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Chemistry and Biology of Non-canonical Nucleic Acids

1. Aufl.

von: Naoki Sugimoto
124,99 €
Verlag:	Wiley-VCH
Format:	EPUB
Veröffentl.:	06.04.2021
ISBN/EAN:	9783527817863
Sprache:	englisch
Anzahl Seiten:	288

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Titelbeschreibung

Discover the fundamentals and intricacies of a subject at the interface of chemistry and biology with this authoritative resource Chemistry and Biology of Non-canonical Nucleic Acids delivers a comprehensive treatment of the chemistry and biology of non-canonical nucleic acids, including their history, structures, stabilities, properties, and functions. You'll learn about the role of these vital compounds in transcription, translation, regulation, telomeres, helicases, cancers, neurodegenerative diseases, therapeutic applications, nanotechnology, and more. An ideal resource for graduate students, researchers in physical, organic, analytical, and inorganic chemistry will learn about uncommon nucleic acids, become the common non-canonical nucleic acids that fascinate and engage academics and professionals in private industry. Split into 15 chapters covering a wide range of aspects of non-canonical nucleic acids, the book explains why these compounds exist at the forefront of a new research revolution at the intersection of chemistry and biology. Chemistry and Biology of Non-canonical Nucleic Acids also covers a broad range of topics critical to understanding these versatile and omnipresent chemicals, including: * A discussion of the dynamic regulation of biosystems by nucleic acids with non-canonical structures * The role played by nucleic acid structures in neurodegenerative diseases and various cancers * An exploration of the future outlook for the chemistry and biology of non-canonical nucleic acids * An introduction to the history of canonical and non-canonical structures of nucleic acids * An analysis of the physicochemical properties of non-canonical nucleic acids Perfect for biochemists, materials scientists, and bioengineers, Chemistry and Biology of Non-canonical Nucleic Acids will also earn a place in the libraries of medicinal and pharmaceutical chemists who wish to improve their understanding of life processes and the role that non-canonical nucleic acids play in them.

