دانلود کتاب Handbook of Chemical Biology of Nucleic Acids

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Preface
Contents
About the Editor
Section Editors
Contributors
Part I: Physical Chemistry of Nucleic Acids
1 High-Pressure Single-Molecule Studies on Non-canonical Nucleic Acids and Their Interactions
Introduction
Why High-Pressure Studies on Biomolecular Systems?
Materials and Methods
Förster Resonance Energy Transfer (Lakowicz 2006)
Confocal Microscopy Setup (Patra et al. 2018, 2019)
Time-Correlated Single Photon Counting (Wahl et al. 2013)
Pulsed Interleaved Excitation (PIE) (Rüttinger et al. 2006)
Data Analysis
Pressure Setup (Patra et al. 2018)
Measuring Kinetics with Immobilized Probes
Results and Discussion
Pressure Effects on Nucleic Acid Structures
Effect of High Hydrostatic Pressure on the Conformational Dynamics of DNA Hairpins
Effect of High Pressure on the Conformational Dynamics of G-Quadruplexes
Effect of High Pressure on the Conformational Dynamics of I-Motifs
Pressure Effects on the Interaction of Proteins with Non-canonical DNA
Conclusion
References
2 Stability Prediction of Canonical and Noncanonical Structures of Nucleic Acids
Introduction
Basics of Stability Prediction of Canonical Structures of Nucleic Acids
Structure and Thermodynamics of the Canonical Structure of Nucleic Acids
Melting Behavior of Nucleic Acid Structures
Measurement of Thermodynamic Stability and Calculation of Thermodynamic Parameters
Nearest-Neighbor (NN) Parameters: Prediction of Thermodynamic Stability and Its Calculation Method
Application of Prediction to Nonmatched Base Pair and Secondary Structure Based on NN Rules
Stability Prediction of Noncanonical Structures
Applicability of Stability Prediction to Noncanonical Structures
Hairpin Loop
Triplex
G-quadruplex
i-motif
Expansion and Application of Stability Prediction
Issues in Application of Stability Prediction Under Cellular Conditions
Stability of DNA Duplex Structure in Different Cation Concentrations
Stability of DNA Duplex Structure in a Molecular Crowding Environment
Extension of Stability Prediction to the DNA Duplex Structure in Various Solution Environments
Prediction of the Stability of the DNA Duplex Under Intracellular Conditions by Measuring the Intracellular Environment
Conclusion
References
3 The Effect of Pressure on the Conformational Stability of DNA
Introduction
Structural Considerations
Thermodynamic Considerations
Pressure Effects on Canonical Duplex DNA
Changes in Volume, ΔV
Changes in Expansibility, ΔE, and Compressibility, ΔKS
Pressure-Temperature Stability Phase Diagram of Duplex DNA
Effects of Cations, Cosolvents, and Sequence and Length of Oligomeric DNA on Transition Volume, ΔV
Pressure Effects on Noncanonical DNA Structures
Hairpins
Z-DNA
Three-Stranded DNA
G-Quadruplexes
i-Motif Structures
Pressure and the Kinetics of Helix Formation
Conclusions
References
4 Quadruplexes Are EverywhereOn the Other Strand Too: The i-Motif
i-Motif Forming Strands and Characters
i-Motif Characterization Methods
Factors Affecting i-Motif Stability
i-Motif Applications
Ligands/Compounds
Physiological Roles
Conclusion
References
5 i-Motif Nucleic Acids
Introduction
i-Motif Structure
Hemi-Protonated Cytosines
Intramolecular i-Motif Formation
Topologies
Grooves
Loops
Stabilizing Cations
i-Motifs and pH
Nanotechnology
i-Motifs at Neutral pH
i-Motifs in Biology
i-Motifs in the Telomeres
i-Motifs in Gene Promoter Regions
i-Motifs in DNA Replication
i-Motifs in Cells
i-Motifs and G-Quadruplexes
i-Motif Ligands and Probes
TMPyP4 and Macrocycles
Carboxyl-Modified Nanotubes and Quantum Dots
Small Molecules
Fluorescent Probes
Synergistic Ligands for i-Motifs and G-Quadruplexes
Conclusion
References
Part II: Structural Chemistry of Nucleic Acids
6 NMR Study on Nucleic Acids
Introduction
Elements of the Structural Buildup of Nucleic Acids and Their Conformational Landscape
Assessment of the Folding Topology by NMR
Assessment of Multimeric State by Translational Diffusion Coefficients
Site-Specific Low-Isotopic Enrichment
Nucleobase Substitutions with Nucleobase Analogs
Natural Abundance Heteronuclear Experiments
Resonance Assignment Through Sequential and Interstrand Interactions
Determination of 3D Structure
Labeling with Stable Heteronuclear 15N and 13C Isotopes
NMR Structural Studies in Combination with Complementary Methods
Challenges in Structural Studies of Biologically Relevant DNA and RNA
Dynamic Processes in RNA and Corresponding NMR Methods
Conclusion
References
7 Z-DNA
Introduction
Chemical and Structural Properties of Z-DNA
Left-Handed Z-DNA
Crystal Structures of Z-DNA in Complex with Chemical Inducers
Crystal Structures of Z-DNA in Complex with Z-DNA Binding Proteins
Crystal Structures of BZ Junctions
NMR Studies of Z-DNA Transition Induced by ZBP
NMR Monitoring on Z-DNA Formation of d(CGCGCG)2 by ZBPs
NMR Monitoring on Intermolecular Interaction of ZBPs with Z-DNA
B-to-Z Transition Mechanism of DNA Induced by ZBPs
NMR Dynamics Study on B-to-Z Transition of DNA Induced by ZBPs
A-to-Z Transition Mechanism of RNA Induced by ZBPs
BZ Junction Formation of DNA Induced by ZBPs
Chemical Biology Strategies Used to Elucidate the Biological Significance of Z-DNA and Z-DNA Binding Proteins
Strategies Used to Determine the Structure and Stability of Z-DNA
Strategies for Developing a Z-DNA Sensor
Strategies Applied to Ascertain the Z-DNA Function
Strategies for Developing Therapeutics Targeting Z-DNA
