairly thoughtful design to field usage and report, is the basis
extensive knowledge of immunology to rely on. In today’s of quality. Our technical and scientific background
research world, antibodies are used for an amazing is what makes Merck Millipore a major designer and
variety of applications, from purification to blocking producer of quality antibodies, and not merely a
of cellular function. Today, antibody users range from distributor. Indeed, there is a whole lot of science in
classic medical anatomists to novice biochemists and every vial of our antibodies.
biomedical engineers. Many users are unaware that
immunogen design is fairly complex and that only
Advanced Collaboration,
immunization Multi-platform discovery &
technologies validation publication
R1
H N C C HN
H O
Innovative Rigorous Customer
immunogen selection experimentation
design & purification
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The science inside your tube of Special validation
Merck Millipore antibodies. To support our multi-step, multi-application validation
process, we have a tissue and blot library with over
1300 lysates, allowing us to precisely determine each
Antigen development and immunization
antibody’s specificity. At Merck Millipore, we have the
Our team of antibody research scientists continually
advantage of having an entire cell analysis technology
monitors and reviews the latest publications and
development team in-house. We validate antibodies for
collaborates with leading research institutions to identify
flow cytometry using our own guava easyCyte™ dual-
the most useful targets and antibodies. We design
laser microcapillary instruments. Similarly, our in-house
multiple immunogens, taking into consideration post-
bead-based immunodetection team helps us validate
translational modifications, structure, cross-reactivity,
antibodies using the trusted Luminex xMAP platform. Our
and homology. We discuss target selection with leaders
microarray system handles development and validation
in key research areas, including neuroscience, cancer,
mainly for antibodies recognizing modified histones.
epigenetics, and signaling research using their expertise
Using confocal microscopes and high-throughput IHC
to guide development and validation.
instruments, we can obtain accurate data faster than
manual imaging. Further scientific review determines
Monoclonal antibody development
whether staining patterns conform to published
Following immunization at our USDA-approved facility,
subcellular expression. For immunohistochemistry, we
we develop monoclonal and polyclonal antibodies using
include negative controls, to confirm the signal.
state-of-the-art processes. For monoclonal antibodies,
we use a robotic cloning and screening system, which
Technical review
handles all the fusions and feeding steps for hybridomas.
The final step in our process is a quality review carried
These highly automated processes use cutting-edge
out by an independent team of scientists. Before
technology to ensure optimum throughput and
releasing the antibody to manufacturing, the team
maximum consistency. Using an array-jet automated
considers all antibody validation data, as well as data
microarray system, we test the fusion and identify
from scientists who participated in the beta testing. If
positive clones. To ensure that the positive signal is from
our antibodies fail to meet our strictest specifications,
the antibody, we screen again using ELISA. Positives are
they are discarded without question, even if they have hit
screened using automated Western blotting of cells with
initial targets. As an integral component of our quality
endogenously expressed antigens. The pool of positives is
process, only antibodies that pass this stringent review
repeatedly diluted to isolate the highest performer until
are made available to customers.
our samples reach 100% clonality. This additional process
is one way that Merck Millipore sets itself apart from the
Customer experimentation
competition. With additional Western blotting, we select
and collaboration
the best possible clone for further validation.
Once produced and released for sale, we support
customers’ research efforts with a highly specialized
Polyclonal antibody development
team of technical support scientists and field engineers.
Polyclonal antibodies are purified using fast protein We work closely with researchers to improve immunogen
liquid chromatography (FPLC) systems, using no column design and antibody performance. We have a growing
more than 10 times. Automated Western blotting is network of beta testers to continue validation. And each
used to determine further purification steps. These new and every one of our antibodies is backed by our 100%
polyclonal antibodies are then validated in a number Antibody Performance Guarantee.
of applications and are also incorporated into kits and
assays for Merck Millipore’s protein and cellular analysis Merck Millipore antibodies are among the most cited,
platforms. trusted, and highly validated on the market today.