Inhaltsverzeichnis

Preface xi 1 History for Canonical and Non-canonical Structures of Nucleic Acids 1 1.1 Introduction 1 1.2 History of Duplex 1 1.3 Non-Watson–Crick Base Pair 5 1.4 Nucleic Acid Structures Including Non-Watson–Crick Base Pairs 7 1.5 Perspective of the Research for Non-canonical Nucleic Acid Structures 8 1.6 Conclusion and Perspective 9 References 9 2 Structures of Nucleic Acids Now 11 2.1 Introduction 11 2.2 Unusual Base Pairs in a Duplex 11 2.2.1 Hoogsteen Base Pair 13 2.2.2 Purine–Pyrimidine Mismatches 13 2.2.3 Purine–Purine Mismatches 14 2.2.4 Pyrimidine–Pyrimidine Mismatches 16 2.3 Non-canonical Backbone Shapes in DNA Duplex 17 2.4 Branched DNA with Junction 19 2.5 Multi-stranded DNA Helices 20 2.6 Structures in RNA 20 2.6.1 Basic Structure Distinctions of RNA 20 2.6.2 Elements in RNA Secondary Structures 21 2.6.2.1 Hairpin Loop 22 2.6.2.2 Bulge Loop 22 2.6.2.3 Internal Loop 23 2.6.3 Elements in Tertiary Interactions of RNA 24 2.6.3.1 A-Minor Interactions 25 2.6.3.2 Ribose Zipper 25 2.6.3.3 T-Loop Motif 26 2.6.3.4 Kissing-Loop Interaction 26 2.6.3.5 GNRA Tetraloop Receptor Interaction 27 2.6.3.6 Pseudoknot Crosslinking Distant Stem Regions 29 2.7 Conclusion 29 References 30 3 Stability of Non-canonical Nucleic Acids 33 3.1 Introduction 33 3.2 Factors Influencing Stabilities of the Canonical Duplexes 34 3.2.1 Hydrogen Bond Formations 34 3.2.2 Stacking Interactions 35 3.2.3 Conformational Entropy 35 3.3 Thermodynamic Analysis for the Formation of Duplex 36 3.4 Factors Influencing Stabilities of the Non-canonical Nucleic Acids 39 3.4.1 Factors Influencing Stability of Triplexes 39 3.4.2 Factors Influencing Stability of Quadruplex 42 3.4.2.1 G-Quadruplexes 42 3.4.2.2 i-Motif 44 3.5 Thermodynamic Analysis for the Non-canonical Nucleic Acids 45 3.5.1 Thermodynamic Analysis for the Intramolecular Triplex and Tetraplex 45 3.5.2 Thermodynamic Analysis for the Intermolecular Triplex 45 3.5.3 Thermodynamic Analysis for the Tetraplex 46 3.6 Conclusion 48 References 49 4 Physicochemical Properties of Non-canonical Nucleic Acids 51 4.1 Introduction 51 4.2 Spectroscopic Properties of Non-canonical Nucleic Acids 51 4.2.1 Effect of Non-canonical Structure on UV Absorption 51 4.2.2 Circular Dichroism of Non-canonical Nucleic Acids 53 4.2.3 NMR Spectroscopy 56 4.2.4 Other Spectroscopic Characteristics of Non-canonical Nucleic Acids 57 4.3 Chemical Interactions on Non-canonical Nucleic Acids 59 4.3.1 Hydration 59 4.3.2 Cation Binding 61 4.3.3 pH Effect 62 4.3.4 Chemical Modification 63 4.4 Chemical Platform on the Non-canonical Structures 64 4.4.1 Specificity of a Ligand to Non-canonical Structures 64 4.4.2 Fluorescence Platform of Non-canonical Structures 67 4.4.3 Interface Between Proteins and Nucleic Acids 68 4.5 Physicochemical Property of Non-canonical Nucleic Acids in Cell 69 4.5.1 Molecular Crowding Condition that Reflects Cellular Environments 69 4.5.2 Effects of Crowding Reagents on Non-canonical Nucleic Acid Structures 70 4.5.3 Quantification of Physical Properties of Non-canonical Structures in Crowding Condition 71 4.5.4 Non-canonical Structures Under Mimicking Organelle Environment 72 4.5.5 Insight for the Formation of Non-canonical Nucleic Acids in Cells 73 4.6 Conclusion 75 References 75 5 Telomere 79 5.1 Introduction 79 5.2 Structural Properties of Telomere 79 5.2.1 Structures of Telomere 79 5.2.2 Structural Properties of Human Telomeric G4s 81 5.2.3 Structure of Repeats of Human Telomeric G4s 84 5.3 Biological Relevance of Telomere G4 86 5.3.1 Telomerase Activity 86 5.3.2 Telomerase Repeated Amplification Protocol (TRAP) Assay 89 5.3.3 Alternative Lengthening of Telomere (ALT) Mechanism 89 5.4 Other Non-canonical Structures Related to Telomere Region 89 5.4.1 Telomere i-Motif 89 5.4.2 Telomere RNA 90 5.5 Conclusion 92 References 93 6 Transcription 95 6.1 Introduction 95 6.2 Transcription Process 96 6.2.1 Transcription Initiation 96 6.2.2 Transcription Elongation 98 6.2.3 Transcription Termination 99 6.3 Transcription Process Perturbed by Certain Sequences of DNA and RNA 101 6.4 Transcription Process Perturbed by Non-canonical Structures of DNA and RNA 103 6.5 Conclusion 110 References 110 7 Translation 113 7.1 Introduction 113 7.2 RNAs Involved in Translation Machinery 113 7.3 General Process of Translation 117 7.3.1 Translation Initiation 117 7.3.2 Translation Elongation 119 7.3.3 Translation Termination 119 7.4 RNA Structures Affecting Translation Reaction 121 7.4.1 Modulation of Translation Initiation in Prokaryotes 121 7.4.2 Modulation of Translation Initiation in Eukaryotes 123 7.4.3 RNA Structures Affecting Translation Elongation 126 7.4.4 RNA Structures Affecting Translation Termination 130 7.5 Conclusion 133 References 134 8 Replication 137 8.1 Introduction 137 8.2 Replication Machineries 137 8.3 Replication Initiation 138 8.3.1 Mechanism of Activation of Replication Origins 138 8.3.2 Activation Control of Origins by