Part I Interphase Systems
1 Biocompatible Inorganic Devices .............................. 1
Thomas Sawitowski
2.1 Introduction ............................................ 1
1.2 Implant Coatings ........................................ 1
1.2.1 Stents ........................................... 2
1.2.2 Seeds ............................................ 7
1.3 Conclusion ............................................. 10
2 Microfluidics Meets Nano: Lab-on-a-Chip Devices and their
Potential for Nanobiotechnology ............................. 13
Holger Bartos, Friedrich Götz, and Ralf-Peter Peters
2.1 Introduction ........................................... 13
2.2 Overview ............................................... 13
2.2.1 Definition and History .......................... 13
2.2.2 Advantages of Microfluidic Devices .............. 14
2.2.3 Concepts for Microfluidic Devices ............... 15
2.2.4 Fluid Transport ................................. 17
2.2.5 Stacking and Sealing ............................ 18
2.3 Methods ................................................ 19
2.3.1 Materials for the Manufacture of Microfluidic
Components ...................................... 19
2.3.1.1 Silicon ................................ 19
2.3.1.2 Glass .................................. 19
2.3.1.3 Polymers ............................... 20
2.3.2 Fluidic Structures .............................. 21
2.3.3 Fabrication Methods ............................. 23
2.3.4 Surface Modifications ........................... 23
2.3.5 Spotting ........................................ 25
2.3.6 Detection Mechanisms ............................ 26
2.4 Outlook ................................................ 26
3 Microcontact Printing of Proteins ........................... 31
Emmanuel Delamarche
3.1 Introduction ........................................... 31
3.2 Strategies for Printing Proteins on Surfaces ........... 33
3.2.1 Contact Processing with Hydrogel Stamps ......... 33
3.2.2 Microcontact Printing ........................... 33
3.2.3 Affinity-Contact Printing ....................... 34
3.3 Microcontact Printing Polypeptides and Proteins ........ 34
3.3.1 Printing One Type of Biomolecule ................ 35
3.3.2 Substrates ...................................... 36
3.3.3 Resolution and Contrast of the Patterns ......... 38
3.4 Activity of Printed Biomolecules ....................... 40
3.5 Printing Multiple Types of Proteins .................... 42
3.5.1 Additive and Subtractive Printing ............... 42
3.5.2 Parallel Inking and Printing of Multiple
Proteins ........................................ 44
3.5.3 Affinity-Contact Printing ....................... 44
3.6 Methods ................................................ 45
3.6.1 Molds and Stamps ................................ 45
3.6.2 Surface Chemistry of Stamps ..................... 47
3.6.3 Inking Methods .................................. 47
3.6.4 Treatments of Substrates ........................ 48
3.6.5 Printing ........................................ 48
3.6.6 Characterization of the Printed Patterns ........ 49
3.7 Outlook ................................................ 49
4 Cell-Nanostructure Interactions ............................. 53
Joachim P. Spatz
4.1 Introduction ........................................... 53
4.2 Methods ................................................ 56
4.3 Outlook ................................................ 63
5 Defined Networks of Neuronal Cells in Vitro ................. 66
Andreas Offenhäusser and Angela K. Vogt
5.1 Introduction ........................................... 66
5.2 Overview: Background and History ....................... 67
5.2.1 Physiology of Information Processing within
Neuronal Networks ............................... 67
5.2.2 Topographical Patterning ........................ 67
5.2.3 Chemical Patterning ............................. 68
5.3 Methods ................................................ 69
5.3.1 Topographical Patterning ........................ 69
5.3.2 Photolithographic Patterning .................... 70
5.3.3 Photochemical Patterning......................... 70
5.3.4 Microcontact Printing ........................... 71
5.4 Outlook ................................................ 72
Part II Protein-based Nanostructures
6 S-Layers .................................................... 77
Uwe B. Sleytr, Eva-Maria Egelseer, Dietmar Pum, and
Bemhard Schuster
6.1 Overview ............................................... 77
Abbreviations ............................................... 77
6.1.1 Chemistry and Structure ......................... 78
6.1.2 Genetics and Secondary Cell-Wall Polymers ....... 80
6.1.3 Assembly ........................................ 82
6.1.3.1 Self-Assembly in Suspension ............ 82
6.1.3.2 Recrystallization at Solid Supports .... 83
6.1.3.3 Recrystallization at the Air/Water
Interface and on Langmuir Lipid
Films .................................. 83
6.2 Methods ................................................ 84
