Nanobioelectronics : for electronics, biology, and medicine

Chapter 1. DNA-Mediated Assembly of Metal Nanoparticles: Fabrication, Structural Features, and Electrical Properties .......................... 11 Monika Fischler, Melanie Homberger, and Ulrich Simon 1. Introduction ..................................................................................................... 11 2. Materials Synthesis .......................................................................................... 12 2.1. Liquid Phase Synthesis of Metal Nanoparticles ...................................... 12 2.2. Preparation of DNA-Functionalized Metal Nanoparticles ...................... 15 3. Nanoparticle Assemblies and Properties ......................................................... 18 3.1. Three-Dimensional Assemblies ............................................................... 18 3.2. Two-Dimensional Assemblies ................................................................. 21 3.3. One-Dimensional Assemblies ................................................................. 28 4. Conclusion ....................................................................................................... 37 Chapter 2. DNA-Based Nanoelectronics .................................................................. 43 Rosa Di Felice 1. Introduction ...................................................................................................... 43 1.1. DNA for Molecular Devices .................................................................... 43 1.2. What is Known about DNA’s Ability to Conduct Electrical Currents? ................................................................................. 44 2. Methods, Materials, and Results ...................................................................... 46 2.1. Experimental Investigations ..................................................................... 47 2.2. Theoretical Investigations ........................................................................ 61 3. Summary and Outlook ..................................................................................... 74 v vi CONTENTS Electronics for Genomics ............................................................................................ 81 Chapter 3. DNA Detection with Metallic Nanoparticles ........................................ 83 Robert Möller, Grit Festag, and Wolfgang Fritzsche 1. Introduction ...................................................................................................... 83 2. Nanoparticle-Based Molecular Detection ........................................................ 84 2.1. Nanoparticle Synthesis and Bioconjugation ............................................ 84 2.2. Detection Methods for Nanoparticle-Labeled DNA ................................ 86 3. Conclusion and Outlook .................................................................................. 98 Chapter 4. Label-Free, Fully Electronic Detection of DNA with a Field-Effect Transistor Array ............................................................................ 103 Sven Ingebrandt and Andreas Offenhäusser 1. Introduction ...................................................................................................... 103 2. Materials and Methods .................................................................................... 105 2.1. Field-Effect Transistors and Amplifier Systems for DNA Detection ...... 105 2.2. Immobilization of Probe DNA onto FET Surfaces.................................. 108 2.3. Aligned Microspotting ............................................................................. 111 2.4. DNA Sequences for Hybridization Detection ......................................... 111 3. Results and Discussion .................................................................................... 113 3.1. FET-Based Potentiometric Detection of DNA Hybridization ................. 113 3.2. FET-Based Impedimetric Detection of DNA Hybridization ................... 117 3.3. Underlying Detection Principle ............................................................... 121 4. Conclusion and Outlook .................................................................................. 125 Part B Protein-Based Nanobioelectronics Protein-Based Nanoelectronics .................................................................................. 137 Chapter 5. Nanoelectronic Devices Based on Proteins ........................................... 139 Giuseppe Maruccio and Alessandro Bramanti 1. Proteins in Nanoelectronics ............................................................................. 139 2. Overview and Theory of Charge Transport Mechanisms in Proteins .............. 140 3. Probing and Interconnecting Molecules/Proteins ............................................ 143 4. Experimental Results on Protein Devices ........................................................ 150 5. Reliability of Protein-Based Electronic Devices (Aging of Proteins in Ambient Condition and under High Electric Fields, etc.) ............. 159 6. Outlook: Usefulness of Proteins in Future Robust Molecular Devices, Capability of Reacting to Biological Environment (Biosensors), and Potential Commercial Applications .......................................................... 163 Chapter 6. S-Layer Proteins for Assembling Ordered Nanoparticle Arrays ....... 167 Dietmar Pum and Uwe B. Sleytr 1. Introduction ...................................................................................................... 167 2. Description of S-Layers ................................................................................... 168 3. Methods, Materials, and Results ...................................................................... 169 3.1. Nanoparticle Formation by Self-Assembly on S-Layer Patterned Substrates ................................................................... 169 3.2. Wet Chemical Synthesis of Nanoparticles ............................................... 171 3.3. Binding of Preformed Nanoparticles ....................................................... 174 4. Conclusions ...................................................................................................... 178 Electronics for Proteomics ......................................................................................... 181 Chapter 7. Electrochemical Biosensing of Redox Proteins and Enzymes ............ 183 Qijin Chi, Palle S. Jensen, and Jens Ulstrup 1. Introduction ...................................................................................................... 183 2. Theoretical Considerations .............................................................................. 185 2.1. Electrochemical Electron Transfer .......................................................... 185 2.2. Redox Processes in Electrochemical STM .............................................. 187 3. Experimental Approaches ................................................................................ 190 3.1. Materials and Reagents ............................................................................ 190 3.2. Assembly of Protein Monolayers ............................................................ 192 3.3. Instrumental Methods .............................................................................. 192 4. Experimental Observations and Theoretical Simulations ................................ 193 4.1. Case Observation I: Cytochrome c .......................................................... 193 4.2. Case Observation II: Azurin .................................................................... 195 4.3. Case Observation III: Nitrite Reductase .................................................. 200 4.4. Case Observation IV: Cytochrome c4 ...................................................... 