Fluorescence Sensors and Biosensors 1st Edition
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FLUORESCENCE
SENSORS and
BIOSENSORS
Edited by
Richard B.Thompson
Boca Raton London New York
A CRC title, part of the Taylor & Francis imprint, a member of the
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Preface
This volume originated in the realization that an edited volume on developments in
fluorescence sensing and biosensing was sorely needed. In our frame of reference,
fluorescence-based sensors transduce the presence or level of some chemical analyte
as a change in fluorescence; biosensors use biological (or biomimetic) molecules to
effect the recognition of the analyte. This book is exclusively devoted to fluorescence
(and phosphorescence)-based sensing, which I view as the most powerful approach
for chemical sensing for three reasons. Fluorescence has high intrinsic sensitivity,
with experiments studying the emission of single molecules becoming commonplace.
Fluorescence transduction is very flexible, with many different phenomena being
employed herein to transduce analyte as changes in fluorescence. Finally, fluorescence
sensing is a peerless research tool for addressing biological questions because it
permits analytes to be imaged remotely either in the microscope or through fiber
optics. The enormous impact of fluorescence techniques may be judged by the growth
of the company Molecular Probes, which in 25 years grew from a firm offering a
handful of fluorescent dyes to one offering thousands of fluorescent products (and
which sold for $300 million in 2003). These fluorophores have appeared in thousands
of scholarly papers during this period, and fluorescence has emerged as a mainstream
research and development technology in fields such as fluorescence-activated cell
sorting, DNA sequencing, high-throughput screening, and clinical diagnostics. Thus,
I decided to solicit chapters on many of the most important new developments in the
field, with a view to highlighting technologies with the broadest potential impact.
The chapters are roughly grouped under three headings: new recognition or trans-
duction approaches, other new technology, and selected applications.
Tuan Vo-Dinh was kind enough to contribute an overview of the field from his
unique perspective of leadership over decades. This was especially good of him in
view of the release of his comprehensive Biomedical Photonics Handbook (CRC
Press, 2003). Drs. Yang and Ellington have been the leaders for some time in the
development of aptamers (oligoribonucleotides) for sensing, which is an especially
powerful technique for obtaining recognition chemistry for analytes that have no
other means of being “seen.” Dr. Daunert and her colleagues provide a succinct
overview of one of the most important biorecognition chemistry platforms, that
based on periplasmic binding proteins. Dr. Yao and his colleagues comprehensively
review the use of the molecular beacon approach for DNA recognition, which has
become a dominant method for transducing the recognition of DNA sequences in
array formats. Dr. Blagoi and his colleagues present the use of resonance energy
transfer itself in sensing, an approach that is used by several of the other authors.
Finally, the editor and his colleagues summarize the issues and future prospects for
the use of the carbonic anhydrase recognition platform for metal ion determination
and imaging.
There have been many new developments in fluorophores for fluorescent labeling
and sensing as well as fundamentally new approaches for sensor and assay construc-
tion; three of these are highlighted in this section. Dr. Geddes and his colleagues
make abundantly clear the current fascination and practical interest in metal-enhanced
fluorescence, where, under certain conditions, fluorophores exhibit almost magically
changed emission. Dr. Savitsky introduces a series of phosphorescent labels and
presents persuasive evidence of their advantages in a series of clinically relevant
assays. Dr. Anzenbacher describes a series of fluorescent probes selective for anions,
a heretofore underappreciated (and underserved from the standpoint of analytical
methods) group of analytes compared with metal ions. Finally, Drs. Chang and Yager
introduce us to their unique technology for fluid handling on a nanoscale, which is
a central issue in many analytical and clinical determinations.
The last section of the book deals with application of fluorescence sensing
technology to some rather practical problems. Dr. Herron gives a very lucid summary
of the work of the Utah group on the development of planar waveguide biosensors
and their application to clinical diagnostics. Dr. Tolosa and her colleagues discuss
the issues in adapting fluorescence-based sensing approaches to very demanding
problems in biochemical production by fermentation. Finally, several of my distin-
guished colleagues and I discuss some of the myriad practical problems in measuring
analytes such as free zinc ion at ultratrace levels in biological specimens.