Strategies Applied for Nanotechnology Applications Using Z-DNA
Disease Implications
Z-DNA Is Immunogenic
Z-DNA Forming Sequence (ZFS) Controls the Expression of the Disease-Related Genes
Z-DNA Forming Sequence (ZFS) Is a Hotspot for the Large-Scale Deletion of DNA
Disease Implications of Z-DNA Binding Proteins
Conclusion and Perspective
References
8 Structures of G-Quadruplexes and Their Drug Interactions
Introduction
DNA G-Quadruplexes
Structural Characteristics of DNA G-Quadruplexes
Intramolecular DNA G-Quadruplexes
Human Telomeric DNA G-Quadruplexes
Human Telomeric G-Quadruplex Structures
Human Promoter DNA G-Quadruplexes
Parallel DNA G-Quadruplexes in Gene Promoters
Broken-Strand DNA G-Quadruplexes in Gene Promoters
Promoter DNA G-Quadruplexes with Long Loops and Hairpin Motifs
Left-Handed DNA G-Quadruplexes
Four-Tetrad DNA G-Quadruplexes
Structural Basis of Small Molecule Interactions of DNA G-Quadruplexes
G-Quadruplex Interactions with End-Stacking Compounds
Small Molecule Recognition of G-Quadruplexes with Additional Loop and Capping Interactions
Small Molecule Recognition of Parallel G-Quadruplexes
Small Molecule Interactions with Vacancy G-Quadruplex Bound by Metabolites
Small Molecule Interactions with G-Quadruplex-Duplex Junction
G-Quadruplex Intercalation with Small Molecule
Electrostatic Interactions of G-Quadruplex-Interactive Small Molecules
Conclusion
References
9 In Cell 19F NMR for G-Quadruplex
Introduction
Results and Discussion
In Cell 19F NMR for DNA G-quadruplex
In Cell 19F NMR for RNA G-quadruplex
In-Cell 19F NMR for Hybrid DNA/RNA G-quadruplex
Conclusion
References
10 Structures and Catalytic Activities of Complexes Between Heme and DNA
Introduction
G-quadruplex DNA and RNA
Molecular Recognition Between Heme and G-Quadruplex DNA
Spectroscopic Properties of a Heme(Fe3+)-DNA Complex
NMR Characterization of Heme-DNA Complexes
CO Adducts of Heme(Fe2+)-DNA Complexes
Resonance Raman Studies of CO Adducts of Heme(Fe2+)-DNA Complexes
pH-Dependence of a Heme(Fe3+)-DNA Complexes
Imidazole Adducts of Heme(Fe3+)-DNA Complexes
Peroxidase Activity of Heme(Fe3+)-DNA Complexes
Peroxidation Cycle of Heme(Fe3+)-DNA Complexes
Conclusion
References
11 Studying Nucleic Acid-Ligand Binding by X-Ray Crystallography
Introduction
The Crystallization of DNA-Ligand Complexes
The X-Ray Diffraction Experiment
Phasing of Data
Model Building and Refinement
Crystallographic Software
Some Key Features of Ligand-DNA Crystal Structures
DNA Duplexes, Junctions, and Mismatches
Classical Intercalation
Bisintercalation
Intercalative Binding to DNA Junctions
Intercalation by Metal Complexes
G-Quadruplexes
Conclusion
References
12 Predicting the 3D Structure of RNA from Sequence
Introduction
RNA 3D Structure
Experimental Determination of RNA 3D Structure
Predicting RNA 3D Structure
Protein 3D Structure Prediction
Challenges in RNA 3D Structure Prediction
Overview of the Chapter
RNA Basepairs, Loops, and Secondary Structure
Watson-Crick Basepairs and Secondary Structure
RNA Secondary Structure Prediction
Non-Watson-Crick Basepairs and Base-Backbone Interactions
RNA Hairpin, Internal, and Junction Loops
Long-Range Interactions in RNA
RNA Loop Motif Libraries and Prediction Methods
Fragment Assembly and Simulation-Based Methods for Predicting RNA 3D Structure
Fragment Assembly Methods
Computational Simulation Methods
Scoring RNA 3D Structure Predictions Using Machine Learning
RNA-Puzzles Evaluation of Blind RNA 3D Structure Prediction
Protein 3D Structure Prediction and CASP
AlphaFold in CASP13 and CASP14
Comparison of Protein and RNA 3D Structure Prediction
Machine Learning Methods for RNA 3D Structure Prediction
Prediction of RNA Contacts Using Correlation Analysis
RNA Contact Prediction Techniques Based on Machine Learning
RNA Distance Prediction and 3D Structure Prediction Based on Machine Learning
Learning a Foundation Model from RNA Sequence Databases
Conclusions
References
Part III: Organic Chemistry of Nucleic Acids
13 Hexitol Nucleic Acid (HNA): From Chemical Design to Functional Genetic Polymer
Introduction
Chemical and Enzymatic Synthesis of HNA and Related Nucleic Acids
Biophysical and Structural Properties of HNA and Related Six-Membered Nucleic Acids
In Vitro and In Vivo Synthetic Biology Applications of HNA and Akin Oligonucleotides
Biomedical Applications of HNA and Similarly Modified Oligonucleotides
Conclusion
References
14 The Effects of FANA Modifications on Non-canonical Nucleic Acid Structures
Introduction
FANA: A Historical Perspective
Synthesis of FANA: Beyond AraF-N Nucleosides
FANA/RNA Duplexes: Investigating Their Superior Stability
FANA in Triple Helical Structures
FANA in G-Quadruplexes
Structural Effects of Modifying G-Quadruplexes with AraF-G
Effects of Substituting Anti-dG and Syn-dG Residues with AraF-G
Comparing the Potency of AraF-G and RiboF-G in Stabilizing One of Two Forms of a (3 + 1) Hybrid G-Quadruplex
Comparing the Effect of Systematic Single AraF-G, RiboF-G, or LNA-G Substitutions on G-Quadruplex Topology
Structural Characterization of G-Quadruplex Stabilization by AraF-G
Studying the Compatibility of Thrombin-Binding Aptamer with AraF-N Modifications
Improving the Nuclease Resistance of Thrombin-Binding Aptamer and its Binding Affinity to Thrombin
Using Microarray Technology to Find Optimal Positions for AraF-N Stabilization of Thrombin-Binding Aptamer (TBA)
Understanding the Dramatic Effect of a Single AraF-T Substitution at Position T3 of TBA1 on the Enhancement of Binding Affinit...
