Chemistry and Biology of Non-canonical Nucleic Acids

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Naoki Sugimoto. Chemistry and Biology of Non-canonical Nucleic Acids

Table of Contents

List of Tables

List of Illustrations

Guide

Pages

Chemistry and Biology of Non-Canonical Nucleic Acids

Preface

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

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

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

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

4.3.1 Hydration

4.3.2 Cation Binding

4.3.3 pH Effect

4.3.4 Chemical Modification

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

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

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

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

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

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

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

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

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

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

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

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

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Naoki Sugimoto

As I mentioned in the Introduction in Chapter 1, there is close to 70 years history in nucleic acid research after the discovery of the double helix DNA structure (B-form) as the canonical one by James Dewey Watson and Francis Harry Compton Crick in 1953 and chemical biology of nucleic acids are facing to new aspect today, that is, non-canonical nucleic acids. Through this book, I expect that readers understand how uncommon structure of nucleic acids became one of the common structures as non-canonical nucleic acids that fascinate us now. This new research field for non-canonical nucleic acids will soon big-spark at the interface of chemistry and biology.

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T-loop motif is well-observed motif in the loop–loop interaction regions, which have been identified in a variety of RNAs [30]. T-loop motif generally consists of five consecutive nucleotides assuming a compact U-turn-like loop structure, in which the first and the fifth nucleobases form a base pair irrespective of whether it is canonical Watson–Crick or unusual one. When the T-loop motif is involved in the loop–loop interaction, the fourth and fifth nucleobases in the T-loop sandwich an extra nucleobase, which is derived from separated loop region, to make continuous base stacks. The sandwiched nucleobase usually interacts with the second nucleobase of the T-loop through hydrogen bonding [30]. In crystal structure of phenylalanyl-tRNA derived from Saccharomyces cerevisiae, in which T-loop motif was originally discovered, UUCGA loop of pentanucleotides accommodates guanine nucleobase from different tRNA loop region to form stable tertiary interaction (Figure 2.14).

Kissing-loop interaction is a basic type loop-loop interaction that causes cross-linkage between different helices, which are located in intrastrand or interstrand (Figure 2.15). The basic interaction of the kissing loop is formation of base pairing by complementary sequences in the apical loops of two hairpins. Intramolecular kissing complexes have been found in many RNA structures, ranging from transfer RNA (tRNA), in which length is shorter than 100 nucleotides, to ribosomal RNA (rRNA) with more than 1000 nucleotides [31]. The kissing-loop complex is usually stabilized by coaxial stacking of nucleobases included in the interhelical duplex (Figure 2.15) [32]. On the other hand, even if the sequence in the loop forms only two G·C base pairs without the coaxial stacking, a simplest kissing interaction is observed between hairpins each with a GACG tetraloop [33]. In that case, kissing base pairs are stabilized through cross-strand interactions caused by adjacent adenines in the loop [33].

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