We hope you enjoy the book and find it valuable as well.
Richard Thompson
About the Editor
Richard B. Thompson, Ph.D. is Associate Professor of Biochemistry and Molec-
ular Biology at the University of Maryland School of Medicine in Baltimore. He
was educated at Northwestern University (B.A.) and the University of Illinois (Ph.D.,
biochemistry), was a postdoctoral fellow at the University of Maryland, and was a
National Research Council Associate at and later joined the staff of the Naval
Research Laboratory in Washington, D.C., before joining the faculty in Maryland.
Dr. Thompson’s primary professional interest is in the area of fluorescence-based
biosensors, particularly those employing fiber optics. He has published numerous
articles in refereed journals and symposium proceedings, as well as book chapters.
He has served on review panels for agencies including the National Institutes of
Health, National Science Foundation, Department of Energy, and Department of
Defense, as well as three journal editorial boards. He has cochaired and coedited
the proceedings of the conference series “Advances in Fluorescence Sensing Tech-
nology” as well as a CD-ROM compendium of 1000 papers on fluorescence science
and technology and other proceedings. He received the U.S. Navy Special Act Award
for his work in support of Operation Desert Storm. He is a member of the Biophysical
Society, American Association for the Advancement of Science, American Society
for Biochemistry and Molecular Biology, American Chemical Society, Society of
Photo-Optical Instrumentation Engineers, and U.S. Naval Institute.
Acknowledgments
The Editor wishes to express his gratitude not only to the contributors for their
respective chapters but also to his co-workers for their efforts, his sponsors for their
support, and his colleagues for their interest. Special thanks are owed to his wife
Karen and his family for their patience and to Krystyna Gryczynska for drawing
many of the figures.
Contributors
Pavel Anzenbacher, Jr., Ph.D. Douglas A. Christensen, Ph.D.
Department of Chemistry and Center Department of Bioengineering
for Photochemical Sciences University of Utah
Bowling Green State University Salt Lake City, Utah
Bowling Green, Ohio
Michele L. Cramer, M.S.
Kadir Aslan, Ph.D. Department of Biochemistry and
University of Maryland Molecular Biology
Biotechnology Institute University of Maryland School
Baltimore, Maryland of Medicine
Baltimore, Maryland
Mark E. Astill, M.S.
ARUP Institute for Clinical and Sylvia Daunert, Ph.D.
Experimental Pathology Department of Chemistry
ARUP Laboratories University of Kentucky
Salt Lake City, Utah Lexington, Kentucky
Gabriela Blagoi, B.S. Sapna K. Deo, Ph.D.
Department of Chemistry Department of Chemistry
University of New Orleans University of Kentucky
New Orleans, Louisiana Lexington, Kentucky
Rebecca A. Bozym, B.S.
Jacob D. Durtschi, B.S.
Department of Biochemistry and
Department of Pharmaceutics and
Molecular Biology
Pharmaceutical Chemistry
University of Maryland School
University of Utah
of Medicine
Salt Lake City, Utah
Baltimore, Maryland
Stacy Z. Brown, B.S. Andrew Ellington, Ph.D.
Department of Pharmaceutics and Department of Chemistry and Institute
Pharmaceutical Chemistry for Cellular and Molecular Biology
University of Utah University of Texas at Austin
Salt Lake City, Utah Austin, Texas
Hugh N. Chang, M.S.E. Carol A. Fierke, Ph.D.
Department of Bioengineering Department of Chemistry
University of Washington University of Michigan
Seattle, Washington Ann Arbor, Michigan
Christopher J. Frederickson, Ph.D. Karolina Jursíková, M.S.
NeuroBioTex, Inc. Department of Chemistry and Center
Houston, Texas for Photochemical Sciences
Bowling Green State University
Chris D. Geddes, Ph.D. Bowling Green, Ohio
University of Maryland
Biotechnology Institute Yordan Kostov, Ph.D.
