Chemistry and Biology of Non-canonical Nucleic Acids

Description

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. Cover Title Page Copyright Contents Preface Chapter 1 History for Canonical and Non‐canonical Structures of Nucleic Acids 1.1 Introduction 1.2 History of Duplex 1.3 Non‐Watson–Crick Base Pair 1.4 Nucleic Acid Structures Including Non‐Watson–Crick Base Pairs 1.5 Perspective of the Research for Non‐canonical Nucleic Acid Structures 1.6 Conclusion and Perspective References Chapter 2 Structures of Nucleic Acids Now 2.1 Introduction 2.2 Unusual Base Pairs in a Duplex 2.2.1 Hoogsteen Base Pair 2.2.2 Purine–Pyrimidine Mismatches 2.2.3 Purine–Purine Mismatches 2.2.4 Pyrimidine–Pyrimidine Mismatches 2.3 Non‐canonical Backbone Shapes in DNA Duplex 2.4 Branched DNA with Junction 2.5 Multi‐stranded DNA Helices 2.6 Structures in RNA 2.6.1 Basic Structure Distinctions of RNA 2.6.2 Elements in RNA Secondary Structures 2.6.2.1 Hairpin Loop 2.6.2.2 Bulge Loop 2.6.2.3 Internal Loop 2.6.3 Elements in Tertiary Interactions of RNA 2.6.3.1 A‐Minor Interactions 2.6.3.2 Ribose Zipper 2.6.3.3 T‐Loop Motif 2.6.3.4 Kissing‐Loop Interaction 2.6.3.5 GNRA Tetraloop Receptor Interaction 2.6.3.6 Pseudoknot Crosslinking Distant Stem Regions 2.7 Conclusion References Chapter 3 Stability of Non‐canonical Nucleic Acids 3.1 Introduction 3.2 Factors Influencing Stabilities of the Canonical Duplexes 3.2.1 Hydrogen Bond Formations 3.2.2 Stacking Interactions 3.2.3 Conformational Entropy 3.3 Thermodynamic Analysis for the Formation of Duplex 3.4 Factors Influencing Stabilities of the Non‐canonical Nucleic Acids 3.4.1 Factors Influencing Stability of Triplexes 3.4.2 Factors Influencing Stability of Quadruplex 3.4.2.1 G‐Quadruplexes 3.4.2.2 i‐Motif 3.5 Thermodynamic Analysis for the Non‐canonical Nucleic Acids 3.5.1 Thermodynamic Analysis for the Intramolecular Triplex and Tetraplex 3.5.2 Thermodynamic Analysis for the Intermolecular Triplex 3.5.3 Thermodynamic Analysis for the Tetraplex 3.6 Conclusion References Chapter 4 Physicochemical Properties of Non‐canonical Nucleic Acids 4.1 Introduction 4.2 Spectroscopic Properties of Non‐canonical Nucleic Acids 4.2.1 Effect of Non‐canonical Structure on UV Absorption 4.2.2 Circular Dichroism of Non‐canonical Nucleic Acids 4.2.3 NMR Spectroscopy 4.2.4 Other Spectroscopic Characteristics of Non‐canonical Nucleic Acids 4.3 Chemical Interactions on Non‐canonical Nucleic Acids 4.3.1 Hydration 4.3.2 Cation Binding 4.3.3 pH Effect 4.3.4 Chemical Modification 4.4 Chemical Platform on the Non‐canonical Structures 4.4.1 Specificity of a Ligand to Non‐canonical Structures 4.4.2 Fluorescence Platform of Non‐canonical Structures 4.4.3 Interface Between Proteins and Nucleic Acids 4.5 Physicochemical Property of Non‐canonical Nucleic Acids in Cell 4.5.1 Molecular Crowding Condition that Reflects Cellular Environments 4.5.2 Effects of Crowding Reagents on Non‐canonical Nucleic Acid Structures 4.5.3 Quantification of Physical Properties of Non‐canonical Structures in Crowding Condition 4.5.4 Non‐canonical Structures Under Mimicking Organelle Environment 4.5.5 Insight for the Formation of Non‐canonical Nucleic Acids in Cells 4.6 Conclusion References Chapter 5 Telomere 5.1 Introduction 5.2 Structural Properties of Telomere 5.2.1 Structures of Telomere 5.2.2 Structural Properties of Human Telomeric G4s 5.2.3 Structure of Repeats of Human Telomeric G4s 5.3 Biological Relevance of Telomere G4 5.3.1 Telomerase Activity 5.3.2 Telomerase Repeated Amplification Protocol (TRAP) Assay 5.3.3 Alternative Lengthening of Telomere (ALT) Mechanism 5.4 Other Non‐canonical Structures Related to Telomere Region 5.4.1 Telomere i‐Motif 5.4.2 Telomere RNA 5.5 Conclusion References Chapter 6 Transcription 6.1 Introduction 6.2 Transcription Process 6.2.1 Transcription Initiation 6.2.2 Transcription Elongation 6.2.3 Transcription Termination 6.3 Transcription Process Perturbed by Certain Sequences of DNA and RNA 6.4 Transcription Process Perturbed by Non‐canonical Structures of DNA and RNA 6.5 Conclusion References Chapter 7 Translation 7.1 Introduction 7.2 RNAs Involved in Translation Machinery 7.3 General Process of Translation 7.3.1 Translation Initiation 7.3.2 Translation Elongation 7.3.3 Translation Termination 7.4 RNA Structures Affecting Translation Reaction 7.4.1 Modulation of Translation Initiation in Prokaryotes 7.4.2 Modulation of Translation Initiation in Eukaryotes 7.4.3 RNA Structures Affecting Translation Elongation 7.4.4 RNA Structures Affecting Translation Termination 7.5 Conclusion References Chapter 8 Replication 8.1 Introduction 8.2 Replication Machineries 8.3 Replication Initiation 