G4s 139 8.3.3 Control of Timing of Replication Initiation by G4s 142 8.4 DNA Strand Elongation 142 8.4.1 Mechanism of DNA Strand Elongation 142 8.4.2 Impact of G4 and i-Motif Formations on DNA Strand Synthesis 144 8.4.3 Relationship Between G4 and Epigenetic Modification 145 8.4.4 Expansion and Contraction of Replicating Strand Induced by Hairpin Structures 147 8.5 Termination of Replication 148 8.6 Chemistry of the Replication and Its Regulation 148 8.6.1 Cellular Environments 148 8.6.2 Control of Replication by Chemical Compounds 150 8.7 Conclusion 151 References 152 9 Helicase 155 9.1 Introduction 155 9.2 Function and Structure of Helicases 155 9.3 Unwinding of Non-canonical DNA Structures by Helicases 158 9.4 G4 Helicases in Gene Expressions 162 9.5 G4 Helicases in Replication 163 9.6 G4 Helicases in Telomere Maintenance 164 9.7 Relation to Diseases by Loss of G4 Helicases 165 9.8 Insight into Specific Properties of Activities of G4 Helicase Under Cellular Conditions 165 9.9 Conclusion 167 References 167 10 Dynamic Regulation of Biosystems by Nucleic Acids with Non-canonical Structures 171 10.1 Introduction 171 10.2 Time Scale of Biological Reactions 171 10.2.1 Cell Cycle 172 10.2.2 Central Dogma 172 10.2.3 Dynamic Structures of Nucleic Acids 174 10.3 Processes in the Central Dogma Affected by Dynamics of Nucleic Acid Structures 176 10.3.1 Epigenetic Regulation Caused by Chemical Modification of DNA 176 10.3.2 Co-transcriptional Formation of Metastable RNA Structures 178 10.3.3 Co-transcriptional Translation and Transcription Attenuation 180 10.3.4 Co-transcriptional Ligand Binding and Gene Regulation 181 10.3.5 Translation Elongation and Co-translational Protein Folding 183 10.4 Conclusion 184 References 185 11 Cancer and Nucleic Acid Structures 189 11.1 Introduction 189 11.2 Detail Mechanism of Cancer 189 11.2.1 Cancer Incidence 189 11.2.2 The Relationship Between Genes and Cancer 192 11.3 Non-canonical Structures of Nucleic Acids in Cancer Cells 192 11.3.1 Structural Characteristics of Nucleic Acids in Cancer Cells 192 11.3.2 Non-canonical Structures Perturb Gene Expression of Cancer-Related Genes 195 11.4 Roles of Non-canonical Structures of Nucleic Acids in Cancer Cells 197 11.4.1 Monitoring of Non-canonical Structures in Cancer Cells 197 11.4.2 Regulation of Gene Expressions by the Non-canonical Structures in Cancer Cells 198 11.5 Conclusion 199 References 199 12 Neurodegenerative Diseases and Nucleic Acid Structures 203 12.1 Introduction 203 12.2 Protein Aggregation-Induced Neurodegenerative Diseases 203 12.3 DNA Shows Key Role for Neurodegenerative Diseases 205 12.4 RNA Toxic Plays a Key Role for Neurological Diseases 210 12.5 Conclusion 212 References 212 13 Therapeutic Applications 215 13.1 Introduction 215 13.2 Oligonucleotide Therapeutics 216 13.2.1 Antisense Oligonucleotide 216 13.2.2 Functions of Antisense Oligonucleotide Therapeutics 217 13.2.3 Chemical Modifications in Therapeutic Oligonucleotides 220 13.2.3.1 Backbone Modified Oligonucleotides 220 13.2.3.2 Ribose Modified Oligonucleotides 221 13.2.3.3 Oligonucleotides with Unnatural Backbone 221 13.2.4 Oligonucleotide Therapeutics Other Than Antisense Oligonucleotide 223 13.2.4.1 Oligonucleotide Therapeutics Functioning Through RNA Interference 224 13.2.4.2 Oligonucleotide Therapeutics Functioning Through Binding to Protein 224 13.3 Non-canonical Nucleic Acid Structures as Therapeutic Targets 224 13.3.1 Traditional Antibiotics Targeting Structured Region of RNAs 225 13.3.2 Strategies for Constructing Therapeutic Materials Targeting Structured Nucleic Acids 226 13.4 Non-canonical Nucleic Acid Materials for Inducing Non-canonical Structures 230 13.5 Conclusion 231 References 232 14 Materials Science and Nanotechnology of Nucleic Acids 235 14.1 Introduction 235 14.2 Non-canonical Structure-Based Nanomaterials Resembling Protein Functions 235 14.2.1 Aptamer 235 14.2.2 DNAzyme 238 14.2.3 Ion Channel 240 14.3 Protein Engineering Using G4-Binding Protein 240 14.4 Regulation of Gene Expression by G4-Inducing Materials 242 14.5 Environmental Sensing 246 14.5.1 Sensing Temperature in Cells 246 14.5.2 Sensing pH in Cells 248 14.5.3 Sensing K+ Ion in Cells 248 14.5.4 Sensing Crowding Condition in Cells 249 14.6 Conclusion 250 References 250 15 Future Outlook for Chemistry and Biology of Non-canonical Nucleic Acids 253 15.1 Introduction 253 15.2 Exploring Potential: Properties of Non-canonical Structures in Unusual Media 253 15.3 Systemizing Properties: Prediction of the Formation of Non-canonical Nucleic Acids Structures 259 15.4 Advancing Technology: Applications of Non-canonical Structures Taking Concurrent Reactions into Account 262 15.4.1 Co-transcriptional Dynamics of G-Quadruplex 263 15.4.2 Co-transcriptional Functionalization of Riboswitch-Like Sensor 263 15.4.3 Co-transcriptional RNA Capturing for Selection of Functional RNAs 266 15.5 Conclusion 267 References 268 Index 271

