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Nanobiotechnology Concepts, Applications and Perspectives

by: Niemeyer, Christof M.; Mirkin, Chad A.

Nanobiotechnology Concepts, Applications and Perspectives

by: Niemeyer, Christof M.; Mirkin, Chad A.

ISBN 13:
9783527306589
ISBN 10:
3527306587
Edition: 1st
Format: Hardcover
Copyright: 03/12/2004
Publisher: Wiley-VCH

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Summary

Nanotechnology is the key technology of the 21st century. The possibility to exploit the structures and processes of biomolecules for novel functional materials, biosensors, bioelectronics and medical applications has created the rapidly growing field of nanobiotechnology.Designed as a broad survey of the field, this book combines contributions from bioorganic and bioinorganic chemistry, molecular biology, materials science and bioanalytics to fathom the full scope of current and future developments.It is divided into four main sections: Interphase Systems Protein-based Nanostructures DNA-based Nanostructures NanoanalyticsEach chapter describes in detail currently available methods and contains numerous references to the primary literature, making this the perfect "field guide" for chemists, biologists and materials scientists who want to explore the fascinating world of nanobiotechnology.

Part I Interphase Systems

1 Biocompatible Inorganic Devices

(12)

Thomas Sawitowski

1.1 Introduction

(1)

1.2 Implant Coatings

(9)

1.2.1 Stents

(5)

1.2.2 Seeds

(3)

1.3 Conclusion

(3)

2 Microfluidics Meets Nano: Lab-on-a-Chip Devices and their Potential for Nanobiotechnology

(18)

Holger Bartos, Friedrich Gotz, and Ralf-Peter Peters

2.1 Introduction

(1)

2.2 Overview

(6)

2.2.1 Definition and History

(1)

2.2.2 Advantages of Microfluidic Devices

(1)

2.2.3 Concepts for Microfluidic Devices

(2)

2.2.4 Fluid Transport

(1)

2.2.5 Stacking and Sealing

(1)

2.3 Methods

(7)

2.3.1 Materials for the Manufacture of Microfluidic Components

(1)

2.3.1.1 Silicon

(1)

2.3.1.2 Glass

(1)

2.3.1.3 Polymers

(1)

2.3.2 Fluidic Structures

(2)

2.3.3 Fabrication Methods

(1)

2.3.4 Surface Modifications

(2)

2.3.5 Spotting

(1)

2.3.6 Detection Mechanisms

(1)

2.4 Outlook

(5)

3 Microcontact Printing of Proteins

(22)

Emmanuel Delamarche

3.1 Introduction

(2)

3.2 Strategies for Printing Proteins on Surfaces

(1)

3.2.1 Contact Processing with Hydrogel Stamps

(1)

3.2.2 Microcontact Printing

(1)

3.2.3 Affinity-Contact Printing

(1)

3.3 Microcontact Printing Polypeptides and Proteins

(6)

3.3.1 Printing One Type of Biomolecule

(1)

3.3.2 Substrates

(2)

3.3.3 Resolution and Contrast of the Patterns

(2)

3.4 Activity of Printed Biomolecules

(2)

3.5 Printing Multiple Types of Proteins

(3)

3.5.1 Additive and Subtractive Printing

(2)

3.5.2 Parallel Inking and Printing of Multiple Proteins

(1)

3.5.3 Affinity-Contact Printing

(1)

3.6 Methods

(4)

3.6.1 Molds and Stamps

(2)

3.6.2 Surface Chemistry of Stamps

(1)

3.6.3 Inking Methods

(1)

3.6.4 Treatments of Substrates

(1)

3.6.5 Printing

(1)

3.6.6 Characterization of the Printed Patterns

(1)

3.7 Outlook

(4)

4 Cell-Nanostructure Interactions

(13)

Joachim P. Spatz

4.1 Introduction

(3)

4.2 Methods

(7)

4.3 Outlook

(3)

5 Defined Networks of Neuronal Cells in Vitro

(11)

