| | Contents | |
| | | |
| |
| | Preface | XIII |
| | List of Contributors | XV |
| 1 | Bioelectronics – An Introduction
Itamar Willner and Eugenii Katz | 1 |
| | References | 12 |
| 2 | Electron Transfer Through Proteins
Jay R.Winkler,Harry B. Gray,Tatiana R. Prytkova, IgorV.Kurnikov, and David N. Beratan | 15 |
| 2.1 | Electronic Energy Landscapes | 15 |
| 2.2 | Theory of Electron Tunneling | 15 |
| 2.3 | Tunneling Pathways | 17 |
| 2.4 | Coupling-limited ET Rates and Tests of the Pathway Model | 19 |
| 2.5 | Multiple Tunneling Pathway Models | 23 |
| 2.6 | Interprotein Electron Transfer: Docking and Tunneling | 27 |
| 2.7 | Some New Directions in Electron Transfer Theory and Experiment | 28 |
| 2.8 | Concluding Remarks | 31 |
| | References | 31 |
| 3 | Reconstituted Redox Enzymes on Electrodes:From Fundamental Understanding of Electron Transfer at Functionalized Electrode Interfaces to Biosensor and Biofuel Cell Applications
Bilha Willner and Itamar Willner | 35 |
| 3.1 | Introduction | 35 |
| 3.2 | Electrodes Functionalized with Reconstituted Redox Proteins | 43 |
| 3.2.1 | Reconstituted Flavoenzyme-Electrodes Using Molecular or Polymer Relay Systems | 43 |
| 3.2.2 | Electrical Contacting of Flavoenzymes by Reconstitution on Carbon Nanotubes and Conducting Polymer Wires | 53 |
| 3.2.3 | Electrical Contacting of Flavoenzymes by Means of Metallic Nanoparticles | 57 |
| 3.2.4 | Integrated Electrically Contacted Electrodes Composed of Reconstituted Quinoproteins | 65 |
| 3.2.5 | Reconstituted Electrically Contacted Hemoproteins | 67 |
| 3.2.6 | Reconstituted de novo Hemoproteins on Electrodes | 69 |
| 3.3 | Electrical Contacting of Redox Proteins by Cross-linking of Cofactor-Enzyme Affinity Complexes on Surfaces | 73 |
| 3.3.1 | Integrated NAD(P)+-Dependent Enzyme-Electrodes | 73 |
| 3.3.2 | Integrated Electrically Contacted Hemoprotein Electrodes | 80 |
| 3.4 | Reconstituted Enzyme-Electrodes for Biofuel Cell Design | 83 |
| 3.5 | Conclusions and Perspectives | 91 |
| | References | 93 |
| 4 | Application of Electrically Contacted Enzymes for Biosensors
Frieder W. Scheller, Fred Lisdat, and Ulla Wollenberger | 99 |
| 4.1 | Introduction | 99 |
| 4.2 | Biosensors – Precursors of Bioelectronics | 99 |
| 4.3 | Via Miniaturization to Sensor Arrays – The Biochip | 102 |
| 4.4 | The Route to Electrically Contacted Enzymes in Biosensors | 104 |
| 4.5 | Routine Applications of Enzyme Electrodes | 107 |
| 4.6 | Research Applications of Directly Contacted Proteins | 109 |
| 4.6.1 | Protein Electrodes for the Detection of Oxygen-derived Radicals | 109 |
| 4.6.2 | Cytochrome P 450 – An Enzyme Family Capable of Direct Electrical Communication | 117 |
| 4.7 | Conclusions | 123 |
| | References | 123 |
| 5 | Electrochemical DNA Sensors
Emil Palecek and Miroslav Fojta | 127 |
| 5.1 | Introduction | 127 |
| 5.1.1 | Indicator Electrodes | 128 |
| 5.1.2 | Electrochemical Methods | 128 |
| 5.2 | Natural Electroactivity and Labeling of Nucleic Acids | 129 |
| 5.2.1 | Electroactivity of Nucleic Acid Components | 129 |
