Indicator Displacement Assays (IDAs): An Innovative Molecular Sensing Approach E-Book

Ishfaq Ahmad Rather

• Herausgeber: Bentham Science Publishers
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 272

Veröffentlichungsjahr: 2024

Beschreibung

This book explores a revolutionary sensing technique called Indicator Displacement Assays (IDAs). It is designed to provide readers with a comprehensive understanding of the conceptual foundation and wide-ranging applications of IDAs. The book aims to fulfill a crucial gap in the existing references on the subject.
The content starts by explaining fundamental concepts, design strategies, and the scope of IDAs. Subsequent chapters elaborate on the intricate molecular recognition of various analytes, offering insights into sensing mechanisms for cationic, anionic, and neutral molecules. The design and construction of colorimetric, fluorescence, and metal complexing IDAs are also thoroughly explored in later chapters, followed by recent extensions of IDAs, including enantioselective indicator displacement assays, intramolecular indicator displacement assays, reaction-based indicator displacement assays, and more. Innovative applications of IDAs, such as sensory arrays and electrochemical sensors, are also discussed in detail, providing a comprehensive understanding of their conceptual foundations and practical implementations.
The book is a primer on IDAs for researchers who want to understand the fundamentals of the technique, as well as postgraduate students aiming to specialize in supramolecular and analytical chemistry.

Leseprobe

Table of Contents

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FOREWORD

PREFACE

LIST OF ABBREVIATIONS

List of Abbreviations

Background and Basic Concepts of Indicator Displacement Assays

Abstract

1. INTRODUCTION

2. Commonly used Synthetic Receptors and Indicators for the Design of IDAs

3. Various Physical and Chemical Phenomena Involved in Chemical Sensing

3.1. Photoinduced Electron Transfer (PET)

3.2. Fluorescence Resonance Energy Transfer (FRET)

3.3. Charge-Transfer (CT)

3.4. Excited-State Intramolecular Proton Transfer (ESIPT)

3.5. Photon Upconversion (UC)

3.6. Aggregation-Induced Emission (AIE)

4. Classification of Chemical Sensors

4.1. Electrical and Electrochemical Sensors

4.2. Thermometric Sensors

4.3. Optical Sensors

5. Usefulness and Applications of Indicator Displace- ment Assays

6. IDA-Based Thermodynamic Equilibrium

7. Role of Intermolecular Interactions in Designing IDAs

7.1. Hydrogen Bonding (H-bonding)

7.2. Halogen Bonding

7.3. Cation-π and Anion-π Interactions

7.4. CH-π and π –π Stacking Interactions

7.5. Van Der Waals Interactions

8. Design Strategies of IDAs

9. Supramolecular Tandem Assays

10. Advantages and Disadvantages of IDA-Based Sensors

Conclusion

ACKNOWLEDGEMENTS

REFERENCES

Colorimetric Indicator Displacement Assays (C-IDAs)

Abstract

1. Introduction

2. Chromogenic Sensing Ensemble

2.1. Thermodynamic Equilibrium

2.2. Molecular Design Setup and Environmental Factors

2.3. Signal Transduction Mechanism

3. Classification of Sensing Ensembles

3.1. Two-Component Sensing Ensembles

3.2. Three-Component Sensing Ensembles

3.3. Multicomponent Sensing Ensembles

3.4. Inorganic-Organic Hybrid Sensing Ensembles

4. C-IDA Based Anion Sensors

4.1. Phosphate Anion Sensors

5. C-IDA Based Cation Sensors

6. C-IDA Based Saccharide Sensors

Conclusion

ACKNOWLEDGEMENTS

REFERENCES

Fluorescence Indicator Displacement Assays (F-IDAs)

Abstract

1. INTRODUCTION

2. F-IDA Based Anion Sensors

2.1. Phosphate Anion F-IDA Sensors

2.2. Sensors for Fluoride, Bicarbonate and Citrate Ions

3. Sensors for Saccharides

4. Sensors for Biomarkers

5. Sensors for Pharmacological Drugs

6. Sensors for Neurotransmitters

7. Sensors for Explosives and Toxic Substances

8. Sensors for Peptides and Metabolic Waste Products

CONCLUSION

ACKNOWLEDGEMENTS

REFERENCES

Metal Complexing Indicator Displacement Assays (M-IDAs)