Andreas Offenhausser and Angela K. Vogt

5.1 Introduction

(1)

5.2 Overview Background and History

(2)

5.2.1 Physiology of Information Processing within Neuronal Networks

(1)

5.2.2 Topographical Patterning

(1)

5.2.3 Chemical Patterning

(1)

5.3 Methods

(3)

5.3.1 Topographical Patterning

(1)

5.3.2 Photolithographic Patterning

(1)

5.3.3 Photochemical Patterning

(1)

5.3.4 Microcontact Printing

(1)

5.4 Outlook

(5)

Part II Protein-based Nanostructures

6 S-Layers

(16)

Uwe B. Sleytr, Eva-Maria Egelseer, Dietmar Pum, and Bernhard Schuster

6.1 Overview

(7)

Abbreviations

(1)

6.1.1 Chemistry and Structure

(2)

6.1.2 Genetics and Secondary Cell-Wall Polymers

(2)

6.1.3 Assembly

(1)

6.1.3.1 Self-Assembly in Suspension

(1)

6.1.3.2 Recrystallization at Solid Supports

(1)

6.1.3.3 Recrystallization at the Air/Water Interface and on Langmuir Lipid Films

(1)

6.2 Methods

(5)

6.2.1 Diagnostics

(1)

6.2.2 Lipid Chips

(2)

6.2.3 S-Layers as Templates for the Formation of Regularly Arranged Nanoparticles

(2)

6.3 Outlook

(4)

7 Engineered Nanopores

(20)

Hagan Bayley, Ont Braha, Stephen Cheley, and Li-Qun Gu

7.1 Overview

(11)

7.1.1 What is a Nanopore?

(3)

7.1.2 Engineering Nanopores

(1)

7.1.3 What Can a Nanopore Do?

(3)

7.1.4 What are the Potential Applications of Nanopores?

100

(3)

7.1.5 Keeping Nanopores Happy

103

(1)

7.2 Methods

104

(2)

7.2.1 Protein Production

104

(1)

7.2.2 Protein Engineering

104

(1)

7.2.3 Electrical Recording

105

(1)

7.2.4 Other Systems

105

(1)

7.3 Outlook

106

(16)

7.3.1 Rugged Pores

106

(1)

7.3.2 Supported Bilayers

106

(1)

7.3.3 Membrane Arrays

106

(1)

7.3.4 Alternative Protein Pores

107

(1)

7.3.5 Pores with New Attributes and Applications

108

(1)

7.3.6 Theory

108

(5)

8 Genetic Approaches to Programmed Assembly

113

(13)

Stanley Brown

8.1 Introduction

113

(1)

8.2 Order from Chaos

113

(3)

8.3 Monitoring Enrichment

116

(3)

8.4 Quantification of Binding and Criteria for Specificity

119

(1)

8.5 Unselected Traits and Control of Crystallization/Reactivity

119

(1)

8.6 Dominant Traits, Interpretation of Gain-of-Function Mutants

120

(1)

8.7 Interpretation and Requirement for Consensus Sequences

120

(2)

8.8 Sizes of Proteins and Peptides

122

(1)

8.9 Mix and Match, Fusion Proteins, and Context-Dependence

122

(1)

8.10 Mix and Match, Connecting Structures

122

(1)

8.11 Outlook

123

(3)

9 Microbial Nanoparticle Production

126

(10)

Murali Sastry, Absar Ahmad, M. Islam Khan, and Rajiv Kumar

9.1 Overview

126

(7)

9.2 Outlook

133

(3)

10 Magnetosomes: Nanoscale Magnetic Iron Minerals in Bacteria

136

(1)

Richard B. Frankel and Dennis A. Bazylinski

10.1 Introduction

136

(7)

10.1.1 Magnetotactic Bacteria

136

(1)

10.1.2 Magnetosomes

137

(1)

10.1.3 Cellular Magnetic Dipole and Magnetotaxis

138

(1)

10.1.4 Magneto-Aerotaxis

139

(1)