203 5. Conclusions and Outlook ................................................................................. 204 Chapter 8. Ion Channels in Tethered Bilayer Lipid Membranes on Au Electrodes ................................................................................................. 211 Ingo Köper, Inga K. Vockenroth, and Wolfgang Knoll 1. Introduction ...................................................................................................... 211 2. Materials and Methods .................................................................................... 215 2.1. Electrochemical Impedance Spectroscopy .............................................. 215 2.2. Surface Plasmon Resonance Spectroscopy .............................................. 215 3. Protein Incorporation ....................................................................................... 215 3.1. Assembly of the System .......................................................................... 215 3.2. Valinomycin ............................................................................................. 219 3.3. Gramicidin ............................................................................................... 219 3.4. M2δ .......................................................................................................... 220 4. Conclusion ....................................................................................................... 221 Chapter 9. Fluorescent Nanocrystals and Proteins ................................................. 225 Pier Paolo Pompa, Teresa Pellegrino, and Liberato Manna .................................... 225 1. Colloidal Nanocrystals as Versatile Fluorescent Bioprobes ............................ 226 2. Synthesis of Semiconductor Nanocrystals ....................................................... 229 3. Water Solubilization Strategies ........................................................................ 231 4. Protein–QD Hybrid Systems ........................................................................... 238 5. Fluorescence Imaging without Excitation ....................................................... 250 CONTENTS vii Part C Cell-Based Nanobioelectronics Neuron-Based Information Processing ..................................................................... 259 Chapter 10. Spontaneous and Synchronous Firing Activity in Solitary Microcultures of Cortical Neurons on Chemically Patterned Multielectrode Arrays ........................................................................................ 261 T.G. Ruardij, W.L.C. Rutten, G. van Staveren, and B.H. Roelofsen 1. Introduction ...................................................................................................... 261 2. Methods ........................................................................................................... 264 2.1. Cortical Neuron Isolation and Procedures ............................................... 264 2.2. Preparation of PDMS Microstamps ......................................................... 265 2.3. Fabrication of Multielectrode Arrays ...................................................... 265 2.4. Microprinting of Polyethylenimine on Multielectrode Arrays ................ 265 2.5. Morphological Assessment of Neuronal Tissue ...................................... 266 2.6. Bioelectrical Recording ........................................................................... 266 3. Results .............................................................................................................. 267 4. Discussion and Conclusion .............................................................................. 270 Chapter 11. Nanomaterials for Neural Interfaces: Emerging New Function and Potential Applications ........................................................ 277 Allison J. Beattie, Adam S.G. Curtis, Chris D.W. Wilkinson, and Mathis Riehle 1. Introduction ...................................................................................................... 277 2. Nanofabrication ............................................................................................... 279 2.1. Materials .................................................................................................. 280 3. Orientation, Migration, and Extension ............................................................ 281 3.1. Network Patterns ...................................................................................... 282 3.2. Order and Symmetry ................................................................................ 282 3.3. Gene Expression ...................................................................................... 283 4. Electrodes (Extracellular) ................................................................................ 284 5. Summary .......................................................................................................... 284 Chapter 12. Interfacing Neurons and Silicon-Based Devices ................................ 287 Andreas Offenhäusser, Sven Ingebrandt, Michael Pabst, and Günter Wrobel 1. Introduction ...................................................................................................... 287 2. Theoretical Considerations .............................................................................. 289 3. Methods ........................................................................................................... 293 3.1. Field Effect Transistors for Extracellular Recordings ............................. 293 3.2. Characterization of the Cell–Device Interface ......................................... 295 4. Neuron Transistor Hybrid Systems .................................................................. 297 5. Conclusions ...................................................................................................... 299 viii CONTENTS CONTENTS ix Electronics for Cellomics ............................................................................................ 303 Chapter 13. Hybrid Nanoparticles for Cellular Applications ................................ 305 Franco Calabi 1. Introduction ...................................................................................................... 305 2. Properties of Hybrid Nanoparticles for Cellular Applications ........................ 306 2.1. Semiconductor Colloidal Nanocrystals (Quantum Dots) ........................ 306 2.2. Gold Nanoparticles .................................................................................. 308 2.3. Superparamagnetic Nanoparticles ........................................................... 309 3. Nanoparticle–Cell Interactions ........................................................................ 310 3.1. Cell Labeling In Vitro .............................................................................. 310 3.2. In Vivo Targeting ..................................................................................... 315 4. Cell/Animal Biological Applications of Hybrid Nanoparticles ....................... 317 4.1. Dynamics of Cellular Receptors .............................................................. 317 4.2. Sensing/Sensitizing .................................................................................. 319 4.3. Molecular Interactions ............................................................................. 320 4.4. Gene Control ............................................................................................ 320 4.5. In Vivo Imaging ....................................................................................... 320 4.6. Cell Tracking ........................................................................................... 322 4.7. Targeted Therapy ..................................................................................... 324