Abstract

1. Introduction

2. M-IDA Based Sensors for Phosphate and Other Vital Anions

3. Sensors for the Saccharides, Warfare Agents and Biomarkers

4. Sensors for Amino Acids, Neurotransmitters, Sulfides, and T-DNA

Conclusion

ACKNOWLEDGEMENTS

REFERENCES

Recent Extensions of IDA-based Sensing Protocols

Abstract

1. Introduction

2. Enantioselective Indicator Displacement Assays (e-IDAs)

3. Indicator Catalyst Displacement Assay (ICDA)

4. Intramolecular Indicator Displacement Assays (I-IDAs)

5. Reaction Based Indicator Displacement Assays (R-IDAs)

6. Allosteric Indicator Displacement Assay (A-IDA)

7. Mechanically Controlled Indicator Displacement Assays (MC-IDAs)

8. Dimer Dye Assembly Assay (DDA)

9. Quencher Displacement Assay (QDA)

10. Catalytic Chemosensing Assay (CCA)

Conclusion and Outlook

ACKNOWLEDGEMENTS

REFERENCES

IDA-based Differential Sensory Arrays and Assays

Abstract

1. Introduction

2. IDA Operated Single Analyte Sensing Verses Differential Sensing

3. Sensory Array Experimental Data Analysis

4. Differential Sensing of ATP and Glycosaminoglycans

5. Differential Sensing of Proteins, Amino Acids and Glycoproteins

6. Differential Sensing of Organophosphates and Other Vital Anions

7. Differential Sensing of Saccharides and Metabolites

8. Differential Sensing of Polyphenols and Ginsenosides

9. IDA-Based Molecularly Imprinted Polymeric Sensory Arrays

Conclusion and Outlook

REFERENCES

Electrochemical Sensors Based on Indicator Displacement Assays

Abstract

1. Introduction

2. Types of Electrochemical Sensors

2.1. Potentiometric Sensors

2.1.1. Ion-Selective Electrodes (ISEs)

2.1.2. Coated Wire Electrodes (CWEs)

2.1.3. Ion Selective Field Effect Transistors (ISFET)

2.2. Amperometric Sensors

2.3. Conductometric Sensors

3. Techniques Used in Electrochemical Sensing

3.1. Voltammetry

3.1.1. Sweep Type Methods

3.1.1a. Cyclic Voltammetry (CV)

3.1.1b. Linear Sweep Voltammetry (LSV)

3.1.1c. Staircase Voltammetry (SCV)

3.1.2. Polarographic Techniques

3.1.2a. Normal Pulse Voltammetry (NPV)

3.1.2b. Reverse Pulse Voltammetry (RPV)

3.1.2c. Differential Pulse Voltammetry (DPV)

3.1.2d. Squarewave Pulse Voltammetry (SPV)

3.2. Amperometry

3.3. Electrochemical Impedance Spectroscopy

4. IDA Based Electrochemical Sensors for Saccharides

5. IDA-Based Electrochemical Sensors for Biomarkers

6. Miscellaneous Examples

Conclusion

ACKNOWLEDGEMENTS

REFERENCES

Indicator Displacement Assays (IDAs): An Innovative Molecular Sensing Approach

Authored by

Ishfaq Ahmad Rather

Organic and Supramolecular Functional Materials Research Laboratory,

Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, Okhla,

New Delhi-110025, India

&

Rashid Ali

Organic and Supramolecular Functional Materials Research Laboratory,

Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, Okhla,

New Delhi-110025, India

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FOREWORD

The introduction of diverse indicators to study the molecular recognition (binding/sensing) in various supramolecular receptors opened up a new gateway to mimic nature-based specific and selective host-guest interactions. Taking a step forward from the indicator spacer receptor (ISR) approach involving covalent linkages between receptors and indicators via a spacer, the indicator displacement assay (IDA) offers an innovative and powerful sensing approach for various target analytes in the arena of host-guest chemistry. The intense research in the arena of supramolecular analytical chemistry has led to the development of numerous IDA-based sensors for real-world applications.