Baltimore, Maryland Department of Chemical and
Biochemical Engineering
University of Maryland Baltimore
Ignacy Gryczynski, Ph.D. County
Department of Biochemistry and Catonsville, Maryland
Molecular Biology
University of Maryland School Joseph R. Lakowicz, Ph.D.
of Medicine University of Maryland
Baltimore, Maryland Biotechnology Institute
Baltimore, Maryland
Anson V. Hatch, Ph.D.
Department of Bioengineering Frances S. Ligler, D.Phil., D.Sc.
University of Washington Center for Bio/Molecular Science
Seattle, Washington and Engineering
U. S. Naval Research Laboratory
Washington, D.C.
Kenneth R. Hawkins, B.S.
Department of Bioengineering
Govind Rao, Ph.D.
University of Washington
Department of Chemical and
Seattle, Washington
Biochemical Engineering
University of Maryland Baltimore
James N. Herron, Ph.D. County
Department of Pharmaceutics and Catonsville, Maryland
Pharmaceutical Chemistry
University of Utah Nitsa Rosenzweig, Ph.D.
Salt Lake City, Utah Department of Chemistry
University of New Orleans
New Orleans, Louisiana
Michal Hershfinkel, Ph.D.
Zlotowski Center for Neuroscience
Zeev Rosenzweig, Ph.D.
Ben-Gurion University of the Negev
Department of Chemistry
Beer Sheva, Israel
University of New Orleans
New Orleans, Louisiana
M. Shelly John, Ph.D.
Department of Chemistry and UF Brain Alexander P. Savitsky, Ph.D., D.Sc.
Institute A. N. Bach Institute of Biochemistry
University of Florida Russian Academy of Science
Gainesville, Florida Moscow, Russia
Bethel V. Sharma, B.S. Alan H. Terry, M.S.
Department of Chemistry Department of Pharmaceutics and
University of Kentucky Pharmaceutical Chemistry
Lexington, Kentucky University of Utah
Salt Lake City, Utah
Suresh S. Shrestha, Ph.D.
Department of Chemistry Richard B. Thompson, Ph.D.
University of Kentucky Department of Biochemistry and
Lexington, Kentucky Molecular Biology
University of Maryland School
of Medicine
Eric M. Simon, M.E. Baltimore, Maryland
Dexterity Design, Inc.
Salt Lake City, Utah Samuel E. Tolley, Ph.D.
Department of Bioengineering
University of Utah
Richard S. Smith, Ph.D. Salt Lake City, Utah
Department of Bioengineering
University of Utah Leah Tolosa, Ph.D.
Salt Lake City, Utah Department of Chemical and
Biochemical Engineering
University of Maryland Baltimore
Andrea V. Stoddard, B.S. County
Department of Chemistry Catonsville, Maryland
University of Michigan
Ann Arbor, Michigan
Tuan Vo-Dinh, Ph.D.
Center for Advanced Biomedical
Chris R. Taitt, Ph.D. Photonics
Center for Bio/Molecular Science Oak Ridge National Laboratory
and Engineering Oak Ridge, Tennessee
U. S. Naval Research Laboratory
Washington, D.C. Hsu-Kun Wang, M.S.
Department of Pharmaceutics and
Weihong Tan, Ph.D. Pharmaceutical Chemistry
Department of Chemistry and UF Brain University of Utah
Institute Salt Lake City, Utah
University of Florida
Gainesville, Florida Nissa K. Westerberg, Ph.D.
Department of Biochemistry and
Molecular Biology
Lyndon Tan, B.S. University of Maryland School
Lumenal Technologies, L.P. of Medicine
Salt Lake City, Utah Baltimore, Maryland
Paul Yager, Ph.D. Litao Yang, M.S.
Department of Bioengineering Department of Chemistry and Institute
University of Washington for Cellular and Molecular Biology
Seattle, Washington University of Texas at Austin
Austin, Texas
Gang Yao, Ph.D.
