Foreword / Dr Hamaguchi |
Preface / Dr Noyori |
Control of DNA Packaging by Block Catiomers for Systemic Gene Delivery System / Kensuke Osada1: |
Introduction / 1.1: |
Packaging of pDNA by Block Catiomers / 1.2: |
Rod-Shaped Packaging of pDNA / 1.2.1: |
Rod Shape or Globular Shape / 1.2.2: |
Polyplex Micelles as a Systemic Gene Delivery System / 1.3: |
Stable Encapsulation of pDNA Within Polyplex Micelles for Systemic Delivery / 1.3.1: |
Polyplex Micelles for Efficient Cellular Entry / 1.3.2: |
Polyplex Micelles for Safe Endosome Escape / 1.3.3: |
Polyplex Micelles for Nuclear Translocation / 1.3.4: |
Polyplex Micelles for Efficient Transcription / 1.3.5: |
Design Criteria of Block Catiomers Toward Systemic Gene Therapy / 1.4: |
Rod Shape or Toroid Shape / 1.5: |
Summary / 1.6: |
References |
Manipulation of Molecular Architecture with DNA / Akinori Kuzuya2: |
Molecular Structure of DNA / 2.1: |
Immobile DNA Junctions / 2.3: |
Topologically Unique DNA Molecules / 2.4: |
DNA Tiles and Their Assemblies / 2.5: |
DNA Origami / 2.6: |
DNA Origami as a Molecular Peg Board / 2.7: |
Molecular Machines Made of DNA Origami / 2.8: |
DNA Origami Pinching Devices / 2.9: |
Novel Design Principles / 2.10: |
DNA-PAINT: An Application of DNA Devices / 2.11: |
Prospects / 2.12: |
Chemical Assembly Lines for Skeletally Diverse Indole Alkaloids / Hiroki Oguri3: |
Macmillan's Collective Total Synthesis by Means of Organocascade Catalysis / 3.1: |
Systematic Synthesis of Indole Alkaloids Employing Cyclopentene Intermediates by the Zhu Group / 3.3: |
Biogenetically Inspired Synthesis Employing a Multipotent Intermediate by the Oguri Group / 3.4: |
Molecular Technology for Injured Brain Regeneration / Itsuki Ajioka4: |
Biology of Angiogenesis / 4.1: |
Angiogenesis for Injured Brain Regeneration / 4.3: |
Molecular Technology to Promote Angiogenesis / 4.4: |
Biology of Cell Cycle / 4.5: |
Biology of Neurogenesis / 4.6: |
Molecular Technology to Promote Neuron Regeneration / 4.7: |
Conclusion / 4.8: |
Engineering the Ribosomal Translation System to Introduce Non-proteinogenic Amino Acids into Peptides / Takayuki Katoh5: |
Decoding the Genetic Code / 5.1: |
Aminoacylation of tRNA by Aminoacyl-tRNA Synthetases / 5.3: |
Methods for Preparing Noncanonical Aminoacyl-tRNAs / 5.4: |
Ligation of Aminoacyl-pdCpA Dinucleotide with tRNA Lacking the 3'-Terminal CA / 5.4.1: |
Post-aminoacylation Modification of Aminoacyl-tRNA / 5.4.2: |
Misacylation of Non-proteinogenic Amino Acids by ARSs / 5.4.3: |
Flexizyme, an Aminoacylation Ribozyme / 5.4.4: |
Methods for Assigning Non-proteinogenic Amino Acids to the Genetic Code / 5.5: |
The Nonsense Codon Method / 5.5.1: |
Genetic Code Reprogramming / 5.5.2: |
The Four-base Codon Method / 5.5.3: |
The Nonstandard Base Method / 5.5.4: |
Limitation of the Incorporation of Noncanonical Amino Acids: Substrate Scope / 5.6: |
Improvement of the Substrate Tolerance of Ribosomal Translation / 5.7: |