10.1.5 Magnetite Crystals in Magnetosomes

140

(1)

10.1.6 Greigite Crystals in Magnetosomes

141

(1)

10.1.7 Biochemistry and Gene Expression in Magnetosome Formation

141

(2)

10.1.8 Applications of Magnetosomes

143

(1)

10.2 Research Methods

143

(1)

10.3 Conclusion and Future Research Directions

143

(3)

11 Bacteriorhodopsin and its Potential in Technical Applications

146

(1)

Norbert Hampp and Dieter Oesterhelt

11.1 Introduction

146

(1)

11.2 Overview. The Molecular Properties of Bacteriorhodopsin

147

(8)

11.2.1 Haloarchaea and their Retinal Proteins

147

(3)

11.2.2 Structure and Function of Bacteriorhodopsin

150

(3)

11.2.3 Genetic Modification of Bacteriorhodopsin

153

(1)

11.2.4 Biotechnological Production of Bacteriorhodopsins

154

(1)

11.3 Overview. Technical Applications of Bacteriorhodopsin

155

(10)

11.3.1 Photoelectric Applications

156

(1)

11.3.1.1 Preparation of Oriented PM Layers

156

(1)

11.3.1.2 Interfacing the Proton-Motive Force

158

(1)

11.3.1.3 Application Examples

158

(1)

11.3.2 Photochromic Applications

159

(1)

11.3.2.1 Photochromic Properties of Bacteriorhodopsin

159

(1)

11.3.2.2 Preparation of Bacteriorhodopsin Films

161

(1)

11.3.2.3 Interfacing the Photochromic Changes

161

(1)

11.3.2.4 Application Examples

161

(1)

11.3.3 Applications in Energy Conversion

161

(4)

11.4 Methods

165

(1)

11.5 Outlook

165

(3)

12 Polymer Nanocontainers

168

(1)

Alexandra Graff, Samantha M. Benito, Corinne Verbert, and Wolfgwng Meier

12.1 Introduction

168

(1)

12.2 Overview

168

(7)

12.2.1 From Liposomes in Biotechnology to Polymer Nanocontainers in Therapy

168

(1)

12.2.2 Dendrimers

169

(1)

12.2.3 Layer by Layer (LbL) Deposition

170

(2)

12.2.4 Block Copolymer Self-Assembly

172

(1)

12.2.4.1 Shell Cross-linked Knedel's (SCKs)

173

(1)

12.2.4.2 Block Copolymer Nanocontainers

174

(1)

12.3 Polymer Nanocontainers with Controlled Permeability

175

(4)

12.3.1 Block Copolymer Protein Hybrid Systems

175

(3)

12.3.2 Stimuli-responsive Nanocapsules

178

(1)

12.4 Nanoparticle Films

179

(1)

12.5 Biomaterials and Gene Therapy

180

(1)

12.6 Outlook

181

(4)

13 Biomolecular Motors Operating in Engineered Environments

185

(1)

Stefan Diez, Jonne H. Helenius, and Jonathon Howard

13.1 Overview

185

(5)

13.2 Methods

190

(5)

13.2.1 General Conditions for Motility Assays

190

(1)

13.2.2 Temporal Control

191

(1)

13.2.3 Spatial Control

191

(3)

13.2.4 Connecting to Cargoes and Surfaces

194

(1)

13.3 Outlook

195

(5)

14 Nanoparticle-Biomaterial Hybrid Systems for Bioelectronic Devices and Circuitry

200

(1)

Eugenii Katz and Itamar Willner

14.1 Introduction

200

(2)

14.2 Biomaterial-Nanoparticle Systems for Bioelectronic and Biosensing Applications

202

(13)

14.2.1 Bioelectronic Systems Based on Nanopaticle-Enzyme Hybrids

202

(3)

14.2.2 Bioelectronic Systems for Sensing of Biorecognition Events Based on Nanoparticles

205

(10)

14.3 Biomaterial-based Nanocircuitry

215

(6)

