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MICROARR AY
METHODS
AND
PROTOCOLS
Robert S. Matson
Boca Raton London New York
CRC Press is an imprint of the
Taylor & Francis Group, an informa business
46659_C00a.indd 3 11/26/08 3:49:59 PM
CRC Press
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© 2009 by Taylor & Francis Group, LLC
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International Standard Book Number-13: 978-1-4200-4665-6 (Softcover)
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Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and are
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Library of Congress Cataloging-in-Publication Data
Microarray methods and protocols / edited by Robert S. Matson.
p. ; cm.
Includes bibliographical references and index.
ISBN-13: 978-1-4200-4665-6 (hardcover : alk. paper)
ISBN-10: 1-4200-4665-9 (hardcover : alk. paper)
1. DNA microarrays--Laboratory manuals. 2. Protein microarrays--Laboratory
manuals. I. Matson, Robert S. II. Title.
[DNLM: 1. Microarray Analysis--methods--Laboratory Manuals. 2. Analytic
Sample Preparation Methods--Laboratory Manuals. 3. Gene Expression
Profiling--methods--Laboratory Manuals. 4. Laboratory Techniques and
Procedures--Laboratory Manuals. QU 25 M6258 2009]
QP624.5.D726M513 2009
572.8’636--dc22 2008035383
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Dedication
To my mentors: SeaBong Chang, Tokuji
Kimura, T.T. Tchen, and Armand Fulco
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Contents
Preface.......................................................................................................................ix
Editor.........................................................................................................................xi
Authors.................................................................................................................... xiii
Chapter 1. Introduction to Microarray Technologies............................1
Robert S. Matson
Chapter 2. Nucleic Acid Sample Preparation.....................................13
Robert S. Matson
Chapter 3. Solid-Phase Substrates for Nucleic Acid
Microarrays.....................................................................51
Robert S. Matson
Chapter 4. Protein Sample Preparation for Microarrays.....................71
Robert S. Matson
Chapter 5. Solid-Phase Chemistries for Protein Microarrays..............83
Robert S. Matson
Chapter 6. Protein Microarrays: The Link between Genomics and
Proteomics......................................................................93
Persis P. Wadia and David B. Miklos
vii
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viii Contents
Chapter 7. Bead Arrays: An Introduction to Multiplexed
Bead-Based Assays for Proteins.................................... 111
Yong Song
Chapter 8. Carbohydrate Arrays......................................................127
Denong Wang
Chapter 9. Lectin Microarrays......................................................... 141
Masao Yamada
Chapter 10. Printing Methods...........................................................157
Todd Martinsky
Appendix A: Microarray Reagent, Materials, and
Equipment Sources...........................................................................201
Appendix B: Image Analysis............................................................. 209
Index.................................................................................................. 213
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Preface
The concepts that define microarray were developed in the late 1980s. Less than
a decade later we witnessed large-scale efforts to commercialize microarrays, and
today they are seasoned tools eagerly employed by a world of scientists. This multi-
plexing technology (formatted as slides, plates, biochips, or beads) now is undergoing
the scrutiny required for the standardization that is essential to drive its adoption in
future prognostic and diagnostic applications. Microarray technology continues to
evolve, taking on different forms: Originating with the glass microscope slide and
biochip, it is now pressing onward into the nanotechnology frontier. From the spotting
of cDNA and the in situ synthesis of oligonucleotide arrays now come microarrays
comprising proteins, carbohydrates, drugs, tissues, and cells. For myself, it has been
a great adventure into the multidisciplinary approach to research. I am indebted
to Jim Osborne, who championed our cause from the helm of Beckman Coulter’s
Advanced Technology Center, and to Ed Southern, who inspired us all. I would also
like to thank my co-authors for their hard work and dedication in providing such
excellent contributions to this book.
I remain hopeful for these arrays of small spots, with the expectation that
microarrays will ultimately reduce the cost of healthcare. I invite you to join us in
that endeavor.
Robert S. Matson, Ph.D., F.A.C.B.
Orange, California
ix
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Editor
Robert Matson, Ph.D., F.A.C.B., has been involved
in microarray technology research for the past
17 years at Beckman Coulter. He participated in
NIST’s Advanced Technology Program–sponsored
Genosensor Consortium, and collaborated with Sir
Edwin Southern on the development of an in situ oligo-
nucleotide array synthesis platform for the corporation.
Other work included development of a microplate-
based array platform for multiplexed micro-ELISA.
Dr. Matson has been granted 12 U.S. patents, as well
as several European patents on nucleic acid and pro-
tein microarray technology. He was inducted into
Beckman Coulter’s Inventors Hall of Fame in 2006,
and was recently elected a Fellow of the National Academy of Clinical Biochemistry.
He has previously served in several technical management roles including R&D
director, BioProbe International; R&D director, Costar–Nuclepore; and chemistry
R&D group leader at BioRad Laboratories.
