Introduction to Fluorescence Sensing: Volume 2: Target Recognition and Imaging

772 Pages·2023·26.625 MB·English

by  Alexander P. Demchenko

Alexander P. Demchenko
Introduction
to Fluorescence
Sensing
Volume 2: Target Recognition
and Imaging
Third Edition
Introduction to Fluorescence Sensing
Alexander P. Demchenko
Introduction to Fluorescence
Sensing
Volume 2: Target Recognition and Imaging
Third Edition
Alexander P. Demchenko
National Academy of Sciences of Ukraine
Palladin Institute of Biochemistry
Kyiv, Ukraine
Yuriy Fedkovych National University
Chernivtsi, Ukraine
ISBN 978-3-031-19088-9 ISBN 978-3-031-19089-6 (eBook)
https://doi.org/10.1007/978-3-031-19089-6
1st edition: © Springer Science + Business Media B.V. 2009
2nd edition: © Springer International Publishing Switzerland 2015
3rd edition: © Springer Nature Switzerland AG 2023
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Dedicated to the memory of my wife Tetiana
Ivanchenko
Preface
This book is the second part of third edition on fluorescence sensing that was deeply
revised with many additions and now appeared in two volumes. It was written with
an intension to combine a textbook, a reference book and a critical review of recent
achievements with the vision of future developments. Observing vast literature and
realizing how many researchers, their groups and institutions are involved in this
research and how strong the public request is for the results of their activities provides
a strong motivation for its writing. Indeed, among other sensing and imaging tech-
nologies that develop in parallel, the technologies based on fluorescence are unique.
They are the most sensitive; their sensitivity reached the absolute limit of single
molecules. They offer very high spatial resolution, so that with overcoming the light
diffraction limit has reached a molecular scale. They are also the fastest; their response
develops on the scale of fluorescence lifetime and can be as short as 10−8–10−10 s.
But their greatest advantage is versatility. Fluorescence sensing can be provided in
solid, liquid and gas media and at all kinds of interfaces between these phases. It
is because the fluorescence reporter and the detecting instrument are connected via
light emission, fluorescence detection can be made non-invasive and equally well
suited for remote industrial control and for sensing different targets within the living
cells. All these features explain the high popularity of fluorescence sensing, many
aspects are explored now and many remain for the future.
The field of chemical and biological sensing is immense. It is nearly the whole
world of natural and synthetic compounds that have to be analyzed in a broad variety
of conditions and for a broad variety of purposes. In the human body, we need to
detect and quantify virtually all the genes (genomics) and the products of these
genes (proteomics). We need to know how they interact performing their functions
(interactomics). In our surrounding, there is a need to analyze a huge number of
compounds including millions of newly synthesized products. Among them, we
have to select potentially useful compounds (e.g. drugs) and discriminate those that
are inefficient and harmful. No less important is to control agricultural production
and food processing. There is also a practical necessity to provide control in industrial
product technologies, especially in those that produce pollution. Permanent moni-
toring is needed to maintain safety of our environment. Protection from harmful
vii
viii Preface
microbes, clinical diagnostics and control of patient treatment are the key issues of
modern medicine. New problems and challenges appear with the advancement of
human society in the twenty-first century. We have to be ready to meet them.
Fluorescence sensing technology is the field of research and development in which
basic science and technical developments successfully meet. Enrichment of each
other and revealing of unexplored areas is an indicator of its rapid growth. Many
directions in the present accomplishments and future efforts are overviewed in this
book. After the publication of its previous editions, tremendous progress is observed
in all fields of research, development and application related to its subject. In order
to follow this progress, in the new third edition a number of changes and additions
have been made. The present edition is separated into two volumes, V.1 “Materials
and Devices” and V.2 “Target Recognition and Imaging”. In V.1, the reader may
find critical analysis of methodology in fluorescence sensing and of fluorescence
and related methods that can be applied. The properties of different types of fluo-
rescent materials that are molecules and nanoparticles, organic, inorganic or their
mixed compositions are analyzed. The present Volume 2 is focused on the practical
realization of molecular recognition that is in the background of sensor-target inter-
actions. Different objects of the inorganic and organic world can be used as targets.
Of particular interest is the detection of ions, analysis of biological macromolecules,
and sensing within living cells and tissues.
The fascinating field of fluorescence sensing needs fresh brains. Therefore, the
book is primarily addressed to students and young scientists. Together with basic
knowledge, they will get an overview of different ideas in research and technology
and guide to their own creative activity. Providing a link between basic sciences
needed to understand the sensor performance and frontier of research, where new
ideas are explored and new products developed, the book will make a strong link
between research and education. For the active researcher, it will also be a source
