| |
| |
| |
| The Quest for Nanotechnology | |
| |
| |
| Biotechnology and the Two-Week Revolution | |
| |
| |
| From Biotechnology to Bionanotechnology | |
| |
| |
| What is Bionanotechnology? | |
| |
| |
| |
| Bionanomachines in Action | |
| |
| |
| The Unfamiliar World of Bionanomachines | |
| |
| |
| Gravity and inertia are negligible at the nanoscale | |
| |
| |
| Nanomachines show atomic granularity | |
| |
| |
| Thermal motion is a significant force at the nanoscale | |
| |
| |
| Bionanomachines require a water environment | |
| |
| |
| Modern Biomaterials | |
| |
| |
| Most natural bionanomachines are composed of protein | |
| |
| |
| Nucleic acids carry information | |
| |
| |
| Lipids are used for infrastructure | |
| |
| |
| Polysaccharides are used in specialized structural roles | |
| |
| |
| The Legacy of Evolution | |
| |
| |
| Evolution has placed significant limitations on the properties of natural biomolecules | |
| |
| |
| Guided Tour of Natural Bionanomachinery | |
| |
| |
| |
| Biomolecular Design and Biotechnology | |
| |
| |
| Recombinant DNA Technology | |
| |
| |
| DNA may be engineered with commercially available enzymes | |
| |
| |
| Site-directed mutagenesis makes specific changes in the genome | |
| |
| |
| Fusion proteins combine two functions | |
| |
| |
| Monoclonal Antibodies | |
| |
| |
| Biomolecular Structure Determination | |
| |
| |
| X-ray crystallography provides atomic structures | |
| |
| |
| NMR spectroscopy may be used to derive atomic structures | |
| |
| |
| Electron microscopy reveals molecular morphology | |
| |
| |
| Atomic force microscopy probes the surface of biomolecules | |
| |
| |
| Molecular Modeling | |
| |
| |
| Bionanomachines are visualized with computer graphics | |
| |
| |
| Computer modeling is used to predict biomolecular structure and function | |
| |
| |
| The protein folding problem | |
| |
| |
| Docking simulations predict the modes of biomolecular interaction | |
| |
| |
| New functionalities are developed with computer-assisted molecular design | |
| |
| |
| |
| Structural Principles of Bionanotechnology | |
| |
| |
| Natural Bionanomachinery is Designed for a Specific Environment | |
| |
| |
| A Hierarchical Strategy Allows Construction of Nanomachines | |
| |
| |
| The Raw Materials: Biomolecular Structure and Stability | |
| |
| |
| Molecules are composed of atoms linked by covalent bonds | |
| |
| |
| Dispersion and repulsion forces act at close range | |
| |
| |
| Hydrogen bonds provide stability and specificity | |
| |
| |
| Electrostatic interactions are formed between charged atoms | |
| |
| |
| The hydrophobic effect stabilizes biomolecules in water | |
| |
| |
| Protein Folding | |
| |
| |
| Not all protein sequences adopt stable structures | |
| |
| |
| Globular proteins have a hierarchical structure | |
| |
| |
| Stable globular structure requires a combination of design strategies | |
| |
| |
| Chaperones provide the optimal environment for folding | |
| |
| |
| Rigidity can make proteins more stable at high temperatures | |
| |
| |
| Many proteins make use of disorder | |
| |
| |
| Self-Assembly | |
| |
| |
| Symmetry allows self-assembly of stable complexes with defined size | |
| |
| |
| Quasisymmetry is used to build assemblies too large for perfect symmetry | |
| |
| |
| Crowded conditions promote self-assembly | |
| |
| |
| Self-Organization | |
| |
| |
| Lipids self-organize into bilayers | |
| |
| |
| Lipid bilayers are fluid | |
| |
| |
| Proteins may be designed to self-organize with lipid bilayers | |
| |
| |
| Molecular Recognition | |
| |
| |
| Crane principles for molecular recognition | |
| |
| |
| Atomicity limits the tolerance of combining sites | |
| |
| |
| Flexibility | |
| |
| |
| Biomolecules show flexibility at all levels | |
| |
| |
| Flexibility poses great challenges for the design of bionanomachines | |
| |
| |
| |
| Functional Principles of Bionanotechnology | |
| |
| |
| Information-Driven Nanoassembly | |
| |
| |
| Nucleic acids carry genetic information | |
| |
| |
| Ribosomes construct proteins | |
| |
| |
| Information is stored in very compact form | |
| |
| |
| Energetics | |
| |
| |
| Chemical energy is transferred by carrier molecules | |
| |
| |
| Light is captured with specialized small molecules | |
| |
| |
| Protein pathways transfer single electrons | |
| |
| |
| Electrical conduction and charge transfer have been observed in DNA | |
| |
| |
| Electrochemical gradients are created across membranes | |
| |
| |
| Chemical Transformation | |
| |
| |
| Enzymes reduce the entropy of a chemical reaction | |
| |
| |
| Enzymes create environments that stabilize transition states | |