| 5.2.2 | Analysis of Unlabeled Nucleic Acids | 131 |
| 5.2.3 | Electroactive Labels of Nucleic Acids | 136 |
| 5.2.4 | Signal Amplification | 140 |
| 5.3 | Sensors for DNA and RNA Hybridization | 140 |
| 5.3.1 | DNA Hybridization | 142 |
| 5.3.2 | Electrochemical Detection in DNA Sensors | 143 |
| 5.3.3 | Single-surface Techniques | 143 |
| 5.3.4 | Double-surface Techniques | 153 |
| 5.3.5 | Concluding Remarks to DNA Hybridization Sensors | 158 |
| 5.4 | Sensors for DNA Damage | 159 |
| 5.4.1 | DNA Damage | 159 |
| 5.4.2 | Relations Between DNA Damage and its Electrochemical Features | 162 |
| 5.4.3 | DNA-modified Electrodes as Sensors for DNA Damage | 167 |
| 5.4.4 | Sensors for DNA Strand Breaks | 168 |
| 5.4.5 | Detection of Covalent Damage to DNA Bases | 170 |
| 5.4.6 | Genotoxic Substances Interacting with DNA Noncovalently | 173 |
| 5.4.7 | Electrochemically Induced DNA Damage | 176 |
| 5.4.8 | Analytical Applications of Electrochemical Sensors for DNA Damage | 177 |
| 5.4.9 | Concluding Remarks to DNA Damage Sensors | 180 |
| | References | 181 |
| 6 | Probing Biomaterials on Surfaces at the Single Molecule Level for Bioelectronics
Barry D. Fleming, Shamus J. O’Reilly, and H. Allen O. Hill | 193 |
| 6.1 | Methods for Achieving Controlled Adsorption of Biomolecules | 194 |
| 6.2 | Methods for Investigating Adsorbed Biomolecules | 195 |
| 6.3 | Surfaces Patterned with Biomolecules | 197 |
| 6.4 | Attempts at Addressing Single Biomolecules | 201 |
| 6.5 | Conclusions | 205 |
| | References | 207 |
| 7 | Interfacing Biological Molecules with Group IV Semiconductors for Bioelectronic Sensing
Robert J. Hamers | 209 |
| 7.1 | Introduction | 209 |
| 7.2 | Semiconductor Substrates for Bioelectronics | 210 |
| 7.2.1 | Silicon | 210 |
| 7.2.2 | Diamond | 211 |
| 7.3 | Chemical Functionalization | 213 |
| 7.3.1 | Covalent Attachment of Biomolecules to Silicon Surfaces | 213 |
| 7.3.2 | Hybridization of DNA at DNA-modified Silicon Surfaces | 215 |
| 7.3.3 | Covalent Attachment and Hybridization of DNA at Diamond Surfaces | 217 |
| 7.4 | Electrical Characterization of DNA-modified Surfaces | 219 |
| 7.4.1 | Silicon | 219 |
| 7.4.2 | Impedance Spectroscopy of DNA-modified Diamond Surfaces | 225 |
| 7.5 | Extension to Antibody–Antigen Detection | 225 |
| 7.6 | Summary | 227 |
| | References | 228 |
| 8 | Biomaterial-nanoparticle Hybrid Systems for Sensing and Electronic Devices
Joseph Wang,Eugenii Katz,and Itamar Willner | 231 |
| 8.1 | Introduction | 231 |
| 8.2 | Biomaterial–nanoparticle Systems for Bioelectrochemical Applications | 232 |
| 8.2.1 | Bioelectrochemical Systems Based on Nanoparticle-enzyme Hybrids | 232 |
| 8.2.2 | Electroanalytical Systems for Sensing of Biorecognition Events Based on Nanoparticles | 235 |
| 8.3 | Application of Redox-functionalized Magnetic Particles for Triggering and Enhancement of Electrocatalytic and Bioelectrocatalytic Processes | 250 |
| 8.4 | Conclusions and Perspectives | 259 |
| | References | 261 |
| 9 | DNA-templated Electronics
Kinneret Keren, Uri Sivan, and Erez Braun | 265 |