AraF-G-Modified Parallel G-Quadruplexes in Telomere Biology
AraF-G-Modified Parallel G-Quadruplexes Are a Substrate of Telomerase
Probing the Mechanism of Telomerase Extension of Parallel Telomeric G-Quadruplexes
FANA in i-Motif Structures
Effects of Modifying i-Motifs with AraF-C
AraF-C Stabilizes i-Motifs at Neutral pH
Structural Insights on i-Motif Stabilization by AraF-C
Comparing the Effects of AraF-C and 5-Methyl-araF-C on i-Motif Stability
Simultaneously Stabilizing Complementary i-Motifs and G-quadruplexes Using AraF-C and AraF-G, Respectively
Conclusion and Outlook
References
15 Isomorphic Fluorescent Nucleoside Analogs
Introduction
Enzymatic Reactions of Nucleosides and Nucleobases
Enzymatic Reactions of Nucleobase-Based Cofactors
RNA and DNA Oligonucleotide Constructs
RNA Folding and Ribozyme Activity
RNA/DNA-Protein Interactions
DNA Constructs and Conformations
Conclusions
References
16 Bridged Nucleic Acids for Therapeutic Oligonucleotides
Introduction
Concept and Chemistry of Bridged Nucleic Acids
Synthesis and Biophysical Properties of Bridge Nucleic Acids
Five-Membered Bridged Nucleic Acids
Development of Parent 2′-O,4′-C-Methylene-Bridged Nucleic Acid
Phosphate Linkage Modifications in Bridged Nucleic Acids
Base Modifications in Bridge Nucleic Acids
Sugar Modification in Bridge Nucleic Acids
SeLNA and SeOLNA
6′-Mercapto-thioBNA
Amide-Bridged Nucleic Acids (AmNAs)
Guanidine-Bridged Nucleic Acid (GuNA)
2′-O, 4′-C-Spirocyclopropylene-Bridged Nucleic Acid (scpBNA)
2′,4′-BNA/LNA-2-Thiothymine: scpBNA-S2T, scpBNA-Se2T, and ThioAmNA-S2T
Methyleneoxy-Bridged 2′-Deoxyribonucleic Acid (MoDNA)
Triazole- and Tetrazole-Bridged Nucleic Acids
2′,4′-BNA/LNA Derivative with Expanded Ring Size
Six-Membered Bridged Nucleic Acid
Ethylene-Bridged Nucleic Acid (ENA)
2′,4′-BNANC
Hydroxamate-Bridged Nucleic Acid (HxNA)
Six-Membered AmNA (6-AmNA)
Sulfonamide-Bridged Nucleic Acids (SuNAs)
2′-C,4′-C-Ethyleneoxy-Bridged 2′-Deoxyribonucleic Acids (Methylene-EoDNAs)
Seven-Membered Bridged Nucleic Acids
2′-O,4′-C-Methyleneoxymethylene BNA (2′,4′-BNACOC)
Benzylidene Acetal-Type Bridged Nucleic Acids (BA-BNAs)
Urea-Type BNA
2′-O, 4′-C-Ethyleneoxy Bridged Nucleic Acid (EoNA)
Conclusion
References
17 Mesyl Phosphoramidate Oligonucleotides: A New Promising Type of Antisense Agents
Introduction
Structure and Synthesis
Duplex Formation with Complementary DNA and RNA
Circular Dichroism (CD) Spectra
Thermal Stability
Formation of G-Quadruplexes
Enzymatic Stability
RNase H Recruitment
Cellular Uptake
RNase H-Dependent Antisense Application
Splice-Switching Application
Immunomodulatory Activity
Toxicity
Future Prospects
Conclusion
References
18 Chemistry of Cyclic Dinucleotides and Analogs
Introduction
Basic Strategies for Chemical Synthesis of CDNs and Their Analogs
Chemical Synthesis of CDNs Using a Phosphotriester-Phosphotriester Approach
Chemical Synthesis of CDNs Using a H-Phosphonate-H-Phosphonate Approach
Chemical Synthesis of CDNs Using a Phosphoramidite-H-Phosphonate Approach
Chemical Synthesis of CDNs Using a Phosphoramidite-Phosphotriester Approach
Chemical Synthesis of CDNs Using a Phosphoramidite-Phosphoramidite Approach
Synthesis of Synthetic CDN Analogs
CDN Analogs with Modified Phosphodiester Linkages
Phosphorothioates
Others
Sugar-Modified CDN Analogs
Nucleobase-Modified CDN Analogs
Conclusion
References
19 Labeling and Detection of Modified Nucleic Acids
Introduction
Labeling and Detection of DNA Modifications
5mC: The Predominant DNA Modification
5hmC: The First Step Intermediate in the Active Demethylation Pathway
5fC: The Second Step Intermediate in the Active Demethylation Pathway
5caC: The Final Oxidized Derivative of 5mC
N6-Methyldeoxyadenosine (6mA): Predominantly Present in Prokaryotes and a Limited Number of Eukaryotes
5-Formyluracil (5fU)
Deoxyuridine (dU)
Labeling and Detection of RNA Modifications
N6-Methyladenosine (m6A): The Most Abundant Internal mRNA Modification
N1-Methyladenosine (m1A)
5-Methylcytosine (m5C)
N4-Acetylcytidine (ac4C)
Inosine(I): From A-to-I RNA Editing
Pseudouridine (Ψ): The Rotation Isomerization of Uridine
N7-Methylguanosine (m7G): A Well-Known mRNA Cap Modification
Conclusion and Outlook
References
20 Cross-Linking Duplex of Nucleic Acids with Modified Oligonucleotides
Introduction
Cross-Linked Double-Stranded DNA with ONs Containing Nonnatural Nucleic Acids in Both Strands
Cross-Linked Duplex for Biological Tools
Cross-Linked Duplex by Photoirradiation with ODNs Containing Nonnatural Nucleic Acids in Both Strands
Cross-Linked Duplex by Click Chemistry
ONs with Cross-Linking Reactivity Targeting Natural-Type DNA and RNA
CFOs Activated by Photoirradiation
Cross-Linking Via [2 + 2] Reaction by Photoirradiation
Photo-Cross-Linking Using Thionucleobases
Other Photo-Cross-Linking
CFOs Activated by Chemical Reactions
Cross-Linking Reactions Without External Stimuli
Vinyl Purine Derivatives as Cross-Linking Agents
Vinyl Pyrimidine Derivatives as Cross-Linking Agents
Conclusion
References
21 Enzymatic Synthesis of Base-Modified Nucleic Acids
Introduction
General Concepts on Polymerase-Mediated Synthesis of Modified Nucleic Acids
Natural Modifications of Nucleobases: Synthesis and Polymerase-Mediated Incorporation
Epigenetic Base-Modification Patterns on DNA
Epigenetic Base-Modifications on RNA
Pseudouridine (Ψ)
Methylated Adenosine Analogs m1A (8) and m6A (7)
5-methylcytosine m5C (9)
N4-acetylcytidine ac4C (10)
7-Methylguanosine m7G (11)
Base Modifications for Aptamer and Catalytic Nucleic Acid Generation Via SELEX
Aptamer Selection with Base-Modified Nucleotides
Expansion of the Genetic Alphabet and Aptamers
Selection of Base-Modified Catalytic Nucleic Acids
Overview of Other Applications
Generation of Chemically Modified mRNA Vaccines
Controlled Enzymatic Synthesis
Conclusion
References
Further Readings
22 Charge Transfer in Natural and Artificial Nucleic Acids
Introduction
What We Have Learned from Charge Transfer Studies Through DNA
Charge Transfer in Natural and Artificial Nucleic Acids
Charge Transfer in RNA
Charge Transfer in Peptide Nucleic Acids (PNA)
Charge Transfer in Locked Nucleic Acids (LNA)
Charge Transfer Inducing Moieties: Are the Donor and Acceptor Systems the Clandestine Key Players?
