BioMEMS Science and Engineering Perspectives

Transcription

1 BioMEMS Science and Engineering Perspectives Simona Badilescu Muthukumaran Packirisamy 4P \ CRC Press Taylor & Francis Group Boca Raton London New York CRC Press is an imprint of the Taylor St Francis Group, an inform a business

2 Preface The Authors xv xvii Chapter 1 Introduction Introduction to BioMEMS Application Areas Intersection of Science and Engineering Evolution of Systems Based on Size Commercialization, Potential, and Market 4 References 8 Chapter 2 Substrate Materials Used in BioMEMS Devices Introduction Metals Glasses and Ceramics Silicon and Silicon-Based Surfaces Polymers Biopolymers Organic Molecules (Functional Groups) Involved in the Formation of Self-Assembled Monolayers 20 References 22 Review Questions 23 Chapter 3 Biomolecules and Complex Biological Entities: Structure and Properties Amino Acids Polypeptides and Proteins Lipids Fatty Acids and Their Esters Phospholipids Lipoproteins Nucleotides and Nucleic Acids Nucleotides Nucleic Acids DNA Sensing Strategies Carbohydrates Introduction Monosaccharides Oligosaccharides and Polysaccharides Biosensing Applications Enzymes Definition and Nomenclature Mechanism of the Enzymatic Catalysis Catalysis by RNA 53 vii

3 viii Applications of Enzymes in Biotechnology and Biosensing Cells Cellular Organization Cell Movement Whole Cell Biosensors: Applications Bacteria and Viruses Bacterial Cell Structure Virus Structure Biosensors and BioMEMS Sensor Systems for the Detection of Pathogenic Microorganisms and Bacterial Toxins 64 References 65 Review Questions 66 Chapter 4 Engineering of Bioactive Surfaces Introduction Plasma Treatment and Plasma-Mediated Surface Modification Surface Modifications Mediated by Self-Assembled Monolayers (SAMs) Langmuir-Blodgett and Layer-by-Layer Assembly Biosmart Hydrogcls Immobilization and Detection of Biomolecules by Using Gold Nanoparticles: Case Studies Gold Nanoparticles Functionalized by Dextran Gold Nanoparticles in Hybridization Experiments Enhanced Biomolecular Binding Sensitivity by Using Gold Nanoislands and Nanoparticles Study of Antigen-Antibody Interactions by Gold Nanoparticle Localized Surface Plasmon Resonance Spectroscopy Array of Gold Nanoparticles for Binding of Single Biomolecules Biomimetic Surface Engineering Attachment of Proteins to Surfaces Surface Modification of Biomaterials for Tissue Engineering Applications Temperature-Responsive Intelligent Interfaces 93 References 93 Review Questions 94 Chapter 5 Methods of Study and Characterization of Surface-Modified Substrates Contact Angle Introduction to Contact Angle and Surface Science Principles Contact Angle Measurement Evaluation of Hydrophobicity of the Modified Surfaces by Contact Angle Measurements: Case Studies Sensitivity of Contact Angle to Surface Treatment Contact Angle Measurements of Surfaces Functionalized with Polyethyleneglycol (PEG) Study of Surface Wettability of Polypyrrole for Microfluidics Applications Wetting Properties of an Open-Channel Microfluidic System Contact Angle Analysis of the Interfacial Tension 101

4 5.2 Atomic Force Microscopy (AFM) Basic Concepts of AFM and Instrumentation AFM Imaging of Biological Sample Surfaces Ex Situ and In Situ AFM Characterization of Phospholipid Layers Formed by Solution Spreading (Casting) on a Mica Substrate Study of Bacterial Surfaces in Aqueous Solution AFM Study of Native Polysomes of Saccharomyces in a Physiological Buffer Solution Single DNA Molecule Stretching Experiments by Using Chemical Force Microscopy AFM Measurements of Competitive Binding Interactions between an Enzyme and Two Ligands Study of Antigen-Antibody Interactions by Molecular Recognition Force Microscopy (MRFM) Study of Cancer Alterations of Single Living Cells by AFM X-Ray Photoelectron Spectroscopy Introduction X-Ray Photoelectron Spectroscopy of Biologically Important Materials Peptide Nucleic Acids on Gold Surfaces as DNA Affinity Biosensors Application of XPS to Probing Enzyme-Polymer Interactions at Biosensor Interfaces Detection of Adsorbed Protein Films at Interfaces Confocal Fluorescence Microscopy Introduction Biological Confocal Microscopy: Case Studies Bioconjugated Carbon Nanotubes for Biosensor Applications Attenuated Total Reflection (Internal Reflection) Infrared Spectroscopy Introduction: ATR-FTIR Basics Applications of ATR-FTIR Spectroscopy to Biomolecules and Biomedical Samples: Case Studies Hydration Studies of Surface Adsorbed Layers of Adenosine-5'-Phosphoric Acid and Cytidine-5'- Phosphoric Acid by Freeze-Drying ATR-FTIR Spectroscopy Study of the Interaction of Local Anesthetics with Phospholipid Model Membranes Assessment of Synthetic and Biologic Membrane Permeability by Using ATR-FTIR Spectroscopy ATR Measurement of the Physiological Concentration of Glucose in Blood by Using a Laser Source Application of ATR-FTIR Spectroscopic Imaging in Pharmaceutical Research Mechanical Methods: Use of Micro- and Nanocantilevers for Characterization of Surfaces 121 References 122 Review Questions 123