| 9.1 | Introduction and Background | 265 |
| 9.2 | DNA-templated Electronics | 266 |
| 9.3 | DNA Metallization | 268 |
| 9.4 | Sequence-specific Molecular Lithography | 271 |
| 9.5 | Self-assembly of a DNA-templated Carbon Nanotube Field-effect Transistor | 276 |
| 9.6 | Summary and Perspective | 279 |
| | References | 284 |
| 10 | Single Biomolecule Manipulation for Bioelectronics
Yoshiharu Ishii and Toshio Yanagida | 287 |
| 10.1 | Single Molecule Manipulation | 287 |
| 10.1.1 | Glass Microneedle | 289 |
| 10.1.2 | Laser Trap | 289 |
| 10.1.3 | Space and Time Resolution of Nanometry | 290 |
| 10.1.4 | Molecular Glues | 291 |
| 10.1.5 | Comparisons of the Microneedle and Laser Trap Methods | 291 |
| 10.2 | Mechanical Properties of Biomolecules | 291 |
| 10.2.1 | Protein Polymers | 291 |
| 10.2.2 | Mechanically Induced Unfolding of Single Protein Molecules | 294 |
| 10.2.3 | Interacting Molecules | 296 |
| 10.3 | Manipulation and Molecular Motors | 297 |
| 10.3.1 | Manipulation of Actin Filaments | 298 |
| 10.3.2 | Manipulation of a Single Myosin Molecule | 300 |
| 10.3.3 | Unitary Steps of Myosin | 300 |
| 10.3.4 | Step Size and Unconventional Myosin | 302 |
| 10.3.5 | Manipulation of Kinesin | 303 |
| 10.4 | Different Types of Molecular Motors | 304 |
| 10.5 | Direct Measurements of the Interaction Forces | 304 |
| 10.5.1 | Electrostatic Force Between Positively Charged Surfaces | 305 |
| 10.5.2 | Surface Force Property of Myosin Filaments | 305 |
| | References | 306 |
| 11 | Molecular Optobioelectronics
Eugenii Katz and Andrew N. Shipway | 309 |
| 11.1 | Introduction | 309 |
| 11.2 | Electronically Transduced Photochemical Switching of Redox-enzyme Biocatalytic Reactions | 310 |
| 11.2.1 | Electronic Transduction of Biocatalytic Reactions Using Redox Enzymes Modified with Photoisomerizable Units | 312 |
| 11.2.2 | Electronic Transduction of Biocatalytic Reactions Using Interactions of Redox Enzymes with Photoisomerizable ‘‘Command Interfaces’’ | 316 |
| 11.2.3 | Electronic Transduction of Biocatalytic Reactions of Redox Enzymes Using Electron Transfer Mediators with Covalently Bound Photoisomerizable Units | 322 |
| 11.3 | Electronically Transduced Reversible Bioaffinity Interactions at Photoisomerizable Interfaces | 323 |
| 11.3.1 | Reversible Immunosensors Based on Photoisomerizable Antigens | 326 |
| 11.3.2 | Biphasic Reversible Switch Based on Bioaffinity Recognition Events Coupled to a Biocatalytic Reaction | 330 |
| 11.4 | Photocurrent Generation as a Transduction Means for Biocatalytic and Biorecognition Processes | 332 |
| 11.4.1 | Enzyme-Biocatalyzed Reactions Coupled to Photoinduced Electron Transfer Processes | 332 |
| 11.4.2 | Biorecognition Events Coupled to Photoinduced Electron Transfer Processes | 334 |
| 11.5 | Conclusions | 335 |
| | References | 336 |
| 12 | The Neuron-semiconductor Interface
Peter Fromherz | 339 |
| 12.1 | Introduction | 339 |
| 12.2 | Ionic–Electronic Interface | 340 |
| 12.2.1 | Planar Core-coat Conductor | 343 |
| 12.2.2 | Cleft of Cell-silicon Junction | 346 |