Conclusion
References
23 Nucleic Acid Aptamers: From Basic Research to Clinical Applications
Introduction
Aptamer Discovery Technologies
Standard SELEX
Magnetic Bead SELEX
Cell-SELEX
In Vivo SELEX
Challenges of the Clinical Application of Aptamers
Strategies to Overcome the Challenges Associated with Clinical Applications of Aptamers
Improvement of Aptamers´ Nuclease Susceptibility
Ribose Modifications and Alternative Sugar Entities
Substitution of Phosphodiester Linkage
Spiegelmers
Reduction of Renal Clearance of Aptamers
Nucleobase Modifications
Aptamers Bearing an Expanded Genetic Alphabet
Aptamers as Drug Delivery Vehicles
Conclusion
References
Part IV: Ligand Chemistry of Nucleic Acids
24 Targeting Quadruplex Nucleic Acids: The Bisquinolinium Saga
Introduction
Bisquinolinium Pyridodicarboxamide (PDC) and PhenDC3: Prototypic G4 Ligands
Genesis and Design of Bisquinolinium Ligands: The Preorganization Concept
In Vitro Binding: Affinity, Selectivity, and Ligand-Induced Conformation Changes
Binding to Alternative Quadruplexes (VK2)
Biological Effects of Bisquinolinium Ligands
Telomeric Effects
Genetic Instability and Inhibition of Helicases
Miscellaneous DNA- or RNA-Related Effects
Functionalized Bisquinolinium Ligands for Detection and Manipulation of G4 Structures
Biotinylated PDC and PhenDC3 Derivatives
Fluorescent Derivatives for In Vitro Detection and Cellular Imaging of G-Quadruplexes
G4 Cross-Linking and Alkylating Agents
Immunotagged G4 Ligands
Other Bisquinolinium Derivatives as G4 Ligands
Dimeric Derivatives
Variations of the PDC Core
Variations in Linker Groups and Quinolinium Residues
Conclusion
References
25 Compound Shape and Substituent Effects in DNA Minor Groove Interactions
Introduction
AT Sequence-Specific MG Compounds That Can Also Bind at GC Sequences by Intercalation
Diversity in the Recognition of AT MG Sequences
Heterocyclic Diamidines That Recognize Some AT Sequences as Dimers
Curvature Determination for MG Binders
Out-of-Shape DNA MG Binders: Inclusion of Interfacial Water for Induced Fit Interactions of Heterocyclic Dications with DNA
Development of Heterocyclic Amidine MG Binders with GC Recognition
Pyridine Compound Design
N-Alkyl-Benzimidazole-Thiophene Compound Design
Azabenzimidazole Compound Design
MG Binders with Additional GC BP-Binding Capability: Compounds with the Same GC Recognizing Modules
MG Binders with Additional GC BP-Binding Capability: Compounds with Different GC Recognizing Modules
MG Binders with Additional GC BP-Binding Capability: Compounds That Recognize the GGAA Sequence That Is Conserved in the PU.1 ...
Conclusion
References
26 Macrocyclic G-Quadruplex Ligands of Telomestatin Analogs
Introduction
G4 and G4 Ligands
TMPyP4: A Macrocyclic G4 Ligand
Telomestatin: A Natural Macrocyclic G4 Ligand
Macrocyclic Polyoxazoles
HXDVs as Macrocyclic Polyoxazoles (Rice Group)
OTDs as Macrocyclic Polyoxazoles (Nagasawa Group)
7OTDs as G4 Ligands: Chemical-Biology Studies
6OTDs as G4 Ligands
Control of G4 Topologies by 6OTDs
G4-Forming Sequence-Selective 6OTDs
Detection of G4 by Fluorescent 6OTDs In Vitro and In Vivo
Anticancer Activity of 6OTDs
6OTD Multimers as G4 Ligands
6OTD Dimer
6OTD Tetramer
6OTD Dendrimer
Control of G4-Protein Interaction by OTD
G4-3R02 Protein with G4
Rif1 Protein with G4
hnRNPA1 Protein with RNA G4
BLM Helicase with G4
S1 Nuclease with Telomeric G4
Micelle-Type Macrocyclic 4OTDs as G4/i-Motif Ligands
Conclusion
References
27 Cyclic Naphthalene Diimide Derivatives as Novel DNA Ligands
Introduction
Polymorphism of G-Quadruplex DNA
G4 Binders
Properties of NDI and Its Binding to Double-Stranded DNA
Binding of NDI to G4
Interaction of cNDI with G4
Interaction of cNDI with G4 Under Molecular Crowding Conditions
Conversion of G4 Structure by NDI
Telomerase Inhibitory Ability of cNDI and Inhibition of Cell Growth
Ferrocenyl cNDI
cNDI Dimer
Conclusions
References
28 Imaging Study of Small Molecules to G-Quadruplexes in Cells
Introduction
Development of G4 Fluorescent Probes to Study G4s In Vivo
BMVC
o-BMVC
BMVC-nC-P and BMVC-8C3O-P
o-BMVC-nC-P
o-2B-P
Fluorescence Images for Identifying the Existence of Endogenous G4s In Vivo
Visualization of Telomeric G4s in Metaphase Chromosomes by BMVC
Detection of G4s in Live Cancer Cells by o-BMVC
Detection of G4 Foci by BG4 Antibody in Fixed Cells
o-BMVC Foci are G4 Foci in Fixed Cells
Telomeric G4s Detected in Fixed Cells by Antisense DNA
Detection of Mitochondrial G4s in Live Cancer Cells by o-BMVC-12C-P
Binding of Small Molecules to G4s in Fixed Cells
Imaging Study of G4 Ligands Binding to Exogenous G4s in Live Cells
Cellular Response to Exogenous G4s in Live Cells
G4 Dynamics of Exogenous G-Rich Oligonucleotides in Live Cells
o-BMVC Foci as a Biosensor for Clinical Cancer Diagnosis
DNA Damage May Facilitate G4 Formation
o-BMVC Test for Clinical Cancer Diagnosis
Other Fluorescent Probes for the Imaging Study of G4s in Cells
Carbazole Derivatives and BMVC Analogues
NBTE for FLIM Image
DAOTA-M2 for FLIM Image
Conjugates of G4 Fluorescent Probes
Conclusion
References
29 DNA/Metal Cluster-Based Nano-lantern
Introduction
DNA Composition, Structure, and Properties
Double-Helix DNA
Multistranded DNA Structures
Interaction Between DNA and Small Drug Molecules
Covalent Binding (Taatjes et al. 1999)
Noncovalent Binding (Rehman et al. 2015)
Intercalation (Brana et al. 2001)
Groove Binding (Baraldi et al. 2004)
Electrostatic Interaction (Rehman et al. 2015)
Other Interaction Modes
DNA Metallization
Introduction of DNA Metallization
Principle of DNA Metallization
DNA Metallization Methods
Chemical Reduction
Photoreduction
Electrochemical Deposition
DNA Metallization with a Localized Reducing Group
Construction of DNA Nano-Lantern
Applications of DNA Nanostructures in Therapeutics
The Design for DNA Nano-Lantern
The Main Achievement of the Nano-Lantern
Conclusion
References
30 Interaction of Poly(Ethylene Glycol)-b-Poly-L-Lysine Copolymers with DNA Structures: A Thermodynamic Investigation
Introduction
Materials and Methods
Result and Discussion
Conclusion
References
31 Chemical Tools to Target Noncoding RNAs
Introduction
RNA As a Therapeutic Target
Targeting Bacterial RNAs
Targeting Viral RNAs
Targeting Eukaryotic RNAs
RNA Nucleotides Repeats
MicroRNAs
Targeting of Long Noncoding RNAs
Current Trends for the Development of Innovative Chemical Tools for RNA Targeting
RIBOTAC Strategy
Targeting Pre-mRNA Splicing
Conclusion
References
32 Targeting DNA Junctions with Small Molecules for Therapeutic Applications in Oncology
Introduction
Structural Studies
Biological and Pathological Functions
DNA Junction-Targeting Anticancer Agents
Targeting TWJs
Targeting FWJs
Conclusion
References
Part V: Nucleic Acids and Gene Expression
33 DNA Damage and Repair in G-Quadruplexes Impact Gene Expression
Introduction
Reactive Oxygen Species and Endogenous DNA Damage
Oxidation of Guanine in Duplex Versus Quadruplex DNA
Initiation of Base Excision Repair After Oxidative Stress
Cell-Based Assays of Gene Expression
AP Endonuclease-1 Binding to G-Quadruplexes
Conclusion and Outlook
References
34 DNA Structural Elements as Potential Targets for Regulation of Gene Expression
Introduction
Does Gene Expression Depend on DNA Structure?