Dr. Matson received his Ph.D. in biochemistry from Wayne State University.
Following postdoctoral studies at the UCLA Medical School he served as a principal
investigator with the Veterans Administration Medical Center and adjunct profes-
sor of biological chemistry at the University of California–Davis Medical School.
Dr. Matson has also held a faculty lectureship in USC’s Department of Chemistry, and
was assistant professor of chemistry at the University of Southern Maine, Portland.
He is the author of Applying Genomic and Proteomic Microarray Technology in
Drug Discovery (CRC Press, 2005).
xi
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Authors
Todd Martinsky, cofounder of TeleChem
International, Inc., and ArrayIt Corporation, previ-
ously served as director of education and consulting at
the Codd and Date Consulting Group. Mr. Martinsky
has led the ArrayIt Division to play a significant role in
the microarray industry. He has authored several book
chapters and other scientific literature and has become
an internationally recognized lecturer, writer, consul-
tant and teacher. In addition to providing consulting
services, Mr. Martinsky has spearheaded ArrayIt’s
technical support team since 1997. Along with his
daily technical and business direction of the ArrayIt product line, Mr. Martinsky
established successful alliances with corporate partners in manufacturing, reagents,
equipment, and distribution. He is responsible for an educational outreach program
that ensures that the broadly patented ArrayIt Micro Spotting Devices are applied in
the field with optimal scientific and technological accuracy. He is currently serving
on the panel that is crafting future regulatory requirements for microarray manufac-
turing for the U.S. Pharmacopeia.
David Miklos, M.D., Ph.D., assistant professor of
medicine, Stanford University, is a hematopoietic stem
cell transplant (HCT) clinician with special interest in
chronic graft versus host disease (GVHD). His lab has
developed protein microarray technology to measure
allogeneic antibody development after allogeneic
transplantation. Dr. Miklos earned his B.S. from the
University of Notre Dame and his M.D./Ph.D. from
Yale University. He trained in internal medicine at
Brigham and Women’s Hospital, followed by hematol-
ogy and oncology fellowship training at Dana-Farber
Cancer Institute with special emphasis in BMT and
xiii
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xiv Authors
hematologic malignancies. He remains active as both a BMT clinician and basic-
science immunologist.
Yong Song, M.D., Ph.D., is product manager, stra-
tegic marketing, Beckman Coulter, Inc., currently
managing the personal cytometry analyzer business.
Dr. Song obtained his M.D. from Shantou University
Medical College, China, and his Ph.D. from the
University of Hong Kong. He received his postdoctoral
training under Prof. Melvin Silverman at the Canadian
Institutes of Health Research group in membrane biol-
ogy in the Faculty of Medicine, University of Toronto,
Canada. Prior to his current position at Beckman
Coulter, Inc., Dr. Song held senior scientific and R&D
management positions at Bio-Rad Laboratories, Hyseq
Pharmaceuticals, and Beckman Coulter, Inc. Dr. Song has many years of experience
in drug discovery and product development for immunoassays and flow cytometry
applications. He has more than 80 publications and is an inventor of a multiplex
bead-based assay patent for determination of cellular protein modifications, includ-
ing protein phosphorylation.
Persis Wadia, Ph.D., received her B.Sc., M.Sc.,
and Ph.D. from the University of Mumbai, India.
She is presently a postdoctoral scholar in the
Department of Medicine, Division of Blood and
Marrow Transplantation, at Stanford University.
Her main fields of research have been oncology and
immunology. Her current research interests include
identifying minor histocompatibility antigens/bio-
markers after bone marrow transplantation in AML
patients.
Denong Wang, M.D., Ph.D., senior research scientist,
Department of Genetics, Stanford University School of
Medicine, is specialized in the areas of carbohydrate
antigens, anti-carbohydrate antibodies, and carbohy-
drate microarray technologies. His group published
the first description of a carbohydrate-based micro-
array technology in the March 2002 issue of Nature
Biotechnology. His recent efforts have focused on
identification and characterization of immunogenic
sugar moieties of microbes and human cancers, as
well as development of novel platforms of bioarrays.
Dr. Wang is principal investigator and director of the
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Authors xv
Stanford Tumor Glycome Laboratory, which is one of the seven key laboratories of
the National Institutes of Health Alliance of Glycobiologists for Detection of Cancer
and Cancer Risk.
Masao Yamada, Ph.D., is director of the Glycomics
Research Laboratory, Moritex Corporation, Yokohama,
Japan. He received his Ph.D. in electrical and electron-
ics engineering from Nagoya University. He has held
several technical management positions in his career
including director, Advanced Device Development,
Fujitsu, Ltd., and vice president, Nippon Laser and
Electronics Lab. Dr. Yamada also served as a consult-
ing associate professor for the Solid State Electronics
Lab, Stanford University, as well as visiting professor
at Nagoya University. In addition to his role as direc-
tor of the Glycomics Research Laboratory, he is senior
general manager for Moritex Corporation.
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