14.3.1 Protein-based Nanocircuitry

216

(2)

14.3.2 DNA as Functional Template for Nanocircuitry

218

(3)

14.4 Conclusions and Perspectives

221

(6)

Part III DNA-based Nanostructures

15 DNA-Protein Nanostructures

227

(116)

Christof M. Niemeyer

15.1 Overview

227

(11)

15.1.1 Introduction

227

(1)

15.1.2 Oligonucleotide-Enzyme Conjugates

228

(1)

15.1.3 DNA Conjugates of Binding Proteins

229

(2)

15.1.4 Noncovalent DNA-Streptavidin Conjugates

231

(3)

15.1.5 Multifunctional Protein Assemblees

234

(2)

15.1.6 DNA-Protein Conjugates in Microarray Technologies

236

(2)

15.2 Methods

238

(3)

15.2.1 Conjugation of Nucleic Acids and Proteins

238

(1)

15.2.2 Immuno-PCR

239

(1)

15.2.3 Supramolecular Assembly

240

(1)

15.2.4 DNA-directed Immobilization

240

(1)

15.3 Outlook

241

(3)

16 DNA-templated Electronics

244

(1)

Erez Braun and Un Sivan

16.1 Introduction and Background

244

(2)

16.2 DNA-templated Electronics

246

(3)

16.3 Sequence-specific Molecular Lithography

249

(4)

16.4 Summary and Perspectives

253

(3)

17 Biomimetic Fabrication of DNA-based Metallic Nanowires and Networks

256

(1)

Michael Meitig and Wolfgang Pompe

17.1 Introduction

256

(2)

17.2 Template Design

258

(4)

17.2.1 DNA as a Biomolecular Template

258

(1)

17.2.2 Integration of DNA into Microelectronic Contact Arrays

258

(3)

17.2.3 DNA Branching for Network Formation

261

(1)

17.3 Metallization

262

(8)

17.3.1 Controlled Cluster Growth on DNA Templates

263

(4)

17.3.2 First-Principle Molecular Dynamics Calculations of DNA Metallization

267

(3)

17.4 Conductivity Measurements on Metalized DNA Wires

270

(2)

17.5 Conclusions and Outlook

272

(2)

17.6 Methods

274

(4)

17.6.1 Site-Specific DNA Attachment

274

(1)

17.6.2 DNA Junctions

274

(1)

17.6.3 DNA Metallization

274

(4)

18 Mineralization in Nanostructured Biocompartments: Biomimetic Ferritins For High-Density Data Storage

278

(10)

Eric L. Mayes and Stephen Mann

18.1 Overview

278

(1)

18.2 Biomimetic Ferritins

279

(1)

18.3 High-Density Magnetic Data Storage

280

(2)

18.4 Methods

282

(1)

18.5 Results

283

(2)

18.6 Outlook

285

(3)

19 DNA-Gold-Nanoparticle Conjugates

288

(1)

C. Shad Thaxton and Chad A. Mirkin

19.1 Overview

288

(13)

19.1.1 Introduction

288

(1)

19.1.2 Nanoparticles

289

(2)

19.1.3 DNA-functionalized Gold Nanoparticles

291

(1)

19.1.4 Nanoparticle Based DNA and RNA Detection Assays

292

(1)

19.1.4.1 Homogeneous DNA Detection

292

(1)

19.1.4.2 Chip-based (Heterogeneous) DNA Detection Assays

293

(6)

19.1.5 DNA-Nanoparticle Detection of Proteins: Biobarcodes

299

(1)

19.1.6 Conclusion

300

(1)

19.2 The Essentials: Methods and Protocols

301

(3)

19.2.1 Nanoparticle Synthesis

301

(1)

19.2.2 DNA-functionalized Au-NP Probe Synthesis

301

(2)

19.2.3 Chip Functionalization with DNA Target "Capture" Strands

303

(1)

19.2.4 Typical Assay Design

304

(1)

19.3 Outlook

304

(4)

19.3.1 Challenges Ahead

304

(1)