Functions of Non-canonical Structures at Gene Promoters
Targeting G-quadruplexes for Medical Purposes
The Lesson from the Studied Ligands
Alternative G4 Arrangements as More Selective Targets
Physiological Relevance of Alternative G4 Repeats
Epigenetics
Conclusions and Perspectives
References
35 Effects of Molecular Crowding on Structures and Functions of Nucleic Acids
Introduction
Physicochemical and Molecular Factors Influencing Nucleic Acid Structures and Their Stabilities
Structural Factors
Hydrogen Bonding
Stacking Interaction
Conformational Entropy
Environmental Factors
Hydration and Dehydration
Cation Binding
Specific Interaction of Biomolecular Ligands
Model Experimental Systems In Vitro to Investigate the Effects of Molecular Crowding on Biomolecules
Characteristics of Co-solutes to Mimic the Intracellular Molecular Environment
Change in Solution Properties by the Addition of Co-solutes
Effects of Molecular Crowding Environments on Nucleic Acids
Effects of Molecular Crowding on Canonical Duplexes
Structure of Large Genomic DNAs Under a Crowding Environment
Stability of Polymer Nucleotide Duplexes Under a Crowding Environment
Stability of Short Oligonucleotide Duplexes in Crowding Environments with Reduced Water Activity
Effects of Molecular Crowding on Noncanonical DNA Structures and Stabilities
Formation of Left-Handed Duplex Under a Crowding Environment
Stabilization of Blanched Junction Under a Crowding Environment
Stabilization of Multistranded Helix Under a Crowding Environment
Triplex Structures Under a Crowding Environment
G-Quadruplex Structures Under a Crowding Environment
i-Motif Structures Under a Crowding Environment
Effects of Molecular Crowding on RNA Structure and Functions
Tertiary Structure Folding Under the Molecular Crowding Environments
Activities of RNA Catalyst Under the Molecular Crowding Environments
Affinities of RNA Aptamers Under the Molecular Crowding Environments
Biological Reactions Influenced by Nucleic Acid Structures and Their Stabilities
Effects of Nucleic Acid Structures on DNA Replication
Effects of Nucleic Acid Structures on RNA Transcription
Effects of Nucleic Acid Structures on Protein Translation
Effects of Nucleic Acid Structures on Concurrent Reactions
Conclusion
References
36 Structure-Guided Optimization of siRNA and Anti-miRNA Properties
Introduction
RNAi and MicroRNA Pathways
Structures of Argonaute Protein Domains and Argonaute-RNA Complexes
siRNA Modifications Whose Design Was Inspired by Ago2-RNA Complexes
siRNA and Anti-miRNA Modifications from Computational Screening
Conclusions
References
37 Tools for Understanding the Chemical Biology of the tRNA Epitranscriptome
Introduction
Current Tools to Study the tRNA Epitranscriptome and tRNA Reprogramming
Current Tools to Study Codon-Biased Translation
Conclusion
References
Further Reading
38 Sulfur- and Selenium-Modified Bacterial tRNAs
Introduction
Sulfur- and Selenium-Containing Nucleosides in the Wobble Position of the Bacterial tRNAs
Sulfur-Containing Nucleosides in the tRNA Chain
S-geranyl- and Selenonucleosides
The Modification Pathways of Thio-, S-geranyl, and Selenonucleosides
Biosynthesis of 2-Thiouridines
Biosynthesis of S-Geranyl- and 2-Selenonucleosides
Escherichia coli tRNA 2-Selenouridine Synthase (SelU), the Enzyme Modifying the R5-Substituted 2-Thiouridines in the Anticodon...