| |
| |
| Enzymes use chemical tools to perform a reaction | |
| |
| |
| Regulation | |
| |
| |
| Protein activity may be regulated through allosteric motions | |
| |
| |
| Protein action may be regulated by covalent modification | |
| |
| |
| Biomaterials | |
| |
| |
| Helical assembly of subunits forms filaments and fibrils | |
| |
| |
| Microscale infrastructure is built from fibrous components | |
| |
| |
| Minerals are combined with biomaterials for special applications | |
| |
| |
| Elastic proteins use disordered chains | |
| |
| |
| Cells make specific and general adhesives | |
| |
| |
| Biomolecular Motors | |
| |
| |
| ATP powers linear motors | |
| |
| |
| ATP synthase and flagellar motors are rotary motors | |
| |
| |
| Brownian ratchets rectify random thermal motions | |
| |
| |
| Traffic Across Membranes | |
| |
| |
| Potassium channels use a selectivity filter | |
| |
| |
| ABC transporters use a flip-flop mechanism | |
| |
| |
| Bacteriorhodopsin uses light to pump protons | |
| |
| |
| Biomolecular Sensing | |
| |
| |
| Smell and taste detect specific molecules | |
| |
| |
| Light is sensed by monitoring light-sensitive motions in retinal | |
| |
| |
| Mechanosensory receptors sense motion across a membrane | |
| |
| |
| Bacteria sense chemical gradients by rectification of random motion | |
| |
| |
| Self-Replication | |
| |
| |
| Cells are autonomous self-replicators | |
| |
| |
| The basic design of cells is shaped by the processes of evolution | |
| |
| |
| Machine-Phase Bionanotechnology | |
| |
| |
| Muscle sarcomeres | |
| |
| |
| Nerves | |
| |
| |
| |
| Bionanotechnology Today | |
| |
| |
| Basic Capabilities | |
| |
| |
| Natural proteins may be simplified | |
| |
| |
| Proteins are being designed from scratch | |
| |
| |
| Proteins may be constructed with nonnatural amino acids | |
| |
| |
| Peptide nucleic acids provide a stable alternative to DNA and RNA | |
| |
| |
| Nanomedicine Today | |
| |
| |
| Computer-aided drug design has produced effective anti-AIDS drugs | |
| |
| |
| Immunotoxins are targeted cell killers | |
| |
| |
| Drugs may be delivered with liposomes | |
| |
| |
| Artificial blood saves lives | |
| |
| |
| Gene therapy will correct genetic defects | |
| |
| |
| General medicine is changing into personalized medicine | |
| |
| |
| Self-Assembly at Many Scales | |
| |
| |
| Self-assembling DNA scaffolds have been constructed | |
| |
| |
| Cyclic peptides form nanotubes | |
| |
| |
| Fusion proteins self-assemble into extended structures | |
| |
| |
| Small organic molecules self-assemble into large structures | |
| |
| |
| Larger objects may be self-assembled | |
| |
| |
| Harnessing Molecular Motors | |
| |
| |
| ATP synthase is used as a rotary motor | |
| |
| |
| Molecular machines have been built of DNA | |
| |
| |
| DNA Computers | |
| |
| |
| The first DNA computer solved a traveling salesman problem | |
| |
| |
| Satisfiability problems are solved by DNA computing | |
| |
| |
| A Turing machine has been built with DNA | |
| |
| |
| Molecular Design Using Biological Selection | |
| |
| |
| Antibodies may be turned into enzymes | |
| |
| |
| Peptides may be screened with bacteriophage display libraries | |
| |
| |
| Nucleic acids with novel functions may be selected | |
| |
| |
| Functional bionanomachines are surprisingly common | |
| |
| |
| Artificial Life | |
| |
| |
| Artificial protocells reproduce by budding | |
| |
| |
| Self-replicating molecules are an elusive goal | |
| |
| |
| ATP is made with an artificial photosynthetic liposome | |
| |
| |
| Poliovirus has been created with only a genetic blueprint | |
| |
| |
| Hybrid Materials | |
| |
| |
| Nanoscale conductive metal wires may be constructed with DNA | |
| |
| |
| Patterned aggregates of gold nanoparticles are formed with DNA | |
| |
| |
| DNA flexes a sensitive mechanical lever | |
| |
| |
| Researchers are harnessing biomineralization | |
| |
| |
| Biosensors | |
| |
| |
| Antibodies are widely used as biosensors | |
| |
| |
| Biosensors detect glucose levels for management of diabetes | |
| |
| |
| Engineered nanopores detect specific DNA sequences | |
| |
| |
| |
| The Future of Bionanotechnology | |
| |
| |
| A Timetable for Bionanotechnology | |
| |
| |
| Lessons for Molecular Nanotechnology | |
| |
| |
| Three Case Studies | |
| |
| |
| Case study: Nanotube synthase | |
| |
| |
| Case study: A general nanoscale assembler | |
| |
| |
| Case study: Nanosurveillance | |
| |
| |
| Ethical Considerations | |
| |
| |
| Respect for life | |
| |
| |
| Potential dangers | |
| |
| |
| Final thoughts | |
| |
| |
| Literature | |
| |
| |
| Sources | |
| |
| |
| Index | |