| 12.2.3 | Conductance of the Cleft | 349 |
| 12.2.4 | Ion Channels in Cell-silicon Junction | 358 |
| 12.3 | Neuron–Silicon Circuits | 362 |
| 12.3.1 | Transistor Recording of Neuronal Activity | 362 |
| 12.3.2 | Capacitive Stimulation of Neuronal Activity | 367 |
| 12.3.3 | Two Neurons on Silicon Chip | 372 |
| 12.3.4 | Toward Defined Neuronal Nets | 377 |
| 12.4 | Brain–Silicon Chips | 383 |
| 12.4.1 | Tissue-sheet Conductor | 383 |
| 12.4.2 | Transistor Recording of Brain Slice | 385 |
| 12.4.3 | Capacitive Stimulation of Brain Slices | 388 |
| 12.5 | Summary and Outlook | 392 |
| | References | 393 |
| 13 | S-Layer Proteins in Bioelectronic Applications
Stefan H. Bossmann | 395 |
| 13.1 | Introduction | 395 |
| 13.1.1 | Upcoming Nanotechnology Applications | 396 |
| 13.2 | S-layer Proteins and Porins | 396 |
| 13.2.1 | The Building Principles of Tailored S-layer Proteins Layers | 397 |
| 13.2.2 | Chemical Modification of S-layers | 400 |
| 13.2.3 | Interaction by Noncovalent Forces | 401 |
| 13.3 | Experimental Methods Developed for Hybrid Bioelectronic Systems | 402 |
| 13.3.1 | Electron Microscopy | 402 |
| 13.3.2 | Combined X-Ray and Neutron Reflectometry | 402 |
| 13.3.3 | Atomic Force Microscopy Using Protein-functionalized AFM-cantilever Tips | 403 |
| 13.3.4 | Scanning Electrochemical Microscopy | 404 |
| 13.4 | Applications of S-layer Proteins at Surfaces | 404 |
| 13.4.1 | S-layer Proteins as Permeability Barriers | 404 |
| 13.4.2 | S-layer Proteins at Lipid Interfaces | 405 |
| 13.4.3 | Introduction of Supramolecular Binding Sites into S-layer Lattices | 412 |
| 13.5 | Molecular Nanotechnology Using S-layers | 414 |
| 13.5.1 | Patterning of S-layer Lattices by Deep Ultraviolet Irradiation (DUV) | 414 |
| 13.5.2 | Synthesis of Semiconductor and Metal Nanoparticles Using S-layer Templates Design of Gold and Platinum Superlattices Using the Crystalline Surfaces Formed by the S-layer Protein of Bacillus sphaericus as a Biotemplate | 416 |
| 13.5.3 | Generation of S-layer Lattice-supported Platinum Nanoclusters | 418 |
| 13.5.4 | Formation and Selective Metallization of Protein Tubes Formed by the S-layer Protein of Bacillus sphaericus NCTC | 9602 |
| 13.5.5 | S-layer/Cadmium Sulfide Superlattices | 421 |
| 13.6 | Immobilization and Electrochemical Conducting of Enzymes in S-layer Lattices | 421 |
| 13.6.1 | S-layer and Glucose Oxidase-based Amperometric Biosensors | 421 |
| 13.6.2 | S-layer and Glucose Oxidase–based Optical Biosensors | 422 |
| 13.7 | Conclusions | 423 |
| | References | 423 |
| 14 | Computing with Nucleic Acids
Milan N. Stojanovic, Darko Stefanovic, Thomas LaBean, and Hao Yan | 427 |
| 14.1 | Introduction | 427 |
| 14.2 | Massively Parallel Approaches | 428 |
| 14.3 | The Seeman–Winfree Paradigm: Molecular Self-assembly | 435 |
| 14.4 | The Rothemund–Shapiro Paradigm: Simulating State Machines | 439 |
| 14.5 | Nucleic Acid Catalysts in Computation | 442 |
| 14.6 | Conclusion | 453 |
| | References | 454 |
| 15 | Conclusions and Perspectives
Itamar Willner and Eugenii Katz | 457 |
| | Subject Index | 463 |