Structure of SelU
SelU Is a tRNA-Bound Nucleoprotein
Substrate Specificity of SelU
Readout of 5′-NNA-3′ and 5′-NNG-3′ Synonymous mRNA Codons by Sulfur- and Selenium-Modified tRNA Anticodons
Synonymous Codons Specific for Lys, Glu, and Gln
U-A and U-G Base Pairing Modes
Tautomeric Forms of Modified Uridines and Their Base Pairs with Guanosine
Ionizable Tautomeric Forms of 2-Thio- and 2-Selenouridines
Theoretical Modeling of U-G Base Pairs with mnm5S2Ura and mnm5Se2Ura
Crystal Structures of U*-G Base Pairs in tRNA-mRNA at the Ribosome Context
Conclusions
References
39 Chemical-Assisted Epigenome Sequencing
Background
Genomic Mapping of 5mC
Bisulfite Sequencing
The Chemistry of Bisulfite Treatment
The Mapping of Bisulfite Sequencing
Limitations of Bisulfite Sequencing
Degradation of DNA during Bisulfite Treatment
Undistinguishable between 5mC and 5hmC
Improvements on Bisulfite Sequencing
T-WGBS
RRBS
PBAT
Bisulfite-Free Methylome Sequencing
TET-Assisted Pic-Borane Sequencing (TAPS)
Enzymatic Methyl Sequencing (EM-Seq)
Genomic Mapping of Oxidized 5mCs
Genomic Mapping of 5hmC
Affinity-Based Methods
TET-Assisted Bisulfite Sequencing (TAB-Seq)
Oxidative Bisulfite Sequencing (OxBS-Seq)
Bisulfite-Free Hydroxymethylome Sequencing
Chemical-Assisted C-to-T Conversion of 5hmC Sequencing (hmC-CATCH)
Chemical-Assisted Pyridine Borane Sequencing (CAPS)
APOBEC-Seq
Aba-Seq
Genomic Mapping of 5fC and 5caC
fC-Seal and 5fC Chemical-Assisted Bisulfite Sequencing (fCAB-Seq)
Reduced Bisulfite Sequencing (redBS-Seq)
Methylase-Assisted Bisulfite Sequencing MAB-Seq and caMAB-Seq
Chemical-Enabled 5fC-to-T Sequencing (fC-CET)
Long-Read Sequencing for DNA Modifications
Single-Molecule Sequencing of 5-Hydroxymethylcytosine
Long-Read DNA Methylation and Hydroxymethylation Sequencing with TAPS
Single-Cell Profiling Methods for DNA Modifications
Single-Cell Methylome Sequencing
Single-Cell Profiling Methods for Other Cytosine Modifications
Genome Amplification in Single-Cell Profiling Methods
Prospect of Single-Cell Bisulfite-Free Methods
Biological Applications of Single-Cell Methods
Early Mammalian Development
Clinical Purposes
Conclusions
References
40 Telomerase
Introduction
Telomerase Components
Discovery of Telomerase
Telomerase Reverse Transcriptase (TERT)
Telomerase RNA
Telomerase Processivity
Human Telomerase Structure
Telomerase and Telomere Dynamics in Aging and Disease
Aging and Cancer
Telomerase Activation in Cancer
Telomerase Inhibitors
Potential Caveats of Telomerase Inhibition
BIBR1532
NU-1
Imetelstat
Conclusions and Future Directions
References
41 Telomeres: Structure and Function
Introduction
Telomeres
Telomeric DNA and Telomere Secondary Structures
Telomere Binding Proteins
Role of Telomere Binding Proteins in End Protection
Role of Telomere Binding Proteins in Telomere Length Regulation
Telomere Dynamics in Aging and Disease
Aging and Cancer
Alternative Lengthening of Telomeres (ALT)
Telomere Biology Disorders
Conclusions and Future Directions
References
42 Genetic Alphabet Expansion of Nucleic Acids
Introduction
Development of Replicable and Transcribable UBPs
Preparation of DNAs with UBPs
DNA and RNA Sequencing Involving UBPs
UBP Application to PCR Technology
UBP Application to DNA Aptamer Generation
UBP Application to Transcription Systems
Conclusion
References
43 Unnatural Base Pairs to Expand the Genetic Alphabet and Code
Introduction
Rational Design of Unnatural Nucleotides
An Approach to Developing UBPs
Development of a Replicable UBP
UBP in E. coli: Creation of the First SSO
UBP Optimization Using the SSO
UBP Decoding in an SSO
Applications of the SSO
Conclusion
References
44 OGG1 at the Crossroads Between Repair and Transcriptional Regulation
Introduction
Genome-Wide Distribution of 8-OxoG Is not Random
Role of 8-OxoG and OGG1 in Transcriptional Regulation
Regulation of Transcription Mediated by Induction of 8-OxoG at G-Quadruplex Sequences
Regulation of Transcription Mediated by 8-OxoG Induced by the Enzymatic Activity of LSD1
Role of 8-OxoG and OGG1 in the Regulation of Transcription of Inflammatory Genes
Origin of ROS as a Signaling Molecule for the Induction of 8-oxoG
Finding the 8-OxoG in the Chromatin Context: A Challenging Task for OGG1
DNA Packaging into Nucleosomes: A Barrier for OGG1 and BER Activity
BER in the Highly Compacted Nuclear Environment
Interplay Between BER, NER, and Transcription
BER Is Linked to Transcription via the Mediator Complex and the Cohesin Structure
Structure and Function of the Mediator Complex
Nuclear Condensates Related to Transcription Initiation: Mediator and Super-Enhancers
Conclusion
References
45 Phosphorothioate Nucleic Acids: Artificial Modification Envisaged by Nature
Introduction
Polydiastereomerism of PS-Oligomers
Synthesis of P-Stereodefined Phosphorothioate Oligonucleotides
Stereodefined Phosphorothioate Nucleotides
Interactions of P-Stereodefined PS-Oligomers with DNA, RNA, and Protein Molecules
Formation of the Homoduplexes DNA/DNA and RNA/RNA and Heteroduplexes DNA/RNA
Formation of Higher-Order Structures
Stereodefined PS-Oligomers As Tools in Mechanistic Studies
Interactions with Proteins
Metabolism of PS-Oligomers
Biological Activity of Synthetic Nucleic Acids Containing Phosphorothioate Backbone
Physiological Phosphorothioate Modification of Nucleic Acids
References
Part VI: Analytical Methods and Applications of Nucleic Acids
46 Aptamer Molecular Evolution for Liquid Biopsy
Introduction
Molecular Evolution of Aptamers
Generation of Oligonucleotide Library with Increased Diversity
Library Containing Modified Oligonucleotides
Expanded Libraries with Artificial Oligonucleotides
Library of High-Order Structures
Selection of Aptamer Candidates from Library
Efficient Selection Platforms
Various Target Types
Identification and Characterization of Aptamer Candidates
Effective Identification Techniques
Effective Characterization Methods
Synthesis and Modification
Aptamer-Based Detection of CTCs
CTC Isolation and Enrichment
Aptamer-Based Magnetic Isolation
Aptamer-Based Microfluidic Isolation
Microfluidics-Assisted Magnetic Isolation
Multivalent Aptamer Capture Interface
Release of CTCs
Release by Disrupting the Conformations of Aptamers
Release by Digesting Aptamers with Nucleases
Release by Detaching Aptamers from Capture Substrates
Detection of CTCs
Aptamer-Based Detection of EVs
Isolation-Free Homogeneous Detection
Detection on Solid-Liquid Interface
Electrochemical Detection
Fluorescence Detection
Visual Detection
Conclusion
References
47 Single-Molecule DNA Visualization
Introduction
Optical Mapping Based on Single-Molecule DNA Visualization
DNA Visualization Using DNA-Binding Fluorescent Proteins
Damage Visualization on Single DNA Molecules
