Handbook of Chemical Biology of Nucleic Acids

ISBN-13: 9789811997754 / Angielski / Twarda / 2023 / 2630 str.

Naoki Sugimoto

Opis

This handbook is the first to comprehensively cover nucleic acids from fundamentals to recent advances and applications. It is divided into 10 sections where authors present not only basic knowledge but also recent research. Each section consists of extensive review chapters covering the chemistry, biology, and biophysics of nucleic acids as well as their applications in molecular medicine, biotechnology and nanotechnology. All sections within this book will be: Physical Chemistry of Nucleic Acids (Section Editor: Prof. Roland Winter), Structural Chemistry of Nucleic Acids (Section Editor: Prof. Janez Plavec), Organic Chemistry of Nucleic Acids (Section Editor: Prof. Piet Herdewijin), Ligand Chemistry of Nucleic Acids (Section Editor: Prof. Marie-Paule Teulade-Fichou), Nucleic Acids and Gene Expression (Section Editor: Prof. Cynthia Burrows), Analytical Methods and Applications of Nucleic Acids (Section Editor: Prof. Chaoyong Yang), Nanotechnology and Nanomaterial Biology of Nucleic Acids (Section Editor: Prof. Zhen Xi), Nucleic Acids Therapeutics (Section Editor: Prof. Katherine Seley-Radtke), Biotechnology and Synthetic Biology of Nucleic Acids (Section Editor: Prof. Eriks Rozners), Functional Nucleic Acids (Section Editor: Prof. Keith R. Fox).The handbook is edited by outstanding leaders with contributions written by international renowned experts. It is a valuable resource not only for graduate students but also for researchers working in areas related to nucleic acids who would like to learn more about their important role and potential applications. 

Spis treści

Section I. Physical Chemistry of Nucleic Acids

1. High-Pressure Single-Molecule Studies on Non-canonical Nucleic Acids and Their Interactions 2. Stability Prediction of Canonical and Noncanonical Structures of Nucleic Acids 3. The Effect of Pressure on the Conformational Stability of DNA 4. Quadruplexes are everywhere…on the other strand too: the i-motif 5. i-Motif Nucleic Acids

Section II. Structural Chemistry of Nucleic Acids

6. NMR Study on Nucleic Acids 7. Z-DNA 8. Structures of DNA G-quadruplexes and Their Drug Interactions 9. In cell 19F NMR for G-quadruplex 10. Structures and Catalytic Activities of Complexes between Heme and DNA 11. Studying nucleic acid-ligand binding by X-ray crystallography 12. Predicting the 3D structure of RNA from sequence

Section III. Organic Chemistry of Nucleic Acids

13. XNA in Synthetic Biology 14. The Effects of FANA Modifications on Non-Canonical Nucleic Acid Structures 15. Isomorphic Fluorescent Nucleoside Analogs 16. Bridged Nucleic Acids for Therapeutic Oligonucleotides 17. Mesyl Phosphoramidate Oligonucleotides: A New Promising Type of Antisense Agents 18. Chemistry of Cyclic Dinucleotides and Analogs 19. Labeling and Detection of Modified Nucleic Acids 20. Cross linking Duplex of Nucleic Acids with Modified Oligonucleotides 21. Enzymatic Synthesis of Base-Modified Nucleic Acids 22. Charge Transfer in Natural and Artificial Nucleic Acids 23. Nucleic Acid Aptamers: From Basic Research to Clinical Applications 24. LNA in Medical Biology

Section IV. Ligand Chemistry of Nucleic Acids

25. Targeting Quadruplex Nucleic Acids: The Bisquinolinium Saga 26. Compound Shape and Substituent Effects in DNA Minor Groove Interactions 27. Macrocyclic G-Quadruplex Ligands of Telomestatin Analogs 28. Cyclic Naphthalene Diimide Derivatives as Novel DNA Ligands 29. Imaging study of small molecules to G-quadruplexes in cells 30. Bivalent Nucleic Acid Ligands 31. DNA/Metal Cluster–Based Nano-Lantern 32. Interaction of Poly (ethylene glycol)-b-poly-L-lysine Copolymers with DNA Structures: A Thermodynamic Investigation 33. Chemical tools to target non-coding RNAs 34. Targeting DNA junctions with small molecules for therapeutic applications in oncology