19.3.2 Academic and Commercial Applications

305

(3)

20 DNA Nanostructures for Mechanics and Computing: Nonlinear Thinking with Life's Central Molecule

308

(13)

Nadrian C. Seeman

20.1 Overview

308

(1)

20.2 Introduction

308

(3)

20.3 DNA Arrays

311

(2)

20.4 DNA Nanomechanical Devices

313

(2)

20.5 DNA-based Computation

315

(2)

20.6 Summary and Outlook

317

(2)

21 Nanoparticles as Non-Viral Transfection Agents

319

(1)

M.N.V. Ravi Kumar, Udo Bakowsky, and Claus-Michael Lehr

21.1 Introduction to Gene Delivery

319

(2)

21.2 Nanoparticles for Drug and Gene Targeting

321

(1)

21.3 Nonviral Nanomaterials in Development and Testing

321

(17)

21.3.1 Chitosan

321

(6)

21.3.2 Liposomes and Solid Lipids

327

(5)

21.3.3 Poly-L-Lysine and Polyethylenimines

332

(2)

21.3.4 Poly(lactide-co-glycolide)

334

(1)

21.3.5 Silica

335

(1)

21.3.6 Block Copolymers

336

(2)

21.4 Setbacks and Strategies to Improve Specific Cell Uptake of Nonviral Systems

338

(1)

21.5 Prospects for Nonviral Nanomaterials

338

(5)

Part IV Nanoanalytics

22 Luminescent Quantum Dots for Biological Labeling

343

(115)

Xiaohu Gao and Shuming Nie

22.1 Overview

343

(5)

22.2 Methods

348

(1)

22.3 Outlook

349

(4)

23 Nanoparticle Molecular Labels

353

(4)

James F. Hainfeld, Richard D. Powell, and Gerhard W. Hacker

23.1 Introduction

353

(1)

23.2 Immunogold-Silver Staining: A History

354

(2)

23.3 Combined Fluorescent and Gold Probes

356

(1)

23.4 Methodology

357

(30)

23.4.1 Choice of Gold and AMG Type

357

(2)

23.4.2 Iodinization

359

(1)

23.4.3 Sensitivity

359

(1)

23.5 Applications for the Microscopical Detection of Antigens

359

(2)

23.6 Applications for Microscopical Detection of Nucleic Acids

361

(1)

23.8 Technical Guidelines and Laboratory Protocols

362

(1)

23.9 Gold Derivatives of Other Biomolecules

362

(1)

23.9.1 Protein Labeling

363

(1)

23.9.2 Gold Cluster-labeled Peptides

364

(1)

23.9.3 Gold Cluster Conjugates of Other Small Molecules

364

(1)

23.9.4 Gold-Lipids: Metallosomes

365

(1)

23.10 Larger Covalent Particle Labels

366

(1)

23.11 Gold Targeted to His Tags

367

(1)

23.12 Enzyme Metallography

368

(1)

23.13 Gold Cluster Nanocrystals

369

(1)

23.14 Gold Cluster-Oligonucleotide Conjugates: Nanotechnology Applications

369

(3)

23.14.1 DNA Nanowires

370

(1)

23.14.2 3-D Nanostructured Mineralized Biomaterials

370

(2)

23.14.3 Gold-quenched Molecular Beacons

372

(1)

23.15 Other Metal Cluster Labels

372

(15)

23.15.1 Platinum and Palladium

373

(1)

23.15.2 Tungstates

374

(1)

23.15.3 Iridium

375

(12)

24 Surface Biology: Analysis of Biomolecular Structure by Atomic Force Microscopy and Molecular Pulling

387

(1)

Envin Oroudjev, Signe Danielsen and Helen G. Hansma

24.1 Introduction

387

(1)

24.2 Recent Results

388

(7)

24.2.1 DNA

388

(1)

24.2.1.1 DNA Condensation

388

(1)

24.2.1.2 DNA Sequences Recognized by Mica

390

(1)