6.2.1 Diagnostics ..................................... 84
6.2.2 Lipid Chips ..................................... 85
6.2.3 S-Layers as Templates for the Formation of
Regularly Arranged Nanoparticles ................ 87
6.3 Outlook ................................................ 89
7 Engineered Nanopores ........................................ 93
Hagan Bayley, Orit Braha, Stephen Cheley, and Li-Qun Gu
7.1 Overview ............................................... 93
7.1.1 What is a Nanopore? ............................. 93
7.1.2 Engineering Nanopores ........................... 96
7.1.3 What Can a Nanopore Do? ......................... 97
7.1.4 What are the Potential Applications of
Nanopores? ..................................... 100
7.1.5 Keeping Nanopores Happy ........................ 103
7.2 Methods ............................................... 104
7.2.1 Protein Production ............................. 104
7.2.2 Protein Engineering ............................ 104
7.2.3 Electrical Recording ........................... 105
7.2.4 Other Systems .................................. 105
7.3 Outlook ............................................... 106
7.3.1 Rugged Pores ................................... 106
7.3.2 Supported Bilayers ............................. 106
7.3.3 Membrane Arrays ................................ 106
7.3.4 Alternative Protein Pores ...................... 107
7.3.5 Pores with New Attributes and Applications ..... 108
7.3.6 Theory ......................................... 108
8 Genetic Approaches to Programmed Assembly .................. 113
Stanley Brown
8.1 Introduction .......................................... 113
8.2 Order from Chaos ...................................... 113
8.3 Monitoring Enrichment ................................. 116
8.4 Quantification of Binding and Criteria for
Specificity ........................................... 119
8.5 Unselected Traits and Control of Crystallization/
Reactivity ............................................ 119
8.6 Dominant Traits, Interpretation of Gain-of-Function
Mutants ............................................... 120
8.7 Interpretation and Requirement for Consensus
Sequences ............................................. 120
8.8 Sizes of Proteins and Peptides ........................ 122
8.9 Mix and Match, Fusion Proteins, and Context-
Dependence ............................................ 122
8.10 Mix and Match, Connecting Structures .................. 122
8.11 Outlook ............................................... 123
9 Microbial Nanoparticle Production .......................... 126
Murali Sastry, Absar Ahmad, M. Islam Khan, and Rajiv
Kumar
9.1 Overview .............................................. 126
9.2 Outlook ............................................... 133
10 Magnetosomes: Nanoscale Magnetic Iron Minerals in
Bacteria ................................................... 136
Richard B. Frankel and Dennis A. Bazylinski
10.1 Introduction .......................................... 136
10.1.1 Magnetotactic Bacteria ......................... 136
10.1.2 Magnetosomes ................................... 137
10.1.3 Cellular Magnetic Dipole and Magnetotaxis ...... 138
10.1.4 Magneto-Aerotaxis .............................. 139
10.1.5 Magnetite Crystals in Magnetosomes ............. 140
10.1.6 Greigite Crystals in Magnetosomes .............. 141
10.1.7 Biochemistry and Gene Expression in
Magnetosome Formation .......................... 141
10.1.8 Applications of Magnetosomes ................... 143
10.2 Research Methods ...................................... 143
10.3 Conclusion and Future Research Directions ............. 143
11 Bacteriorhodopsin and its Potential in Technical
Applications ............................................... 146
Norbert Hampp and Dieter Oesterhelt
11.1 Introduction .......................................... 146
11.2 Overview: The Molecular Properties of
Bacteriorhodopsin ..................................... 147
11.2.1 Haloarchaea and their Retinal Proteins ......... 147
11.2.2 Structure and Function of Bacteriorhodopsin .... 150
11.2.3 Genetic Modification of Bacteriorhodopsin ...... 153
11.2.4 Biotechnological Production of
Bacteriorhodopsins ............................. 154
11.3 Overview: Technical Applications of
Bacteriorhodopsin ..................................... 255
11.3.1 Photoelectric Applications ..................... 156
11.3.1.1 Preparation of Oriented PM Layers ..... 156
11.3.1.2 Interfacing the Proton-Motive Force ... 158
11.3.1.3 Application Examples .................. 158
11.3.2 Photochromic Applications ...................... 159
11.3.2.1 Photochromic Properties of
Bacteriorhodopsin ..................... 159
11.3.2.2 Preparation of Bacteriorhodopsin
Films ................................. 162
11.3.2.1 Interfacing the Photochromic
Changes ............................... 161
11.3.2.2 Application Examples .................. 161
11.3.3 Applications in Energy Conversion .............. 163