8.3.1 Mechanism of Activation of Replication Origins 8.3.2 Activation Control of Origins by G4s 8.3.3 Control of Timing of Replication Initiation by G4s 8.4 DNA Strand Elongation 8.4.1 Mechanism of DNA Strand Elongation 8.4.2 Impact of G4 and i‐Motif Formations on DNA Strand Synthesis 8.4.3 Relationship Between G4 and Epigenetic Modification 8.4.4 Expansion and Contraction of Replicating Strand Induced by Hairpin Structures 8.5 Termination of Replication 8.6 Chemistry of the Replication and Its Regulation 8.6.1 Cellular Environments 8.6.2 Control of Replication by Chemical Compounds 8.7 Conclusion References Chapter 9 Helicase 9.1 Introduction 9.2 Function and Structure of Helicases 9.3 Unwinding of Non‐canonical DNA Structures by Helicases 9.4 G4 Helicases in Gene Expressions 9.5 G4 Helicases in Replication 9.6 G4 Helicases in Telomere Maintenance 9.7 Relation to Diseases by Loss of G4 Helicases 9.8 Insight into Specific Properties of Activities of G4 Helicase Under Cellular Conditions 9.9 Conclusion References Chapter 10 Dynamic Regulation of Biosystems by Nucleic Acids with Non‐canonical Structures 10.1 Introduction 10.2 Time Scale of Biological Reactions 10.2.1 Cell Cycle 10.2.2 Central Dogma 10.2.3 Dynamic Structures of Nucleic Acids 10.3 Processes in the Central Dogma Affected by Dynamics of Nucleic Acid Structures 10.3.1 Epigenetic Regulation Caused by Chemical Modification of DNA 10.3.2 Co‐transcriptional Formation of Metastable RNA Structures 10.3.3 Co‐transcriptional Translation and Transcription Attenuation 10.3.4 Co‐transcriptional Ligand Binding and Gene Regulation 10.3.5 Translation Elongation and Co‐translational Protein Folding 10.4 Conclusion References Chapter 11 Cancer and Nucleic Acid Structures 11.1 Introduction 11.2 Detail Mechanism of Cancer 11.2.1 Cancer Incidence 11.2.2 The Relationship Between Genes and Cancer 11.3 Non‐canonical Structures of Nucleic Acids in Cancer Cells 11.3.1 Structural Characteristics of Nucleic Acids in Cancer Cells 11.3.2 Non‐canonical Structures Perturb Gene Expression of Cancer‐Related Genes 11.4 Roles of Non‐canonical Structures of Nucleic Acids in Cancer Cells 11.4.1 Monitoring of Non‐canonical Structures in Cancer Cells 11.4.2 Regulation of Gene Expressions by the Non‐canonical Structures in Cancer Cells 11.5 Conclusion References Chapter 12 Neurodegenerative Diseases and Nucleic Acid Structures 12.1 Introduction 12.2 Protein Aggregation‐Induced Neurodegenerative Diseases 12.3 DNA Shows Key Role for Neurodegenerative Diseases 12.4 RNA Toxic Plays a Key Role for Neurological Diseases 12.5 Conclusion References Chapter 13 Therapeutic Applications 13.1 Introduction 13.2 Oligonucleotide Therapeutics 13.2.1 Antisense Oligonucleotide 13.2.2 Functions of Antisense Oligonucleotide Therapeutics 13.2.3 Chemical Modifications in Therapeutic Oligonucleotides 13.2.3.1 Backbone Modified Oligonucleotides 13.2.3.2 Ribose Modified Oligonucleotides 13.2.3.3 Oligonucleotides with Unnatural Backbone 13.2.4 Oligonucleotide Therapeutics Other Than Antisense Oligonucleotide 13.2.4.1 Oligonucleotide Therapeutics Functioning Through RNA Interference 13.2.4.2 Oligonucleotide Therapeutics Functioning Through Binding to Protein 13.3 Non‐canonical Nucleic Acid Structures as Therapeutic Targets 13.3.1 Traditional Antibiotics Targeting Structured Region of RNAs 13.3.2 Strategies for Constructing Therapeutic Materials Targeting Structured Nucleic Acids 13.4 Non‐canonical Nucleic Acid Materials for Inducing Non‐canonical Structures 13.5 Conclusion References Chapter 14 Materials Science and Nanotechnology of Nucleic Acids 14.1 Introduction 14.2 Non‐canonical Structure‐Based Nanomaterials Resembling Protein Functions 14.2.1 Aptamer 14.2.2 DNAzyme 14.2.3 Ion Channel 14.3 Protein Engineering Using G4‐Binding Protein 14.4 Regulation of Gene Expression by G4‐Inducing Materials 14.5 Environmental Sensing 14.5.1 Sensing Temperature in Cells 14.5.2 Sensing pH in Cells 14.5.3 Sensing K+ Ion in Cells 14.5.4 Sensing Crowding Condition in Cells 14.6 Conclusion References Chapter 15 Future Outlook for Chemistry and Biology of Non‐canonical Nucleic Acids 15.1 Introduction 15.2 Exploring Potential: Properties of Non‐canonical Structures in Unusual Media 15.3 Systemizing Properties: Prediction of the Formation of Non‐canonical Nucleic Acids Structures 15.4 Advancing Technology: Applications of Non‐canonical Structures Taking Concurrent Reactions into Account 15.4.1 Co‐transcriptional Dynamics of G‐Quadruplex 15.4.2 Co‐transcriptional Functionalization of Riboswitch‐Like Sensor 15.4.3 Co‐transcriptional RNA Capturing for Selection of Functional RNAs 15.5 Conclusion References Index EULA