Department of Chemistry
and UF Brain Institute
University of Florida
Gainesville, Florida
Contents
Chapter 1
Introduction................................................................................................................1
T. Vo-Dinh, Ph.D.
Chapter 2
Prospects for the De Novo Design of Nucleic Acid Biosensors ..............................5
Litao Yang, M.S., and Andrew D. Ellington, Ph.D.
Chapter 3
Biosensors Based on Periplasmic Binding Proteins ...............................................45
Bethel V. Sharma, B.S., Suresh S. Shrestha, Ph.D.,
Sapna K. Deo, Ph.D., and Sylvia Daunert, Ph.D.
Chapter 4
Molecular Beacon DNA Probes Based on Fluorescence Biosensing ....................67
Gang Yao, Ph.D., M. Shelly John, Ph.D., and Weihong Tan, Ph.D.
Chapter 5
Fluorescence Resonance Energy Transfer-Based Sensors for Bioanalysis ............93
Gabriela Blagoi, B.S., Nitsa Rosenzweig, Ph.D., and Zeev Rosenzweig, Ph.D.
Chapter 6
Carbonic Anhydrase-Based Biosensing of Metal Ions: Issues
and Future Prospects .............................................................................................107
Richard B. Thompson, Ph.D., Rebecca A. Bozym, B.S.,
Michele L. Cramer, M.S., Andrea V. Stoddard, B.S.,
Nissa K. Westerberg, Ph.D., and Carol A. Fierke, Ph.D.
Chapter 7
Metal-Enhanced Fluorescence Sensing.................................................................121
Chris D. Geddes, Ph.D., Kadir Aslan, Ph.D., Ignacy Gryczynski, Ph.D.,
and Joseph R. Lakowicz, Ph.D.
Chapter 8
Subpicomolar Assays of Antibodies and DNA
Using Phosphorescence Labels .............................................................................183
A.P. Savitsky, Ph.D., D.Sc.
Chapter 9
Development of Fluorescent Dipyrrolylquinoxaline-Based Anion Sensors.........219
Pavel Anzenbacher, Jr., Ph.D. and Karolina Jursíková, M.S.
Chapter 10
Lab-on-a-Chip and Fluorescence Sensing on the Microscale ..............................233
Hugh N. Chang, M.S.E., Anson V. Hatch, Ph.D.,
Kenneth R. Hawkins, B.S., and Paul Yager, Ph.D.
Chapter 11
The Array Biosensors ............................................................................................263
Frances S. Ligler, D.Phil., D.Sc., and Chris R. Taitt, Ph.D.
Chapter 12
Planar Waveguide Biosensors for Point-of-Care Clinical
and Molecular Diagnostics ....................................................................................283
James N. Herron, Ph.D., Hsu-Kun Wang, M.S., Lyndon Tan,
B.S., Stacy Z. Brown, B.S., Alan H. Terry, M.S., Samuel E. Tolley, Ph.D., Jacob D.
Durtschi, B.S., Eric M. Simon, M.E., Mark E. Astill, M.S., Richard S. Smith, Ph.D.,
and Douglas A. Christensen, Ph.D.
Chapter 13
Fluorescence-Based Sensors for Bioprocess Monitoring .....................................333
Leah Tolosa, Ph.D., Yordan Kostov, Ph.D., and Govind Rao, Ph.D.
Chapter 14
Practical Aspects of Fluorescence Analysis of Free Zinc
Ion in Biological Systems: pZn for the Biologist.................................................351
Richard B. Thompson, Ph.D., Christopher J. Frederickson, Ph.D.,
Carol A. Fierke, Ph.D., Nissa M. Westerberg, Ph.D.,
Rebecca A. Bozym, B.S., Michele L. Cramer, M.S.,
and Michal Hershfinkel, Ph.D.
Index......................................................................................................................377
Dedication
To my parents,
Charles and Alice Thompson,
for their unwavering support