11.4 Methods ............................................... 165
11.5 Outlook ............................................... 165
12 Polymer Nanocontainers ..................................... 168
Alexandra Graff, Samantha M. Benito, Corinne Verbert, and
Wolfgang Meier
12.1 Introduction .......................................... 168
12.2 Overview .............................................. 168
12.2.1 From Liposomes in Biotechnology to Polymer
Nanocontainers in Therapy ...................... 168
12.2.2 Dendrimers ..................................... 169
12.2.3 Layer by Layer (LbL) Deposition ................ 170
12.2.4 Block Copolymer Self-Assembly .................. 172
12.2.4.1 Shell Cross-linked Knedel's (SCKs) .... 173
12.2.4.2 Block Copolymer Nanocontainers ........ 174
12.3 Polymer Nanocontainers with Controlled Permeability ... 175
12.3.1 Block Copolymer Protein Hybrid Systems ......... 175
12.3.2 Stimuli-responsive Nanocapsules ................ 178
12.4 Nanoparticle Films .................................... 279
12.5 Biomaterials and Gene Therapy ......................... 280
12.6 Outlook ............................................... 281
13 Biomolecular Motors Operating in Engineered Environments ... 285
Stefan Diez, Jonne H. Helenius, and Jonathon Howard
13.1 Overview .............................................. 185
13.2 Methods ............................................... 190
13.2.1 General Conditions for Motility Assays ......... 290
13.2.2 Temporal Control ............................... 292
13.2.3 Spatial Control ................................ 292
13.2.4 Connecting to Cargoes and Surfaces ............. 294
13.3 Outlook ............................................... 295
14 Nanoparticle-Biomaterial Hybrid Systems for Bioelectronic
Devices and Circuitry ...................................... 200
Eugenii Katz and Itamar Willner
14.1 Introduction .......................................... 200
14.2 Biomaterial-Nanoparticle Systems for Bioelectronic
and Biosensing Applications ........................... 202
14.2.1 Bioelectronic Systems Based on Nanopaticle-
Enzyme Hybrids ................................. 202
14.2.2 Bioelectronic Systems for Sensing of
Biorecognition Events Based on Nanoparticles ... 205
14.3 Biomaterial-based Nanocircuitry ....................... 215
14.3.1 Protein-based Nanocircuitry .................... 216
14.3.2 DNA as Functional Template for Nanocircuitry ... 218
14.4 Conclusions and Perspectives .......................... 221
Part III DNA-based Nanostructures
15 DNA-Protein Nanostructures ................................. 227
Christof M. Niemeyer
15.1 Overview .............................................. 227
15.1.1 Introduction ................................... 227
15.1.2 Oligonucleotide-Enzyme Conjugates .............. 228
15.1.3 DNA Conjugates of Binding Proteins ............. 229
15.1.4 Noncovalent DNA-Streptavidin Conjugates ........ 231
15.1.5 Multifunctional Protein Assemblies ............. 234
15.1.6 DNA-Protein Conjugates in Microarray
Technologies ................................... 236
15.2 Methods ............................................... 238
15.2.1 Conjugation of Nucleic Acids and Proteins ...... 238
15.2.2 Immuno-PCR ..................................... 239
15.2.3 Supramolecular Assembly ........................ 240
15.2.4 DNA-directed Immobilization .................... 240
15.3 Outlook ............................................... 241
16 DNA-templated Electronics .................................. 244
Erez Braun and Uri Sivan
16.1 Introduction and Background ........................... 244
16.2 DNA-templated Electronics ............................. 246
16.3 Sequence-specific Molecular Lithography ............... 249
16.4 Summary and Perspectives .............................. 253
17 Biomimetic Fabrication of DNA-based Metallic Nanowires
and Networks ............................................... 256
Michael Mertig and Wolfgang Pompe
17.1 Introduction .......................................... 256
17.2 Template Design ....................................... 258
17.2.1 DNA as a Biomolecular Template ................. 258
17.2.2 Integration of DNA into Microelectronic
Contact Arrays ................................. 258
17.2.3 DNA Branching for Network Formation ............ 261
17.3 Metallization ......................................... 262
17.3.1 Controlled Cluster Growth on DNA Templates ..... 263
17.3.2 First-Principle Molecular Dynamics
Calculations of DNA Metallization .............. 267
17.4 Conductivity Measurements on Metalized DNA Wires ...... 270
17.5 Conclusions and Outlook ............................... 272
17.6 Methods ............................................... 274
17.6.1 Site-Specific DNA Attachment ................... 274
17.6.2 DNA Junctions .................................. 274
17.6.3 DNA Metallization .............................. 274
18 Mineralization in Nanostructured Biocompartments:
Biomimetic Ferritins For High-Density Data Storage ......... 278