DNA Modification Labeling
DNA Recombination
In Vitro Observation of DNA Replication
Observation of DNA Replication in Cells
Conclusion
References
48 Tissue-Specific Drug Delivery Platforms Based on DNA Nanoparticles
Introduction
Four Classes of NANPs
Drug Loading in NANPs
In Vivo Stability of NANPs for Targeted Delivery
NANPs for Passive Tumor-Targeting
NANPs for Active Tumor-Targeting
Discovery of Tumor-Specific NANPs Using Library Approach
NANPs for Lung-Targeted Delivery
NANPs for Kidney-Targeted Delivery
NANPs for Liver-Targeted Delivery
NANPs for Brain-Targeted Delivery
NANPs for Spleen-Targeted Delivery
Challenges and Outlook
References
Further Readings
49 Nanobiodevice for Nucleic Acid Sensing
Nanobiodevice for the Preparation of Nucleic Acid
Extraction of Nucleic Acids
Chemical Lysis
Mechanical Lysis
Thermal Lysis
Electrical Lysis
Isolation of Nucleic Acids
Label-Based Isolation
Label-Free and Label-Based Isolation
Nanobiodevice for Detection of Nucleic Acid
Optical-Based Detection
Electrochemical-Based Detection
Electrical-Based Detection
Conclusion
References
50 Functional Nucleic Acid-Protein Complexes: Application to Fluorescent Ribonucleopeptide Sensors
Introduction
Nucleic Acid-Protein Interactions
DNA-Binding Proteins
Nucleic Acid-Protein Complexes
Sequence-Selective DNA Binding by DNA-Binding Peptide Dimers
Preparation of DNA Nanostructure-Protein Complexes Using DNA-Binding Proteins
RNA-Binding Proteins and Peptides
Preparation of Functional Molecules Using RNA-Peptide Complexes
RNP Receptors and Catalysts
Fluorescent RNP Sensors
Conclusion
References
51 Detection Systems Using the Ternary Complex Formation of Nucleic Acids
Introduction
Branched DNA Assays
Enzyme-Free bDNA-Based Signal Amplification ECL Assay
SMART
3WJ-EXPAR
3WJ-PGRCA
SATIC
3WJ DNAzyme-Based Probe Method
Y-Shaped DNA Dual-Probe Transistor Assay
Other Related Techniques
Conclusion
References
52 Nucleic Acid Conjugates for Biosensing: Design, Preparation, and Application
Introduction
Reactions Involved in DNA/RNA Conjugate Formation
Functional Group-Specific Coupling Reactions
Bioorthogonal Reactions
Azide-alkyne Cycloaddition
Staudinger Ligation
Inverse Electron-Demand Diels-Alder Cycloaddition
Unique Binding and Functional Switching
Kinetic and Thermodynamic Stabilization by Conjugation with Click Chemistry
Switching
pH
Metal Ions
Light
Nucleic Acid Conjugates for Sensing and as a Research Tool
Complementary DNA Probes Modified with Reporter Molecules
Spectrophotometry
Electrochemistry
Nucleic Acid Aptamer Conjugates
Spectrophotometry
Electrochemistry
Lipid/Cholesterol-Modified DNAs
Liposome/Micelle Manipulation
Sensing on the Cell Surface
Liposome Fusion
Antibody/Enzyme-Modified DNAs
Preparation of Antibody-DNA Conjugates
Refined iPCR
Proximity Assays
Autonomous DNA Assembly
Caged Nucleic Acids
DNA/RNA Backbone
Nucleobase
Ribose
Conclusions and Perspectives
References
53 Molecular Beacons With and Without Quenchers
Introduction
Molecular Beacons
Structure of Molecular Beacons
Mechanism and Principles of Molecular Beacons
Advantages and Limitations of Molecular Beacons
Modifications of Molecular Beacons
Applications of Molecular Beacons
Quencher-Free Molecular Beacons
Mono-labeled Quencher-Free Molecular Beacons
Quencher-Free Molecular Beacons with Fluorophore at the Loop or Middle of the Oligonucleotide
Quencher-Free Molecular Beacons with Fluorophore at the Stem or Strand-end
Dual-Labeled Quencher-Free Molecular Beacons
Applications of Quencher-Free Molecular Beacons
Conclusion
References
Part VII: Nanotechnology and Nanomaterial Biology of Nucleic Acids
54 Gene Nanovector for Genome Therapy
Introduction
Multiplex Gene Regulation at Different Levels
The Gene Regulation Toolbox for Genome Therapy
Gene Rescue
Gene Silencing
Gene Editing
Gene Activation
RNA Editing
Gene Read-Through
Exon Skipping
Aptamer and Riboswitch
Catalytic Nucleic Acids
The Gene Vectors for Delivery
The Delivery Approaches
The Form of Gene Vectors
Plasmid DNA
Linear DNA
Viral Vector
Nano DNA
The Presumptive Model of Archimedes Solid-like Nanostructures Assembled from Branch-PCR
The Design of ASN-TO Gene Nanovector
Size-Tunability of ASN-TO Gene Nanovector
The Applications of ASN-TO Gene Nanovector in Genome Therapy
The Gene Overexpression of ASN-TO Gene Nanovector
The Gene Silencing of ASN-TO Gene Nanovector
The Genome Editing of ASN-TO Gene Nanovector
Multiplex Gene Regulation of ASN-TO Gene Nanovector for Cancer Therapy
Prospects of ASN-TO Gene Nanovector
Systemic and Targeted Delivery
Stimulus-Responsive DNA Release
Network Target-Based Genome Therapy with Co-Branch PCR Perspective
Conclusion
References
55 The Frame-Guided Assembly of Nucleic Acids
Introduction
The Demonstration and Development of Frame-Guided Assembly
The Demonstration of Frame-Guided Assembly
The Molecular Generality of Frame-Guided Assembly
The Application of Frame-Guided Assembly in Drug Delivery
The Mechanism of Frame-Guided Assembly
Development of Structural DNA Nanotechnology
Structural DNA Nanotechnology Based on Tile-Tile Interactions
DNA Origami
Classic DNA Origami
Single-Stranded RNA and DNA Origami
Wireframe Structures
Single-Stranded Tiles (SST)
FGA Based on DNA Nanotechnology
Frame-Guided Assembly with Inner DNA Frame
Frame-Guided Assembly with Outer DNA Frame
Frame-Guided Assembly with Planar DNA Frame
Polymer Membrane
Lipid Membrane
Conclusion
References
56 Graphene Oxide and Nucleic Acids
Introduction
Nucleic Acid Interaction with GO
Fluorescence Quenching by GO
Mechanism of DNA Adsorption and Desorption on GO
GO in Nucleic Acid Amplification
Functionalization of GO
GO-Mediated Facilitation of Nucleic Acid Amplification
Applications in FRET-Based Nucleic Acid Biosensors
DNA and RNA Detection
Aptamer-Based Detection
Applications in Biomedical Therapeutics
Biopolymer-Conjugated GO for Gene and Drug Delivery
Biocompatible GO Derivatives as Photothermal Therapeutic Reagents
Conclusion
References
57 Carbon Nanotubes and Nucleic Acids
Introduction
Carbon Nanotubes: ``Helical Microtubules of Graphitic Carbon´´
(n,m) Notation
Other Morphologies Making Use of CNTs
Synthesis Methods and Their Evolution
Arc-Discharge Method
Laser Ablation
Chemical Vapor Deposition (CVD)
Control Parameters of CVD
Variants in CVD Technique
Properties of CNTs
Mechanical Properties
Electrical Properties
Other Properties
Applications in Nucleic Acid Research
Gene Delivery (pDNA, siRNA, and miRNA)
Biosensors
Electrochemical Biosensors
Semiconductor-Based Biosensors
Optical Biosensors
Conclusion and Future Perspectives
References
58 Artificial Genetic Switches and DNA Origami: Current Landscape and Prospects as Designer Therapeutics and Visualization Too...