Their quality starts at inception and carries through
manufacturing, production and distribution - into the lab
and onto the bench. From start to finish, it’s the science
in every tube of Merck Millipore antibodies that assures
confidence in the world’s most reliable, defensible, and
publishable antibody performance.
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Table of Contents
Foreword
A Note on Antibody Quality
1 Antibody Theory page 7
1.1 An Introduction to Antibodies 7
1.2 Antigens 7
1.3 Epitopes 8
1.4 Antibodies 9
1.5 Antibody-Antigen Interaction 12
1.6 Nature of Antigen-Antibody Bonds 13
1.7 Factors Affecting Antigen-Antibody Reactions 13
1.8 Generation of Antibodies 14
1.9 Antibody Formats 16
1.10 Biological Effects of Antibodies 17
2 Antibody Practice page 21
2.1 Selection and Use 21
2.2 Antibody Titer and Concentration 22
2.3 Storage and Handling of Antibodies 22
2.4 Conjugated Antibodies 23
2.5 Use of Secondary Antibodies 24
2.6 Proper Controls 25
2.7 Publishing with Antibodies 26
2.8 Validating Antibodies 26
3 Antibody Applications page 29
3.1 Introduction to Antibody Applications 29
3.2 Immunoprecipitation 30
3.3 Chromatin Immunoprecipitation (ChIP) 34
3.4 Western Blotting 42
3.5 Enzyme-linked Immunosorbent Assays (ELISA) 51
3.6 Multiplexed Bead-based Detection 56
3.7 Immunohistochemistry/Immunocytochemistry 60
3.8 Flow Cytometry 68
3.9 Functional Blocking and Stimulation Assays 76
4 Sample Protocols page 81
4.1 Immunoprecipitation 81
4.2 Chromatin Immunoprecipitation (ChIP) 81
4.3 Western Blotting 83
4.4 Enzyme-linked Immunosorbent Assays (ELISA) 85
4.5 Multiplexed Bead-based Detection 86
4.6 Immunohistochemistry/Immunocytochemistry 87
4.7 Flow Cytometry 88
4.8 Functional Blocking and Stimulation Assays 89
Appendix 91
Glossary 93
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A
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Antibody Theory 1 th
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1.1 An Introduction to Antibodies 1.7 Factors Affecting Antigen-Antibody
1.2 Antigens Reactions
1.3 Epitopes 1.8 Generation of Antibodies
1.4 Antibodies 1.9 Antibody Formats
1.5 Antibody-Antigen Interaction 1.10 Biological Effects of Antibodies
1.6 Nature of Antigen-Antibody Bonds
1.1 An Introduction to Antibodies critical tools for most areas of life science research. The
During the first half of the 20th century, a series of basic principle of any immunochemical technique is that
scientific discoveries resolved that antibody-mediated a specific antibody will combine with its specific antigen
immunity is the cornerstone of the specific immune to generate an exclusive antibody-antigen complex. In
response. Since their first use as immunolabeling the following pages we will discuss the nature of this
research tools in the early 1970s, antibody technologies bond, and the use of this robust and specific binding as a
have vastly improved, and antibodies have become molecular tag for research.
1.2 Antigens A variety of molecules such as drugs, simple sugars,
The term antigen is derived from antibody generation, amino acids, small peptides, phospholipids, or
referring to any substance that is capable of eliciting triglycerides may function as haptens. Thus, given
an immune response (e.g., the production of specific enough time, just about any foreign substance will be
antibody molecules). By definition, an antigen (Ag) is identified by the immune system and evoke specific
capable of combining with the specific antibodies formed antibody production. However, this specific immune
by its presence. response is highly variable and depends much in part on
the size, structure, and composition of antigens. Proteins
Generally, antigens are foreign proteins or their or glycoproteins are considered as the most suitable
fragments that enter host body via an infection. antigens due to their ability to generate a strong immune
However, in some cases, the body’s own proteins may response; in other words, they are strongly immunogenic.
act as antigens and induce an autoimmune response.