of useful information in nearly all areas where fluorescence sensing and imaging is
used. Accordingly, this book aims at helping scientists in finding the most appropriate
and up-to-date methods to study their molecular recognition systems and to develop
highly needed devices. Thus, this book is organized with the aim to satisfy both
curious students and busy researchers.
This book looks like light reading but it is not. The chapters are selected and
organized in such a way as to provide a valuable reference and a transparent learning
tool. The list of references in each chapter is an additional resource of information,
and the high-quality figures increase clarity and reading pleasure. At the end of
every chapter, the reader may find the section “Sensing and Thinking”, in which the
most actual and often unresolved issues are raised for the discussion. The series of
questions that follows is formulated with the aim to help the reader to check their
acquired knowledge.
Preface ix
This book could not be written without the involvement of my colleagues, friends
and students. My special thanks to Sergiy Bobrovnik, Vasyl Pivovarenko, Mykhailo
Dvoynenko, Kyrylo Pyrshev, Benoit Michel, Dmytro Dziuba, Sergiy Avilov, Semen
Yesylevskyy and Volodymyr Nazarenko.
Enjoy your reading.
Kyiv, Ukraine Alexander P. Demchenko
December 2021
Contents
1 Principles Governing Molecular Recognition .................... 1
1.1 Multivalency: The Principle of Molecular Recognition ......... 3
1.1.1 Multivalent Pattern of Molecular Interactions ......... 4
1.1.2 Energetics and Kinetics in Molecular Recognition ..... 6
1.1.3 Reversibility in Molecular Interactions and Mass
Action Law ...................................... 10
1.2 Lock-And-Key, Induced Fit, Conformation Selection
and Induced-Assisted Folding Models ....................... 12
1.3 Realization of Principles of Molecular Recognition
in Fluorescence Sensing ................................... 16
1.3.1 The Output Parameters Used in Fluorescence
Sensors .......................................... 16
1.3.2 Different Strategies in Fluorescence Sensing .......... 17
1.4 Molecular Recognition of Different Strength and Specificity .... 20
1.4.1 Sensors Providing Strong Highly Specific Binding ..... 20
1.4.2 Sensors Based on Competitive Target Binding ........ 21
1.4.3 Sensors Based on Reversible Specific Binding
and Operating in a Large Volume ................... 22
1.5 Direct Reagent-Independent Sensing ........................ 22
1.6 Simultaneous Analysis of Multiple Analytes ................. 26
1.6.1 Systems for Detection of Multiple Analytes .......... 27
1.6.2 Specific Target Recognition Versus Pattern
Recognition Sensor Arrays ......................... 28
1.7 Sensing and Thinking. Current Trends that Should Be
Highlighted ............................................. 30
References .................................................... 32
2 Basic Theoretical Description of Sensor-Target Binding ........... 37
2.1 Parameters that Need to Be Optimized in Every Sensor ........ 38
2.1.1 The Limit of Detection and Sensitivity ............... 40
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xii Contents
2.1.2 Dynamic Range of Detectable Target
Concentrations ................................... 41
2.1.3 The Sensor Selectivity ............................. 44
2.1.4 Multivalent Binding and Cooperativity ............... 46
2.2 Determination of Binding Constants ........................ 47
2.2.1 Dynamic Association-Dissociation Equilibrium ....... 47
2.2.2 Determination of K by Titration .................... 49
b
2.2.3 Determination of K by Serial Dilutions .............. 51
b
2.3 Modeling the Analyte Binding Isotherms .................... 52
2.3.1 Receptors Free in Solution or Immobilized
to a Surface ...................................... 53
2.3.2 Bivalent and Polyvalent Reversible Target Binding .... 53
2.3.3 Reversible Binding of Analyte and Competitor ........ 55
2.3.4 Reversible Interactions in a Small Volume ............ 57
2.4 Kinetics of Target Binding ................................. 59
2.5 Formats for Fluorescence Detection ......................... 61
2.5.1 Linear Response Format ........................... 61
2.5.2 Intensity-Weighted Format ......................... 64
2.6 Sensing and Thinking. How to Provide the Optimal
Quantitative Measure of Target Binding? .................... 66
References .................................................... 69
3 Recognition Units Built of Small Macrocyclic Molecules .......... 73
3.1 Crown Ethers and Cryptands: Macrocyclic Hosts for Ions ...... 74
3.2 Cavity-Forming Compounds. Structures and Properties ........ 77
3.2.1 Cyclodextrins .................................... 77
3.2.2 Calix[n]arenes .................................... 81
3.2.3 Cucurbit[n]urils .................................. 85
3.2.4 Pillar[n]arenes .................................... 86
3.2.5 Comparison of Properties and Prospects
of Supramolecular Macrocycles ..................... 87
3.3 Porphyrins and Porphyrinoids. Unique Coupling
of Recognition and Reporting .............................. 90
3.4 Sensing and Thinking. The Recognition Properties
of Parent Binders and of Their Derivatives ................... 96
References .................................................... 97
4 Sensors Based on Peptides and Proteins as Recognition Units ...... 103
4.1 Designed and Randomly Synthesized Peptides ................ 104
4.1.1 The Development of Peptide Sensors ................ 105
4.1.2 Randomly Synthesized Peptides, Why They Do
Not Fold? ........................................ 106
4.1.3 Template-Based Approach ......................... 106
4.1.4 The Exploration of ‘Mini-Protein’ Concept ........... 107
4.1.5 Molecular Display Including Phage Display .......... 109