Ribosomally Synthesized Noncanonical Peptides as Drug Discovery Platforms / 5.8: |
Summary and Outlook / 5.9: |
Development of Functional Nanoparticles and Their Systems Capable of Accumulating to Tumors / Sotoru Karasawa6: |
Accumulation Based on Aberrant Morphology and Size / 6.1: |
Accumulation Based on Aberrant pH Microenvironment / 6.3: |
Accumulation Based on Temperature of Tumor Microenvironment / 6.4: |
Perspective / 6.5: |
Glycan Molecular Technology for Highly Selective In Vivo Recognition / Katsunori Tanaka7: |
Molecular Technology for Chemical Glycan Conjugation / 7.1: |
Conjugation to Lysine / 7.1.1: |
Conjugation to Cysteine / 7.1.2: |
Bioorthogonal Conjugation / 7.1.3: |
Enzymatic Glycosylation / 7.1.4: |
In Vivo Kinetic Studies of Monosaccharide-Modified Proteins / 7.2: |
Dissection-Based Kinetic and Bio distribution Studies: Effects of Protein Modification by Galactose, Mannose, and Fucose / 7.2.1: |
Noninvasive imaging of In Vivo Kinetic and Organ-Specific Accumulation of Monosaccharide-Modified Proteins / 7.2.2: |
In Vivo Kinetic Studies of Oligosaccharide-Modified Proteins / 7.3: |
In Vivo Kinetics of Proteins Modified by a Few Molecules of N-glycans / 7.3.1: |
In Vivo Kinetics of Proteins Modified by Many AT-glycans: Homogeneous N-glycoalbumins / 7.3.2: |
In Vivo Kinetics of Proteins Modified by Many N-glycans: Heterogeneous N-glycoalbumins / 7.3.3: |
Tumor Targeting by JV-glycoalbumins / 7.3.4: |
Glycan Molecular Technology on Live Cells: Tumor Targeting by N-glycas-Engineered Lymphocytes / 7.3.5: |
Glycan Molecular Technology Adapted as Metal Carriers: In Vivo Metal-Catalyzed Reactions within Live Animals / 7.4: |
Concluding Remarks / 7.5: |
Acknowledgments |
Molecular Technology Toward Expansion of Nucleic Acid Functionality / Michiko Kimoto and Kiyohiko Kawai8: |
Molecular Technologies that Enable Genetic Alphabet Expansion / 8.1: |
Nucleotide Modification / 8.2.1: |
Unnatural Base Pairs (UBPs) as Third Base Pairs Toward Expansion of Nucleic Acid Functionality / 8.2.2: |
High-Affinity DNA Aptamer Generation Using the Expanded Genetic Alphabet / 8.2.3: |
Molecular Technologies that Enable Fluorescence Blinking Control / 8.3: |
Single Molecule Detection Based on Blinking Observations / 8.3.1: |
Blinking Kinetics / 8.3.2: |
Control of Fluorescence Blinking by DNA Structure / 8.3.3: |
Triplet Blinking / 8.3.3.1: |
Redox Blinking / 8.3.3.2: |
Isomerization Blinking / 8.3.3.3: |
Conclusions / 8.4: |
Molecular Technology for Membrane Functionalization / Michio Murakoshi and Takahiro Muraoka9: |
Synthetic Approach for Membrane Functionalization / 9.1: |
Formation of Multipass Transmembrane Structure / 9.2.1: |
Formation of Supramolecular Ion Channels / 9.2.2: |
Demonstration of Ligand-Gated Ion Transportation / 9.2.3: |
Light-Triggered Membrane Budding / 9.2.4: |
Semi-biological Approach for Membrane Functionalization / 9.3: |
Mechanical Analysis of the Transmembrane Structure of Membrane Proteins / 9.3.1: |