24.2.1.3 Drug-binding to Single ds-DNA Molecules

390

(1)

24.2.2 Proteins

390

(1)

24.2.2.1 Prion Proteins

391

(1)

24.2.2.2 Membrane Proteins

393

(1)

24.2.2.3 Spider Silk

394

(1)

24.2.3 Fossils

394

(1)

24.2.4 Science and Nature

394

(1)

24.3 Methodology

395

(3)

24.3.1 The Probe

396

(1)

24.3.2 The Sample

397

(1)

24.4 The Future

398

(6)

24.4.1 Unity or Diversity?

398

(1)

24.4.2 World-wide Research

399

(5)

25 Force Spectroscopy

404

(1)

Markus Seitz

25.1 Overview

404

(15)

25.1.1 Dynamic Force Spectroscopy of Specific Biomolecular Bonds

405

(4)

25.1.2 Force Spectroscopy and Force Microscopy of Cell Membranes

409

(1)

25.1.3 Protein (Un-)folding

409

(3)

25.1.4 Elasticity of Individual Polymer Molecules

412

(2)

25.1.5 DNA Mechanics

414

(2)

25.1.6 DNA-Protein Interactions

416

(1)

25.1.7 Molecular Motors

417

(1)

25.1.8 Synthetic Functional Polymers

418

(1)

25.2 Methods

419

(5)

25.2.1 AFM Cantilevers

419

(2)

25.2.2 Microneedles

421

(1)

25.2.3 Optical Tweezers

421

(1)

25.2.4 Magnetic Tweezers

422

(1)

25.2.5 Biomembrane Force Probe

423

(1)

25.3 Outlook

424

(5)

26 Biofunctionalized Nanoparticles for Surface-Enhanced Raman Scattering and Surface Plasmon Resonance

429

(1)

Mahnaz El-Kouedi and Christine D. Keating

26.1 Overview

429

(10)

26.1.1 Introduction

429

(1)

26.1.2 Applications in SPR

430

(1)

26.1.2.1 Nanoparticle Substrates

430

(1)

26.1.2.2 Planar Substrates

431

(3)

26.1.3 Applications in SERS

434

(1)

26.1.3.1 Proteins

434

(1)

26.1.3.2 Nucleic Acids

437

(2)

26.2 Methods

439

(1)

26.2.1 Planar SPR Substrate Preparation

439

(1)

26.2.2 Metal Nanoparticles

439

(1)

26.2.3 Bioconjugates

439

(1)

26.2.4 General Comments

440

(1)

26.3 Future Outlook

440

(4)

27 Bioconjugated Silica Nanoparticles for Bioanalytical Applications

444

(1)

Timothy J. Drake, Xiaojun Julia Zhao, and Weihong Tan

27.1 Overview

444

(1)

27.2 Methods

445

(9)

27.2.1 Fabrication

445

(2)

27.2.2 Particle Probes

447

(1)

27.2.2.1 Dye-doped Silica Nanoparticles

447

(1)

27.2.2.2 Magnetic Silica Nanoparticles

449

(1)

27.2.3 Biofunctionalization of Silica Nanoparticles

449

(1)

27.2.3.1 Amino-Group Cross-Linkage

450

(1)

27.2.3.2 Avidin-Biotin Linking Bridge

451

(1)

27.2.3.3 Disulfide-coupling Chemical Binding

451

(1)

27.2.3.4 Cyanogen Bromide Modification

451

(1)

27.2.4 Bioanlytical Applications for Silica Nanoparticles

452

(1)

27.2.4.1 Cellular Labeling/Detection

452

(1)

27.2.4.2 DNA Analysis

453

(1)

27.2.4.3 Ultrasensitive DNA Detection

453

(1)

27.3 Outlook

454

(4)

Index

458

Rent More, Save More! Use code: KBRENTAL

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Nanobiotechnology Concepts, Applications and Perspectives

Nanobiotechnology Concepts, Applications and Perspectives

9783527306589

3527306587

Summary

Author Biography

Table of Contents

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