Section V. Nucleic Acids and Gene Expression

35. DNA Damage and Repair in G-quadruplexes Impact Gene Expression 36. DNA Structural Elements as Potential Targets for Regulation of Gene Expression 37. Effects of molecular crowding on structures and functions of nucleic acids 38. Structure-guided Optimization of siRNA and anti-miRNA Properties 39. Tools for understanding the chemical biology of the tRNA epitranscriptome 40. Sulfur and Selenium modified bacterial tRNAs 41. Chemical-assisted Epigenome Sequencing 42. Epitranscriptomics 43. Telomeres and Telomerase 44. Genetic Alphabet Expansion of Nucleic Acids 45. Unnatural Base Pairs to Expand the Genetic Alphabet and Code 46. OGG1 at the crossroads between repair and transcriptional regulation 47. Phosphorothioate Nucleic Acids - Artificial Modification Envisaged by Nature

Section VI. Analytical Methods and Applications of Nucleic Acids

48. Aptamer Molecular Evolution for Liquid Biopsy 49. Single-molecule DNA Visualization 50. Tissue-specific Drug Delivery Platforms Based on DNA Nanoparticles 51. Nanobiodevice for Nucleic Acid Sensing 52. Functional Nucleic Acid-Protein Complexes: Application to Fluorescent Ribonucleopeptide Sensors 53. Detection Systems Using the Ternary Complex Formation of Nucleic Acids 54. Nucleic Acid Conjugates for Biosensing – Design, Preparation, and Application 55. Molecular Beacons With and Without Quenchers

Section VII. Nanotechnology and Nanomaterial Biology of Nucleic Acids

56. Gene nanovector for genome therapy 57. The Frame-Guided Assembly of Nucleic Acids 58. Graphene Oxide and Nucleic Acids 59. Carbon Nanotubes and Nucleic Acids 60. Artificial genetic switches and DNA origami: Current landscape and prospects as designer therapeutics and visualization tools 61. Functional Engineering of Synthetic RNA Through Circularization 62. Stimuli-Responsive DNA Nanostructures for Biomedical Applications 63. Gene-Like Precise Construction of Functional DNA Materials 64. Design and Self-Assembly of Therapeutic Nucleic Acid Nanoparticles (NANPs) with Controlled Immunological Properties 65. Nanomaterials for therapeutic nucleic acids delivery

Section VIII. Nucleic Acids Therapeutics

66. Flex-Nucleosides – A Strategic Approach to Antiviral Therapeutics 67. Small Molecules Targeting Repeat Sequences Causing Neurological Disorders 68. Targeted Cancer Therapy: KRAS-Specific Treatments for Pancreatic Cancer 69. Functional XNA and Biomedical Application 70. Controlled Intracellular Trafficking and Gene Silencing by Oligonucleotide-Signal Peptide Conjugates 71. First and second generation nucleoside triphosphate prodrugs: TriPPPro-compounds for antiviral chemotherapy 72. New Molecular Technologies for Oligonucleotide Therapeutics-1: Properties and Synthesis of Boranophosphate DNAs 73. Extracellular Vesicles-mediated CRISPR/Cas Delivery: Their Applications in Molecular Imaging and Precision Biomedicine 74. Advancing XNAzymes as Nucleic Acid Therapeutics 75. New Molecular Technologies for Oligonucleotide Therapeutics-2: A-type nucleic acid duplex-specific binding oligocationic molecules for oligonucleotide therapeutics

