Chemistry and Biology of Non-canonical Nucleic Acids

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