Table Of ContentPlenty of Room for Biology
at the Bottom
An Introduction to Bionanotechnology
Second Edition
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Plenty of Room for Biology
at the Bottom
An Introduction to Bionanotechnology
Second Edition
Ehud Gazit
Tel Aviv University, Israel
Anna Mitraki
University of Crete and IESL-FORTH, Greece
Imperial College Press
ICP
Published by
Imperial College Press
57 Shelton Street
Covent Garden
London WC2H 9HE
Distributed by
World Scientific Publishing Co. Pte. Ltd.
5 Toh Tuck Link, Singapore 596224
USA office: 27 Warren Street, Suite 401-402, Hackensack, NJ 07601
UK office: 57 Shelton Street, Covent Garden, London WC2H 9HE
Library of Congress Cataloging-in-Publication Data
Gazit, Ehud.
Plenty of room for biology at the bottom : an introduction to bionanotechnology / by Ehud Gazit,
Tel Aviv University, Israel & Anna Mitraki,
University of Crete and Institute for Electronic Structure and Laser, Greece. -- Second edition.
pages cm
Includes bibliographical references and index.
ISBN 978-1-84816-930-2 (hardcover : alk. paper)
1. Biotechnology. 2. Biomimetic materials. 3. Biomolecules. 4. Nanotechnology.
5. Biomimetics. I. Mitraki, Anna. II. Title.
QP514.2.G39 2013
610.28--dc23
2012048470
British Library Cataloguing-in-Publication Data
A catalogue record for this book is available from the British Library.
Copyright © 2013 by Imperial College Press
All rights reserved. This book, or parts thereof, may not be reproduced in any form or by any means,
electronic or mechanical, including photocopying, recording or any information storage and retrieval
system now known or to be invented, without written permission from the Publisher.
For photocopying of material in this volume, please pay a copying fee through the Copyright
Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, USA. In this case permission to
photocopy is not required from the publisher.
Typeset by Stallion Press
Email: [email protected]
Printed in Singapore
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This book is dedicated to my family with love (E.G.)
To my two mentors, Professor Jeannine Yon-Kahn
of Université P aris-Sud, France and
Professor Jonathan King
of MIT, USA (A.M.)
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Contents
Preface xiii
Chapter 1 Introduction: Nanobiotechnology
and Bionanotechnology 1
1.1. C lassical Biotechnology: Industrial Production
Using Biological Systems 2
1.2. M odern Biotechnology: From Industrial
Processes to Novel Therapeutics 3
1.3. M odern Biotechnology: Immunological,
Enzymatic, and Nucleic Acid-Based Technology 4
1.4. T he Interface Between Nanotechnology and
Biotechnology: Bionanotechnology 6
1.5. Supramolecular (Bio)Chemistry: The
Theoretical Basis for Self-Assembly 8
1.6. T he Next Steps for Self-Association at the
Nano-Scale 9
1.7. Biology in Nanotechnology and Nano-Sciences
in Biotechnology 11
1.8. The Combination of Bionanotechnology
and Nanobiotechnology 13
1.9. Nanobionics and Bio-Inspired Nanotechnology 14
Chapter 2 A Brief Introduction to Nanotechnology 17
2.1. The Emergence of Nanotechnology:
“There’s Plenty of Room at the Bottom” 17
2.2. Coining the Term “Nanotechnology” and the
Emergence of the Nanotechnology Concept 19
2.3. Manipulating Molecules: The Scanning Probe
Microscopes 19
vii
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viii Plenty of Room for Biology at the Bottom (2nd Edition)
2.4. Carbon Fullerene: A New Form of Carbon 22
2.5. Carbon Nanotubes: Key Building Blocks
for Future Nanotechnological Applications 24
2.6. A Single Layer of Carbon: Graphene 26
2.7. Non-Carbon Nanotubes and Fullerene-Like
Material: The Inorganic Nanomaterials 26
2.8. Quantum Dots and Other Nanoparticles 28
2.9. Nanowires, Nanorods, and Other
Nanomaterials 30
2.10. Magnetic Nanoparticles 30
Chapter 3 Natural Biological Assembly at the Nanometric
Scale 31
3.1. The Process of Self-Assembly and
Self-Organization in Biology 31
3.2. Organization of Bacterial S-Layers 32
3.3. Self-Organization of Viruses 34
3.4. Self-Organization of Phospholipid Membranes 37
3.5. Fibrillar Cytoskeleton Assemblies 39
3.6. Nucleic Acids: The Genetic Information
Media and a Template for Nanotechnological
Applications 42
3.7. Oligosaccharides and Polysaccharides:
Another Class of Biological Polymers 43
3.8. A myloid Fibrils as Self-Assembled
Nano-Scale Bio-Assemblies 44
3.9. S ilk: Natural Fibrillar Supramolecular Protein
Assembly 46
3.10. Ribosome: The Protein Assembly Line
Instrument 46
3.11. Other Complex Machines in the Genetic
Code Expression 47
3.12. Protein Quality-Control Machinery: The
Proteasome 48
3.13. Biological Nano-Motors: Kinesin and Dynein 48
3.14. Other Nano-Motors: Flagella and Cilia 49
3.15. Ion Channels: Nano-Pores of High Specificity 50
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Contents ix
Chapter 4 Nanometric Biological Assemblies: Molecular
and Chemical Basis for Interaction 53
4.1. E mergence of Biological Activity through
Self-Assembly 53
4.2. Molecular Recognition and Chemical Affinity 54
4.3. Affinity and Specificity of Biological
Interactions 56
4.4. The Relation between Thermodynamics
and Kinetics of Dissociation 56
4.5. The Chemical Basis for Molecular Recognition
and Specific Binding 59
4.6. The Formation of Specific Complexes
by an Increase in Entropy 59
Chapter 5 Molecular Recognition and the Assembly
of Biological Structures 63
5.1. Antibodies as the Molecular Sensors
of Recognition 63
5.2. Selection of Antibodies and Equivalent
Systems in the Test Tube 65
5.3. Recognition between Nucleic Acids by Proteins 67
5.4. Interaction between Receptors and Ligands 68
5.5. Molecular Recognition between Nucleic Acids 69
5.6. Aptamers 69
Chapter 6 Self-Assembly of Biological and Bio-Inspired
Nanomaterials 71
6.1. Formation of DNA-Based Materials 71
6.2. Assembly of Peptide-Based Nanomaterials 73
6.3. The First Peptide Nanotubes 75
6.4. Amphiphile and Surfactant-Like Peptide
Building Blocks 77
6.5. Charge Complementary as a Driving Force
for Self-Assembly 79
6.6. Conjugation of Peptides for Self-Assembly 80
6.7. Aromatic Interactions for the Formation
of Nano-Structures 82
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