The authors have chosen the interesting theme of “Indicator Displacement Assays (IDAs): An Innovative Molecular Sensing Approach” and presented a collection of significant topics covering the design, development, and applications of various types of IDAs and sensory arrays operating through IDA. The corresponding author Dr. Rashid Ali and co-author Ishfaq Ahmad Rather have ample experience in the domain of supramolecular chemistry and have published high-impact research articles in reputed journals. Both authors put their efforts to update the knowledge gained in the field of supramolecular chemistry in general and IDA-based systems in particular. The authors have made an effort to cover a wide range of IDA-based sensors developed from diverse supramolecular receptors like pillarenes, calixarenes, calix[4]pyrroles, cucurbit[n]urils, cyclodextrins, tripodals, boronic acid derivatives, etc. This authored book is a single source of literature collection on the selected topic. In the future plan of action to design, synthesize, and apply IDA-based sensors for real applications, this book will surely help the scientists worldwide already working and also those who want to enter into this emerging arena.

Siddharth Pandey Indian Institute of Technology Hauz Khas, New Delhi - 110016 India

PREFACE

Among diverse sensing assays, the indicator displacement assay (IDA)-based competitive experiments employing various indicators are most acknowledged in supramolecular analytical chemistry. IDA experiments have shown a promising role in exploring the interactions between biological hosts (e.g., proteins, nucleic acids, etc.) and various small molecules of interest, which are otherwise difficult to achieve through other sensing methodologies. This particular competitive technique has great potential to accomplish a rapid analysis of desired analytes because of being easily adaptable for different receptors.

In the first chapter of the book “Indicator Displacement Assays (IDAs): An Innovative Molecular Sensing Approach”, we have assembled the background, conceptual details, design, and construction strategies, in addition to the need and urgency to replace indicator spacer receptor (ISR) approach with IDA having numerous advantages. The second, third, and fourth chapter, besides dealing with the molecular recognition of various analytes (cationic, anionic, and neutral), also deal with the design and construction of colorimetric, fluorescence, and metal complexing IDAs, respectively. The fifth chapter deals with various aspects of recent extensions of IDAs like enantioselective indicator displacement assays (e-IDAs), intramolecular indicator displacement assays (I-IDAs), reaction-based indicator displacement assays (R-IDAs), mechanically controlled indicator displacement assays (MC-IDAs), allosteric indicator displacement assays (A-IDAs), dimer dye assembly assay (DDA), and quencher displacement assay (QDA). The sixth chapter discusses conceptual details and various applications of IDA-based sensory arrays. The last chapter of this book deals with the design, fabrication, and applications of IDA-based electrochemical sensors.

This book strives to collectively present the design, construction, and molecular recognition characteristics of IDA-based sensors along with recent advancements, which in turn will provide newer insights to readers as well as young researchers who are willing to work in the field of sensory materials.

Ishfaq Ahmad Rather Organic and Supramolecular Functional Materials Research Laboratory Department of Chemistry Jamia Millia Islamia, Jamia Nagar, Okhla, New Delhi-110025, India &Rashid Ali Organic and Supramolecular Functional Materials Research Laboratory Department of Chemistry

LIST OF ABBREVIATIONS

Rashid Ali1,*,Ishfaq Ahmad Rather1

1 Organic and Supramolecular Functional Materials Research Laboratory, Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, Okhla, New Delhi-110025, India

*Corresponding author Ishfaq Ahmad Rather: Organic and Supramolecular Functional Materials Research Laboratory, Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, Okhla, New Delhi-110025, India;