Autorenportrait

Naoki Sugimoto, PhD, is Professor at Konan University in Japan and Director of the Frontier Institute for Biomolecular Engineering Research. He received his PhD from Kyoto University, Japan in 1985. He has published over 500 scientific papers and books and is a member of the Editorial Board of Nucleic Acids Research and Scientific Reports. He is the First President of the Japan Society of Nucleic Acids Chemistry.

Back cover copy

Discover the fundamentals and intricacies of a subject at the interface of chemistry and biology with this authoritative resource Chemistry and Biology of Non-canonical Nucleic Acids delivers a comprehensive treatment of the chemistry and biology of non-canonical nucleic acids, including their history, structures, stabilities, properties, and functions. You'll learn about the role of these vital compounds in transcription, translation, regulation, telomeres, helicases, cancers, neurodegenerative diseases, therapeutic applications, nanotechnology, and more. An ideal resource for graduate students, researchers in physical, organic, analytical, and inorganic chemistry will learn about uncommon nucleic acids, become the common non-canonical nucleic acids that fascinate and engage academics and professionals in private industry. Split into 15 chapters covering a wide range of aspects of non-canonical nucleic acids, the book explains why these compounds exist at the forefront of a new research revolution at the intersection of chemistry and biology. Chemistry and Biology of Non-canonical Nucleic Acids also covers a broad range of topics critical to understanding these versatile and omnipresent chemicals, including: <ul> <li>A discussion of the dynamic regulation of biosystems by nucleic acids with non-canonical structures</li> <li>The role played by nucleic acid structures in neurodegenerative diseases and various cancers</li> <li>An exploration of the future outlook for the chemistry and biology of non-canonical nucleic acids</li> <li>An introduction to the history of canonical and non-canonical structures of nucleic acids</li> <li>An analysis of the physicochemical properties of non-canonical nucleic acids</li> </ul> Perfect for biochemists, materials scientists, and bioengineers, Chemistry and Biology of Non-canonical Nucleic Acids will also earn a place in the libraries of medicinal and pharmaceutical chemists who wish to improve their understanding of life processes and the role that non-canonical nucleic acids play in them.