Quantifying Interactions of Biomolecules with Inorganic Surfaces (eBook)

Abhijeet Patra obtained his bachelors degree in Electrical and Electronics Engineering from the National Institute of Technology, Tiruchchirappalli, one of the premier institutes in India in 2011. Upon receiving the prestigious NGS scholarship to pursue doctoral studies at National University of Singapore, he joined the research group of Prof T Venkatesan, pioneer of pulsed laser deposition and, after an exciting 4 years, graduated with a PhD in 2015. His research interests are in understanding how inorganic assemblies interact with the biological world, with a sharp focus on translating the science into biomedical applications. 

Supervisor’s Foreword 6
Abstract 8
Acknowledgement 10
Contents 13
Abbreviations 16
1 Introduction 18
Abstract 18
References 22
2 Methods 24
Abstract 24
2.1 Pulsed Laser Deposition 24
2.2 Atomic Force Microscopy 26
2.3 Scanning Electron Microscopy 27
2.4 Contact Angle and Surface Energy Measurement 27
2.4.1 Contact Angle and Surface Energy 27
2.4.2 Description of OWRK Method 28
2.5 Surface Plasmon Resonance 30
2.5.1 Surface Plasmons 30
2.5.2 Excitation of Surface Plasmons 32
2.5.3 Optical Sensing with Surface Plasmon Resonance 34
2.5.4 Working Principle of SPR Biosensors 34
2.6 Rutherford Backscattering Spectroscopy 36
2.7 Mass Spectrometry 37
2.7.1 Matrix Assisted Laser Desorption Ionization 38
2.7.2 Electrospray Ionization 39
2.8 Liquid Chromatography 40
2.8.1 Thin Layer Chromatography 40
2.8.2 High Performance Liquid Chromatography 40
2.8.2.1 Normal Phase HPLC 41
2.8.2.2 Reverse Phase HPLC 41
References 41
3 Quantifying Interactions Between Water and Surfaces 43
Abstract 43
3.1 Introduction 43
3.1.1 Overview 43
3.1.2 Literature Review and the Need for a New Technique 44
3.1.3 Motivation and Rationale 44
3.2 Results and Discussion 45
3.2.1 Measurement of Contact Angles on Surfaces and Calculation of Surface Energies 45
3.2.2 Force Spectroscopy on Surfaces with Native Water Layer 48
3.2.3 Correlating Nanoscale Measurements with Macroscale Measurements 50
3.2.4 Breaking of Hydrogen Bonds on the Surface as a Possible Reason for Nanoscale-Macroscale Hydrophilicity Correlation 52
3.3 Conclusion 54
3.4 Experimental Details 54
3.4.1 Sample Fabrication 54
3.4.2 Contact Angle Measurement Setup 55
3.4.3 Atomic Force Microscopy and Force Spectroscopy 55
References 56
4 Quantifying Interactions Between Lipids and Surfaces 57
Abstract 57
4.1 Introduction 57
4.1.1 Metabolomics 58
4.1.2 Lipidomics 59
4.1.3 The Need for Sample Preparation 61
4.1.3.1 Liquid-Liquid Extraction (LLE) 62
4.1.3.2 The Problem with Phospholipids 63
4.1.3.3 Solid Phase Extraction 64
4.1.3.4 Motivation 64
4.2 Results and Discussion 66
4.2.1 Metal Oxide Coated MALDI Plates for Selective Phospholipid Enrichment 66
4.2.2 Phospholipid Enrichment Using µcolumns 67
4.2.3 Phospholipid Enrichment Using Batch Processing 71
4.2.4 Surface Plasmon Resonance for Quantifying Phospholipid Adhesion 73
4.3 Conclusion 78
4.4 Experimental Details 78
4.4.1 Fabrication of Modified MALDI Plates 78
4.4.2 Lipid Adhesion Studies with Modified MALDI Plates 79
4.4.3 Lipid Adhesion Studies with ?column Approach 79
4.4.4 Lipid Adhesion Studies in Batch Processing Approach 80
4.4.5 Surface Plasmon Resonance 81
References 81
5 Quantifying Interactions Between Serum Proteins and Gold Nanoparticles 84
Abstract 84
5.1 Introduction 84
5.1.1 Overview 84
5.1.2 Existing Methods Used to Study Corona Formation and Their Limitations 85
5.1.3 Need for a New Method and Previously Reported Work 86
5.2 Results and Discussion 86
5.2.1 Immobilization of Gold NPs 86
5.2.2 Studying Interactions of AuNPs with Proteins 88
5.2.3 Effect of PEGylation Observed Through SPR 91
5.2.4 Effect of Varying PEG Chain Length on Resistance to Corona 93
5.2.5 Observation of Hybrid Modifications Effect on NP Targeting Design 94
5.3 Conclusion 96
5.4 Experimental Details 97
5.4.1 Synthesis of AuNPs 97
5.4.2 Immobilization of AuNPs onto the Chip Surface 98
5.4.3 Studying Interactions of Serum Components with Immobilized AuNPs 98
5.4.4 Obtaining Kinetic Parameters from Curve Fitting and Calculating Surface Coverage 99
5.4.5 Studying Interactions of Serum Components with PEGylated AuNPs 101
5.4.6 Studying Effect of PEG Chain Length on Corona Formation 102
5.4.7 Studying the Interaction of Serum and Streptavidin with Model Hybrid NP Systems 102
References 103
6 Conclusion 106
Abstract 106
Appendix A: SPR Sensorgrams for Interactions of 3 Serum Proteins with Gold Nanoparticles 109
Appendix B: SPR Sensorgrams for Interactions of PEG with Chemically Active Chip Surface 113
Appendix B: SPR Sensorgrams for Interactions of PEG with Chemically Active Chip Surface 114
Curriculum Vitae 114