Development of the Nanobiodevice Using a Membrane Protein Expressing in the Inner Ear / 9.3.2: |
Improvement of Protein Performance by Genetic Engineering / 9.3.3: |
Molecular Technology for Degradable Synthetic Hydrogels for Biomaterials / Hiroharu Ajiro and Takamasa Sakai10: |
Scope of the Chapter |
Degradation Behavior of Hydrogels / 10.1: |
Polylactide Copolymer / 10.2: |
Trimethylene Carbonate Derivatives / 10.3: |
Polyurethane / 10.4: |
Molecular Technology for Epigenetics Toward Drug Discovery / Takayoshi Suzuki11: |
Epigenetics / 11.1: |
Isozyme-Selective Histone Deacetylase (HDAC) Inhibitors / 11.3: |
Identification of HDAC3-Selective Inhibitors by Click Chemistry Approach / 11.3.1: |
Identification of HDAC8-Selective Inhibitors by Click Chemistry Approach and Structure-Based Drug Design / 11.3.2: |
Identification of HDAC6-Insensitive Inhibitors Using C-H Activation Reaction / 11.3.3: |
Identification of HDAC6-Selective Inhibitors by Substrate-Based Drug Design / 11.3.4: |
Identification of SIRT1-Selective Inhibitors by Target-Guided Synthesis / 11.3.5: |
Identification of SIRT2-Selective Inhibitors by Structure-Based Drug Design and Click Chemistry Approach / 11.3.6: |
Histone Lysine Demethylase (KDM) Inhibitors / 11.4: |
Identification of KDM4C Inhibitors by Structure-Based Drug Design / 11.4.1: |
Identification of KDM5A Inhibitors by Structure-Based Drug Design / 11.4.2: |
Identification of KDM7B Inhibitors by Structure-Based Drug Design / 11.4.3: |
Identification of LSD1 Inhibitors by Target-Guided Synthesis / 11.4.4: |
Small-Molecule-Based Drug Delivery System Using LSD1 and its Inhibitor / 11.4.5: |
Molecular Technology for Highly Efficient Gene Silencing: DNA/RNA Heteroduplex Oligonucleotides / Kotaro Yoshioka and Kazutaka Nishina and Tetsuya Nagata and Takanori Yokota11.5: |
Therapeutic Oligonucleotides / 12.1: |
siRNA / 12.2.1: |
ASO / 12.2.2: |
Chemical Modifications of Therapeutic Oligonucleotide / 12.3: |
Modifications of Inter nucleotide Linkage / 12.3.1: |
Modifications of Sugar Moiety / 12.3.2: |
Ligand Conjugation for DDS / 12.4: |
Development of Ligand Molecules for Therapeutic Oligonucleotides / 12.4.1: |
Vitamin E for Ligand Molecule / 12.4.2: |
siRNA Conjugated with Tocopherol / 12.4.3: |
ASO Conjugated with Tocopherol / 12.4.4: |
DNA/RNA Heteroduplex Oligonucleotide / 12.5: |
Basic Concept of Heteroduplex Oligonucleotide / 12.5.1: |
HDO Conjugated with Tocopherol (Toc-HDO) / 12.5.2: |
Design of Toc-HDO / 12.5.2.1: |
Potency of Toc-HDO / 12.5.2.2: |
Adverse Effect of Toc-HDO / 12.5.2.3: |
Mechanism of Toc-HDO / 12.5.2.4: |
Future Prospects / 12.6: |
Molecular Technology for Highly Sensitive Biomolecular Analysis: Hyperpolarized NMR/MRI Probes / Shinsuke Sando and Hiroshi Nonaka13: |
HyperpoJarization / 13.1: |
Requirements for HP Molecular Imaging Probes / 13.2: |
HP 13C Molecular Probes for Analysis of Enzymatic Activity / 13.3: |
[1-13C] Pyruvate / 13.3.1: |
HP 13C Probes for Analysis of Glycolysis and Tricarboxylic Acid Cycle / 13.3.2: |