Eric L. Mayes and Stephen Mann
18.1 Overview .............................................. 278
18.2 Biomimetic Ferritins .................................. 279
18.3 High-Density Magnetic Data Storage .................... 280
18.4 Methods ............................................... 282
18.5 Results ............................................... 283
18.6 Outlook ............................................... 285
19 DNA-Cold-Nanoparticle Conjugates ........................... 288
C. Shad Thaxton and Chad A. Mirkin
19.1 Overview .............................................. 288
19.1.1 Introduction ................................... 288
19.1.2 Nanoparticles .................................. 289
19.1.3 DNA-functionalized Gold Nanoparticles .......... 291
19.1.4 Nanoparticle Based DNA and RNA Detection
Assays ......................................... 292
19.1.4.1 Homogeneous DNA Detection ............. 292
19.1.4.2 Chip-based (Heterogeneous) DNA
Detection Assays ...................... 293
19.1.5 DNA-Nanoparticle Detection of Proteins:
Biobarcodes .................................... 299
19.1.6 Conclusion ..................................... 300
19.2 The Essentials: Methods and Protocols ................. 301
19.2.1 Nanoparticle Synthesis ......................... 301
19.2.2 DNA-functionalized Au-NP Probe Synthesis ....... 301
19.2.3 Chip Functionalization with DNA Target
"Capture" Strands .............................. 303
19.2.4 Typical Assay Design ........................... 304
19.3 Outlook ............................................... 304
19.3.1 Challenges Ahead ............................... 304
19.3.2 Academic and Commercial Applications ........... 305
20 DNA Nanostructures for Mechanics and Computing: Nonlinear
Thinking with Life's Central Molecule ...................... 308
Nadrian C. Seeman
20.1 Overview .............................................. 308
20.2 Introduction .......................................... 308
20.3 DNA Arrays ............................................ 311
20.4 DNA Nanomechanical Devices ............................ 313
20.5 DNA-based Computation ................................. 315
20.6 Summary and Outlook ................................... 317
21 Nanoparticles as Non-Viral Transfection Agents ............. 319
M.N.V. Ravi Kumar, Udo Bakowsky, and Claus-Michael Lehr
21.1 Introduction to Gene Delivery ......................... 319
21.2 Nanoparticles for Drag and Gene Targeting ............. 321
21.3 Nonviral Nanomaterials in Development and Testing ..... 321
21.3.1 Chitosan ....................................... 321
21.3.2 Liposomes and Solid Lipids ..................... 327
21.3.3 Poly-l-Lysine and Polyethylenimines ............ 332
21.3.4 Poly(lactide-co-glycolide) ..................... 334
21.3.5 Silica ......................................... 335
21.3.6 Block Copolymers ............................... 336
21.4 Setbacks and Strategies to Improve Specific Cell
Uptake of Nonviral Systems ............................ 338
21.5 Prospects for Nonviral Nanomaterials .................. 338
Part IV Nanoanalytics
22 Luminescent Quantum Dots for Biological Labeling ........... 343
Xiaohu Gao and Shuming Nie
22.1 Overview .............................................. 343
22.2 Methods ............................................... 348
22.3 Outlook ............................................... 349
23 Nanoparticle Molecular Labels .............................. 353
James F. Hainfeld, Richard D. Powell, and Gerhard
W. Hacker
23.1 Introduction .......................................... 353
23.2 Immunogold-Silver Staining: A History ................. 354
23.3 Combined Fluorescent and Gold Probes .................. 356
23.4 Methodology ........................................... 357
23.4.1 Choice of Gold and AMG Type .................... 357
23.4.2 Iodinization ................................... 359
23.4.3 Sensitivity .................................... 359
23.5 Applications for the Microscopical Detection of
Antigens .............................................. 359
23.6 Detection of Nucleic Acid Sequences ................... 360
23.7 Applications for Microscopical Detection of Nucleic
Acids ................................................. 361
23.8 Technical Guidelines and Laboratory Protocols ......... 362
23.9 Gold Derivatives of Other Biomolecules ................ 362
23.9.1 Protein Labeling ............................... 363
23.9.2 Gold Cluster-labeled Peptides .................. 364
23.9.3 Gold Cluster Conjugates of Other Small
Molecules ...................................... 364
23.9.4 Gold-Lipids: Metallosomes ...................... 365
23.10 Larger Covalent Particle Labels ...................... 366
23.11 Gold Targeted to His Tags ............................ 367
23.12 Enzyme Metallography ................................. 368
23.13 Gold Cluster Nanocrystals ............................ 369
23.14 Gold Cluster-Oligonucleotide Conjugates:
Nanotechnology Applications .......................... 369