5 x Chapter 6 Biosensing Fundamentals Biosensors Introduction Classification: Case Studies Enzyme-Based Biosensors Nucleic-Acid-Based Biosensors Antibody-Based Biosensors Microbial Biosensors Immunoassays Introduction Enzyme-Linked Immunosorbent Assay (ELISA) Microfluidic Immunoassay Devices A Compact-Disk-Like Microfluidic Platform for Enzyme-Linked Immunosorbent Assay Portable Low-Cost Immunoassay for Resource-Poor Settings Comparison between Biosensors and ELISA Immunoassays 151 References 153 Review Questions 155 Chapter 7 Fabrication of BioMEMS Devices Basic Microfabrication Processes Introduction Thin-Film Deposition Photolithography Etching Substrate Bonding Micromachining Bulk Micromachining Surface Micromachining High-Aspect-Ratio Micromachining (LIGA Process) Soft Micromachining Introduction Molding and Hot Embossing Micro Contact Printing (ucp) Micro Transfer Molding (utm) Micromolding in Capillaries Microfabrication Techniques for Biodegradable Polymers Nanofabrication Methods Laser Processing, Ablation, and Deposition High-Precision Milling Inductively Coupled Plasma (ICP) Reactive Ion Etching Electron Beam Lithography Dip Pen Nanolithography Nanosphere Lithography (Colloid Lithography) Surface Patterning by Microlenses Electrochemical Patterning Electric-Field-Assisted Nanopatterning Large-Area Nanoscale Patterning 190

6 xi Selective Molecular Assembly Patterning (SMAP) Site-Selective Assemblies of Gold Nanoparticles on an AFM Tip-Defined Silicon Template Highly Ordered Metal Oxide Nanopatterns Prepared by Template-Assisted Chemical Solution Deposition Wetting-Driven Self-Assembly: A New Approach to Template- Guided Fabrication of Metal Nanopatterns Patterned Gold Films via Site-Selective Deposition of Nanoparticles onto Polymer-Templated Surfaces Nanopatterning by PDMS Relief Structures of Polymer Colloidal Crystals 197 References 199 Review Questions 200 Introduction to Microfluidics Introduction Fluid Physics at the Microscale Methods for Enhancing Diffusive Mixing between Two Laminar Flows Controlling Flow and Transport in Microfluidic Channels Physical Processes Underlying Electrokinetics in Electroosmosis Systems Droplet Actuation Based on Marangoni Flows Electrowetting Thermocapillary Pumping Surface Electrodeposition Modeling MicroChannel Flow Introduction The Finite Element Method Simulation of Flow in Microfluidic Channels: Case Studies Case 1: Silicon Microfluidic Platform for Fluorescence-Based Biosensing Case 2: Numerical Simulation of Electroosmotic Flow in Hydrophobic Microchannels: Influence of Electrode's Position Case 3: Prediction of Intermittent Flow Microreactor System Case 4: Modeling of Electrowetting Flow Experimental Methods Flow Visualization at Microscale Fluorescent Imaging Method Particle Streak Velocimetry Particle Tracking Velocimetry Micro Particle Imaging Velocimetry (upiv) Micro-Laser-Induced Fluorescence (ulif) Method for Shape Measurements Caged and Bleached Fluorescence 241 References 241 Review Questions 243

7 xii Chapter 9 BioMEMS 245 Chapter Life Science Applications Introduction to Microarrays Microarrays Based on DNA Introduction to DNA Chips Principles of DNA Microarray: The Design, Manufacturing, and Data Handling Applications of DNA Microarrays Polymerase Chain Reaction (PCR) Introduction PCR Process On-Chip Single-Copy Real-Time Reverse Transcription PCR in Isolated Picoliter Droplets: A Case Study Protein Microarrays Introduction Fabrication of Protein Microarrays Applications of Protein Arrays Cell and Tissue-Based Assays on a Chip Microreactors Introduction MicroChannel Enzyme Reactors Enzymatic Conversions: Case Studies Glycosidase-Promoted Hydrolysis in Microchannels Lactose Hydrolysis by Hyperthermophilic ß-Glycoside Hydrolase with Immobilized Enzyme Photopatterning Enzymes inside Microfluidic Channels Integrated Microfabricated Device for an Automated Enzymatic Assay Silicon Microstructured Enzyme Reactor with Porous Silicon as the Carrier Matrix Enzymatic Reactions Using Droplet-Based Microfluidics Synthesis of Nanoparticles and Biomaterials in Microfluidic Devices Microfluidic Devices for Separation Separation of Blood Cells Cell or Particle Sorting Micro Total Analysis Systems (ptas) and Lab-on-a-Chip (LOC) Lab-on-a-Chip: Conclusion and Outlook Microcantilever BioMEMS Introduction Basic Principles of Sensing Biomechanical Interactions Detection Modes of Biomechanical Interactions Static Mode Dynamic Mode Location of Interaction in the Case of Mass-Dominant BioMEMS Devices Location of Interaction for Stress-Dominant BioMEMS Devices Fabrication and Functionalization of Microcantilevers 307

8 xiii Case l: Detection of Interaction between ssdna and the Thiol Group Using Cantilevers in the Static Mode Case 2: Specific Detection of Enzymatic Interactions in the Static Mode Case 3: Detection of Enzymatic Interactions in the Dynamic Mode 311 References 312 Review Questions 315 Index 317