¿-Glutamyl-[l-13C]glycine: HP 13C Probe for Analysis of ¿-glutamyl Transpeptidase / 13.3.3: |
[1-13C]Alanine-NH2: HP 13C Probes for Analysis of Aminopeptidase N / 13.3.4: |
HP 13C Molecular Probes for Analysis of the Chemical Environment / 13.4: |
[1-13C] Bicarbonate / 13.4.1: |
[l-13C]Ascorbate and Dehydroascorbate / 13.4.2: |
[13C]Benzoylformic Acid for Sensing H202 / 13.4.3: |
[13C,D3]-p-Anisidine for Sensing of HOCl / 13.4.4: |
[13C,D]EDTA for Sensing of Metal Ions / 13.4.5: |
HP 15N Molecular Probes / 13.5: |
A Strategy for Designing HP Molecular Probes / 13.6: |
Scaffold Structure for Design of 15N HP Probes: [15N,D9]TMPA / 13.6.1: |
[15N,D14]TMPA / 13.6.1.1: |
Scaffold Structure for Designing 13C Hyperpolarized Probes / 13.6.2: |
Molecular Technologies in Life Innovation: Novel Molecular Technologies for Labeling and Functional Control of Proteins Under Live Cell Conditions / Itaru Homochi and Shigeki Kiyonaka and Tomonori Tamura and Ryou Kubota13.7: |
General Introduction / 14.1: |
Ligand-Directed Chemistry for Neurotransmitter Receptor Proteins Under Live Cell Condition and its Application / 14.2: |
Affinity-Guided DMAP Reaction for Analysis of Live Cell Surface Proteins / 14.3: |
Coordination Chemistry-Based Chemogenetic Approach to Switch the Activity of Glutamate Receptors in Live Cells / 14.4: |
Molecular Technologies for Pseudo-natural Peptide Synthesis and Discovery of Bioactive Compounds Against Undruggable Targets / Joseph M. Rogers and Hiroaki Suga14.5: |
Peptides Could Target Undruggable Targets / 15.1: |
Druggable Proteins / 15.2.1: |
Undruggable Proteins / 15.2.2: |
Natural Peptides as Drugs / 15.2.3: |
Modification to Peptides can Improve Their Drug-Like Characteristics / 15.2.4: |
Macro cyclization / 15.2.4.1: |
Amino Acids with Unnatural Side Chains / 15.2.4.2: |
Backbone Modifications Including N-Methylation / 15.2.4.3: |
Cyclosporin - A Membrane-Permeable Anomaly / 15.2.4.4: |
Membrane Permeability Cannot be Calculated from Amino Acid Content / 15.2.4.5: |
Cyclosporin - The Inspiration for the Cyclic Peptide Approach to Undruggable Targets / 15.2.5: |
Molecular Technologies to Discover Functional Peptides / 15.3: |
Ribosomal Synthesis of Peptides / 15.3.1: |
Natural Peptide Synthesis is an Efficient Method to Generate Huge Libraries / 15.3.2: |
Selection Methods / 15.3.3: |
Intracellular Peptide Selection / 15.3.3.1: |
Phage Display / 15.3.3.2: |
A Cell-Free Display, mRNA Display / 15.3.3.3: |
Other Methods of Selection / 15.3.4: |
Molecular Technology for Pseudo-natural Peptide Synthesis and Its Use in Peptide Drug Discovery / 15.4: |
The Need for Pseudo-natural Synthesis - The Limitations of SPPS / 15.4.1: |
Intein Cyclization and SICLOPPS / 15.4.2: |
Post-translation Modification / 15.4.3: |
Genetic Code Expansion / 15.4.4: |
Replacing Amino Acids in Translation / 15.4.5: |
Flexizymes / 15.4.6: |
RaPID System / 15.4.6.2: |
Acknowledgment / 15.5: |
Index |