Bacteria and viruses contain antigens, either on their Antigens are recognized by the host body by two distinct
surface, or inside. These antigens can be isolated and processes (1) by B cells and their surface antibodies
used to develop vaccines. (sIgM) and (2) by the T cell receptor on T cells. Although
both B and T cells respond to the same antigen, they
Antigens are generally of high molecular weight, and respond to different parts of the same molecule.
commonly are proteins or polysaccharides. Polypeptides, Antibodies on the surface of B cells can recognize the
lipids, nucleic acids, and many other materials can also tertiary structure of proteins. On the other hand, T cells
function as antigens. Immune responses may also be require antigens that have been ingested and degraded
generated against smaller substances, called haptens, into recognizable fragments by the antigen-presenting
if these are chemically coupled to a larger carrier cells. Commonly employed antigen-presenting cells are
protein, such as bovine serum albumin, keyhole limpet macrophages and dendritic cells. The immune response
hemocyanin (KLH), or other synthetic matrices. is illustrated in Figure 1. For greater detail on the natural
process of antibody production, a suitable immunology
textbook should be consulted.
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y
r
o
e
h
t
y
d
o Bacteria Antigen Receptor Characteristics of a Good Antigen
b
ti
n • Areas of structural stability and chemical
A B Cell
Processed complexity within the molecule
Antigen Fragment
Macrophage • Significant stretches lacking extensive
repeating units
Antigen Fragment
Receptor Activated • A minimal molecular weight of 8,000 to 10,000
Helper B Cell Daltons, although haptens with molecular weights
T-cell
as low as 200 Da have been used in the presence
of a carrier protein
• The ability to be processed by the immune system
Activated Memory B Cell Antibody-
T-cell Producing • Immunogenic regions that are accessible to the
B Cell
antibody-forming mechanism
• Structural elements that are sufficiently different
Infected Antibody from those present in the host
Cell
Antigen-
• For peptide antigens, regions containing at least
Antibody
Cytotoxic Memory Complexes 30% of immunogenic amino acids: K, R, E, D, Q, N
T Cell T Cell
• For peptide antigens, significant hydrophilic or
Cell-Mediated Immunity Humoral Immunity charged residues
Figure 1.
The Immune Response.
1.3 Epitopes
The small site on an antigen to which a complementary
If the target molecule is denatured, e.g., through fixation,
antibody may specifically bind is called an epitope
reduction, pH changes, or during preparation for gel
or antigenic determinant. This is usually one to six
electrophoresis, the epitope may be altered and this
monosaccharides or five to eight amino acid residues on
may affect its ability to interact with an antibody. For
the surface of the antigen. Because antigen molecules
example, some antibodies are ineffective in Western
exist in space, the epitope recognized by an antibody may
blotting (WB) but are suitable for immunohistochemistry
be dependent upon the presence of a specific three-
(IHC) applications, because, in the IHC procedure, a
dimensional antigenic conformation (e.g., a unique site
complex antigenic site might be maintained in the tissue,
formed by the interaction of two native protein loops or
whereas in the WB procedure, the process of sample
subunits). This is known as a conformational epitope. The
preparation alters the protein conformation sufficiently
epitope may also correspond to a simple linear sequence
to destroy the antigenic site, and hence eliminates
of amino acids and such epitopes are known as linear
antibody binding.
epitopes.
The range of possible binding sites on a target molecule Watch Out
(antigen) is enormous, with each potential binding
A very important target, αVβ3 integrin will
site having its own structural properties derived
not work in Western blotting experiments
from covalent bonds, ionic bonds, hydrophilic, and
because the epitope is formed by the proximal
hydrophobic interactions. Indeed, this has important
association of the αV and β3 subunits to
ramifications for antibody choice and performance. For
each other—a conformation destroyed in the
efficient interaction to occur between the target antigen
electrophoresis protocol.
and the antibody, the epitope must be readily available
for binding.
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