23.14.1 DNA Nanowires ................................ 370
23.14.2 3-D Nanostructured Mineralized
Biomaterials ................................. 370
23.14.3 Gold-quenched Molecular Beacons .............. 372
23.15 Other Metal Cluster Labels ........................... 372
23.15.1 Platinum and Palladium ....................... 373
23.15.2 Tungstates ................................... 374
23.15.3 Iridium ...................................... 375
24 Surface Biology: Analysis of Biomolecular Structure
by Atomic Force Microscopy and Molecular Pulling ........... 387
Emin Oroudjev, Signe Danielsen and Helen G. Hansma
24.1 Introduction .......................................... 387
24.2 Recent Results ........................................ 388
24.2.1 DNA ............................................ 388
24.2.1.1 DNA Condensation ...................... 388
24.2.1.2 DNA Sequences Recognized by Mica ...... 390
24.2.1.3 Drug-binding to Single ds-DNA
Molecules ............................. 390
24.2.2 Proteins ....................................... 390
24.2.2.1 Prion Proteins ........................ 391
24.2.2.2 Membrane Proteins ..................... 393
24.2.2.3 Spider Silk ........................... 394
24.2.3 Fossils ........................................ 394
24.2.4 Science and Nature ............................. 394
24.3 Methodology ........................................... 395
24.3.1 The Probe ...................................... 396
24.3.2 The Sample ..................................... 397
24.4 The Future ............................................ 398
24.4.1 Unity or Diversity? ............................ 398
24.4.2 World-wide Research ............................ 399
25 Force Spectroscopy ......................................... 404
Markus Seitz
25.1 Overview .............................................. 404
25.1.1 Dynamic Force Spectroscopy of Specific
Biomolecular Bonds ............................. 405
25.1.2 Force Spectroscopy and Force Microscopy of
Cell Membranes ................................. 409
25.1.3 Protein (Un-)folding ........................... 409
25.1.4 Elasticity of Individual Polymer Molecules ..... 412
25.1.5 DNA Mechanics .................................. 414
25.1.6 DNA-Protein Interactions ....................... 416
25.1.7 Molecular Motors ............................... 417
25.1.8 Synthetic Functional Polymers .................. 418
25.2 Methods ............................................... 419
25.2.1 AFM Cantilevers ................................ 419
25.2.2 Microneedles ................................... 421
25.2.3 Optical Tweezers ............................... 421
25.2.4 Magnetic Tweezers .............................. 422
25.2.5 Biomembrane Force Probe ........................ 423
25.3 Outlook ............................................... 424
26 Biofunctionalized Nanoparticles for Surface-Enhanced
Raman Scattering and Surface Plasmon Resonance ............. 429
Mahnaz El-Kouedi and Christine D. Keating
26.1 Overview .............................................. 429
26.1.1 Introduction ................................... 429
26.1.2 Applications in SPR ............................ 430
26.1.2.1 Nanoparticle Substrates ............... 430
26.1.2.2 Planar Substrates ..................... 431
26.1.3 Applications in SERS ........................... 434
26.1.3.1 Proteins .............................. 434
26.1.3.2 Nucleic Acids ......................... 437
26.2 Methods ............................................... 439
26.2.1 Planar SPR Substrate Preparation ............... 439
26.2.2 Metal Nanoparticles ............................ 439
26.2.3 Bioconjugates .................................. 439
26.2.4 General Comments ............................... 440
26.3 Future Outlook ........................................ 440
27 Bioconjugated Silica Nanoparticles for Bioanalytical
Applications ............................................... 444
Timothy J. Drake, Xiaojun Julia Zhao, and Weihong Tan
27.1 Overview .............................................. 444
27.2 Methods ............................................... 445
27.2.1 Fabrication .................................... 445
27.2.2 Particle Probes ................................ 447
27.2.2.1 Dye-doped Silica Nanoparticles ........ 447
27.2.2.2 Magnetic Silica Nanoparticles ......... 449
27.2.3 Biofunctionalization of Silica Nanoparticles ... 449
27.2.3.1 Amino-Group Cross-Linkage ............. 450
27.2.3.2 Avidin-Biotin Linking Bridge .......... 451
27.2.3.3 Disulfide-coupling Chemical Binding ... 451
27.2.3.4 Cyanogen Bromide Modification ......... 451
27.2.4 Bioanalytical Applications for Silica
Nanoparticles .................................. 452
27.2.4.1 Cellular Labeling/Detection ........... 452
27.2.4.2 DNA Analysis .......................... 453
27.2.4.3 Ultrasensitive DNA Detection .......... 453
27.3 Outlook ............................................... 454
Index ...................................................... 458
|