List of Abbreviations

AIEAggregation-Induced EmissionAchAcetylcholineARSAlizarin Red SA-IDAAmperometric Indicator Displacement AssayAMPAdenosine MonophosphateABAMN-(4-(aminomethyl)benzyl)-1-(anthracen-9-yl)methanamineAMAAmantadineA-IDAAllosteric Indicator Displacement AssayANNArtificial Neural NetworkBPRBromopyrogallol RedBRBButyl Rhodamine BBODIPYBoron DipyrromethaneBHQBlack Hole QuencherBPHAN,N-bis(pyridin-2-ylmethyl)hexan-1-amineBSABovine Serum AlbuminBINOL1,1′-bi-2-NaphtholC4PsCalix[4]pyrrolesCTCharge TransferC-IDAColorimetric Indicator Displacement AssayCHEFChelation Induced Enhanced FluorescenceCCACatalytic Chemosensing AssayDPVDifferential Pulse VoltammetryDDADimer Dye Assembly AssayETEnergy TransferESIPTExcited-State Intramolecular Proton TransferEETElectron Energy Transfere-IDAEnantioselective Indicator Displacement AssayFRETFluorescence Resonance Energy TransferFETField Effect TransistorsF-IDAFluorescence Indicator Displacement AssayGOGraphene OxideGCEGlassy Carbon ElectrodeGAGGlycosaminoglycanGSHGlutathioneHOMOHighest occupied molecular orbitalHcyhomocysteineHCAHierarchical Cluster AnalysisHiPSHuman Induced Pluripotent StemHTSHigh-Throughput ScreeningISRIndicator Spacer ReceptorIDAIndicator Displacement AssayICTIntramolecular Charge-TransferICDAIndicator Catalyst Displacement AssayI-IDAIntramolecular Indicator Displacement AssayLUMOLowest Unoccupied Molecular OrbitalLELocally ExcitedLOQLimit of QuantificationLODLimit of DetectionLDALinear Discrimination AnalysisMBMethylene BlueMLCTMetal-Ligand Charge TransferM-IDAMetal Indicator Displacement AssayMuMurexideMC-IDAMechanically Controlled Indicator Displacement AssayMRSAMethicillin-Resistant Staphylococcus AureusMIPsMolecularly Imprinted PolymersNIRNear InfraredNAGN-acetyl-β-D-GlucosaminidasePETPhotoinduced Electron TransferPhePhenylalaninePVPyrocatechol VioletPPiInorganic PyrophosphatePAPicric AcidPFOSPerfluorooctane SulfonatePFOAPerfluorooctanoic AcidPAR4-(2-pyridylazo) ResorcinolPCAPrincipal Component AnalysisPLS-DAPartial Least Squares Discriminant AnalysisQzzQuadrupole MomentQDAQuencher Displacement AssayROSReactive Oxygen SpeciesRNSReactive Nitrogen SpeciesRSSReactive Sulphur SpeciesRhBRhodamine BRh-6GRhodamine 6GR-IDAReaction Based Indicator Displacement AssaySASialic AcidSTSafranine TSVMSupport Vector MachineSARS-CoV-2Severe Acute Respiratory Syndrome Coronavirus 2TICTTwisted Intramolecular Charge-TransferTrpTryptophanTyrTyrosineTBAFTetrabutylammonium FluorideThTThioflavin TTEATetraethyl AmmoniumTNT2,4,6-TrinitrotolueneTPETetraphenyletheneUCPhoton UpconversionUDUranine Dyeα||Molecular Polarizibility

Background and Basic Concepts of Indicator Displacement Assays

Ishfaq Ahmad Rather1,*,Rashid Ali1

1 Organic and Supramolecular Functional Materials Research Laboratory, Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, Okhla, New Delhi-110025, India

Abstract

Taking a step forward from the indicator spacer receptor (ISR) method comprising covalent linkages between receptors and indicators via a spacer, the indicator displacement assay (IDA) offers an innovative and powerful sensing approach for various target analytes in the realm of host-guest chemistry. In this chapter, we have assembled the background and conceptual details in order to give essence to the readers about this innovative sensing approach. The photophysical phenomenon and diverse non-covalent interactions involved in the sensing mechanism have been detailed. We have elucidated the need and urgency to replace the ISR approach with IDA, one having numerous advantages. The evolutionary extension of IDA for enzymatic conversion known as supramolecular tandem assays has also been described in this chapter. We believe that the present introductory chapter will give a better understanding to readers who are new to this field.

Keywords: Analyte, Competitive binding, Dynamic, Detection, Enantiomeric excess, Enzyme, Fluorescence quenching, Guest, Host, Indicator displacement assay, Indicators, Macrocycle, Non-covalent interaction, Receptors, Reversible, Recognition, Sensors, Signal, Substrate, Tandem assays.

*Corresponding author Ishfaq Ahmad Rather: Organic and Supramolecular Functional Materials Research Laboratory, Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, Okhla, New Delhi-110025, India;