Section IX. Biotechnology and Synthetic Biology of Nucleic Acids

76. Amides and Other Non-Ionic Backbone Modifications in RNA 77. Expanding the RNP World in Cells 78. Design and Biological Application of RTK Agonist Aptamers 79. G-quadruplex-based Aptamers in therapeutic applications 80. Nucleic Acids in Green Chemistry 81. G-Quadruplexes in Human Viruses: A Promising Route to Innovative Antiviral Therapies 82. Non-chromatographic purification of synthetic RNA 83. Genome Editing using CRISPR 84. Biomaterials Based on DNA Conjugates and Assemblies 85. G-quadruplex resolving by specific helicases 86. Binding and modulation of G-quadruplex DNA and RNA structures by proteins

Section X. Functional Nucleic Acids

87. Targeting Triple Helix DNA 88. Metal Ion-induced Change of Stability of DNA Duplex 89. Liquid Phase Separation and Nucleic Acids 90. Functions and Applications of Riboswitches 91. PNA and Quadruplex 92. Peptide Ribonucleic Acid (PRNA)-Programmed Assemblies 93. Structure and Function of Aptamer and Catalytic DNA 94. Origin and Evolution of RNA 95. Targeting RNA with Small Molecules

O autorze

Naoki Sugimoto received Ph.D. degree in 1985 from Kyoto University, Japan. After postdoctoral work at University of Rochester, USA, he joined Konan University, Kobe, Japan in 1988 and is a full professor since 1994. From 2003, he also holds a director of Frontier Institute for Biomolecular Engineering Research (FIBER) at Konan University. He is a member of the Editorial Board of Nucleic Acids Research from 2007 and Scientific Reports from 2015 to the present, was the first President of the Japan Society of Nucleic Acids Chemistry (JSNAC) from 2017 to 2020 and is now the Fellow of JSNAC. He received the Dr. Masao Horiba’s Award in 2004, Distinguished Scientist Award from ICA (International Copper Association), USA in 2005, Hyogo Science Award from Hyogo prefecture, Japan in 2006, the Chemical Society Japan (CSJ) Award for Creative Work in 2007, JSCC Contribution Award, Japan Society of Coordination Chemistry (JSCC) in 2014, The Iue Cultural Award in Science and Technology in 2015, The Imbach-Townsend Award, IS3NA in 2018, The 72th CSJ Award (Top Award in CSJ) in 2019, and so on. His research interests focus on biophysical chemistry, biomaterials, bionano-engineering, molecular design, biofunctional chemistry, biotechnology, and therapeutic application of nucleic acids.

Blurb

This handbook is the first to comprehensively cover nucleic acids from fundamentals to recent advances and applications. It is divided into 10 sections where authors present not only basic knowledge but also recent research. Each section consists of extensive review chapters covering the chemistry, biology, and biophysics of nucleic acids as well as their applications in molecular medicine, biotechnology and nanotechnology. All sections within this book are: Physical Chemistry of Nucleic Acids (Section Editor: Prof. Roland Winter), Structural Chemistry of Nucleic Acids (Section Editor: Prof. Janez Plavec), Organic Chemistry of Nucleic Acids (Section Editor: Prof. Piet Herdewijin), Ligand Chemistry of Nucleic Acids (Section Editor: Prof. Marie-Paule Teulade-Fichou), Nucleic Acids and Gene Expression (Section Editor: Prof. Cynthia Burrows), Analytical Methods and Applications of Nucleic Acids (Section Editor: Prof. Chaoyong Yang), Nanotechnology and Nanomaterial Biology of Nucleic Acids (Section Editor: Prof. Zhen Xi), Nucleic Acids Therapeutics (Section Editor: Prof. Katherine Seley-Radtke), Biotechnology and Synthetic Biology of Nucleic Acids (Section Editor: Prof. Eriks Rozners), Functional Nucleic Acids (Section Editor: Prof. Keith R. Fox).

The handbook is edited by outstanding leaders with contributions written by international renowned experts. It is a valuable resource not only for researchers but also graduate students working in areas related to nucleic acids who would like to learn more about their important role and potential applications.