Introduction
Artificial Genetic Switches for Transcription Therapy
Targeting of the Promoter Region to Control TF-Regulated Gene Expression
Targeting the Coding Region to Control Mutant Gene Expression
Biomimetic Epigenetic Control to Switch ON the Gene Regulatory Network
PIPs as DNA-Based Visualization Tools
DNA Origami to Visualize Single-Molecule Interactions and Epigenetic Events
Direct Observation of Macromolecular Events Using DNA Origami
Force Spectroscopy-Based Biophysical Studies Using DNA Origami
Conclusion
References
59 Functional Engineering of Synthetic RNA Through Circularization
Introduction
Dumbbell siRNA
Buildup siRNA with Circular RNA
Circular RNA for Prokaryotic System
Circular RNA for Eukaryotic System
Chemical Synthesis of Circular RNA
Conclusion
References
60 Stimuli-Responsive DNA Nanostructures for Biomedical Applications
Introduction
DNA Nanostructures
DNA Nanostructures for Bio-Imaging and Drug Delivery
Bio-Imaging
Fluorescent Imaging
Photoacoustic Imaging
Magnetic Resonance Imaging
Positron Emission Computed Tomography/Computed Tomography Imaging
Drug Delivery
Delivery of Small Molecule Drug
Delivery of Functional Nucleic Acid
Delivery of Functional Protein
Delivery of Multiple Therapeutic Components
Conclusion and Future Perspective
References
61 Gene-Like Precise Construction of Functional DNA Materials
Introduction
Design Principle and Assembly Strategies
The Design Principle of DNA Sequence
Assembly Strategies of DNA Materials
Base-Pairing Based Assembly Strategy
Enzyme-Promoted Synthesis and Assembly
Dynamic Assembly
Hybrid Assembly
DNA Biomaterials
DNA Hydrogel
Branched DNA Assembled Hydrogel
RCA Produced DNA Hydrogel
Polymerase Chain Reaction (PCR) Produced DNA Hydrogel
Chemical Cross-Linking DNA Hydrogel
DNA-Based Nanomaterials
Branched DNA Assembled Nanomaterials
RCA Assembled DNA Nanomaterials
HCR Assembled DNA Nanomaterials
DNA Origami Nanomaterials
The Applications of DNA Materials
Cell Engineering
Diagnosis
Therapy
Conclusions and Further Reading
References
62 Design and Self-Assembly of Therapeutic Nucleic Acid Nanoparticles (NANPs) with Controlled Immunological Properties
Introduction
Functional Nucleic Acids
Messenger RNAs
Non-coding RNAs
siRNAs
Riboswitches
Ribozymes
Aptamers
Therapeutic Nucleic Acids (TNAs)
Nucleic Acids as Nanomaterials
Rational Design and Self-Assembly
Sequence Preparation
Incorporating Function into Scaffolds
Optimization of Storage for Increased Nucleic Acid Stability
Methods to Achieve Anhydrous Sample Storage
Light-Assisted Drying (LAD)
NANPs Tolerance of Dehydration Techniques
Recognition of Nucleic Acids and NANPs by the Human Innate Immune System
Pattern Recognition Receptors (PRRs)
Pathogen-Associated Molecular Patterns (PAMPs)
Incorporating Immunological Properties into Design Parameters of NANPs
Design Strategies of NANPs
Composition and Chemical Modifications of NANPs
Purity of NANPs
Route of Delivery of NANPs
Conclusion
References
Further Readings
63 Nanomaterials for Therapeutic Nucleic Acid Delivery
Introduction
Therapeutic Nucleic Acids
ASOs
RNAi
siRNA
miRNA
mRNA
Challenges and Biological Barriers for Delivery of Therapeutic Nucleic Acids
Nanomaterials for the Delivery of Therapeutic Nucleic Acids
Polymeric Nanoparticles
LNPs
Cell-Penetrating Peptides (CPPs)
Inorganic Nanoparticles
Nucleic Acid-Based Nanoparticles
VLPs and Others
Conclusion
References
Part VIII: Nucleic Acid Therapeutics
64 Flex-Nucleosides: A Strategic Approach to Antiviral Therapeutics
Introduction
Background and Significance
Nucleobase Modifications
Distal Fleximers
Proximal Fleximers
Reverse Fleximers
Click Fleximers and Other Triazole Fleximers
Fleximer Bases
Sugar Modifications
2′ Modifications
3′ Modifications
Carboxylic Modifications
Acyclic Modifications
Conclusion
References
65 Small Molecules Targeting Repeat Sequences Causing Neurological Disorders
Introduction
Contractions of Trinucleotide Repeats in HD Targeting CAG Repeats
Alleviation of Splicing Defects in DM1 Targeting CUG Repeat
Alleviation of RNA Toxicity in SCA31 by a Small Molecule Targeting UGGAA Repeat
Conclusion
References
66 Targeted Cancer Therapy: KRAS-Specific Treatments for Pancreatic Cancer
Introduction
Sequence Determinants That Control KRAS Gene Expression
The Biological Function of the KRAS Oncogene
The Role of G4 in the KRAS Promoter
Antigene Strategies Based on G4-Binding Small Molecules
G4-Binding Compounds Binding to the 5′-UTR Region of the KRAS Gene
RG4-Binding Alkyl Porphyrins Promote Cell Death by Apoptosis and Ferroptosis
Transcription Factor Decoy G-Quadruplex Oligonucleotides against the KRAS Gene
Suppression of the KRAS Gene by miRNAs
Conclusion
References
67 Functional XNA and Biomedical Application
Introduction
Functional Nucleic Acids
Threose Nucleic Acid (TNA)
Polymerases Capable of Recognizing TNA Substrates
TNA Aptamers
TNAzymes
2′-Deoxy-2′-Fluoroarabinose Nucleic Acid (FANA)
Polymerases Capable of Recognizing FANA Substrates
FANA Aptamers
FANAzymes
Other XNAs
Polymerases for Other XNAs
Aptamers Selected from Other XNA Chemistries
Enzymes Selected from Other XNA Chemistries
XNA-Modified Existing DNAzymes
Conclusion
References
68 Controlled Intracellular Trafficking and Gene Silencing by Oligonucleotide-Signal Peptide Conjugates
Introduction
Synthesis of Oligonucleotide-Peptide Conjugate
Solution Phase Synthesis
Solid Phase Synthesis
Synthesis of Oligonucleotide Conjugates by SPFC
Syntheses of Oligonucleotide-Peptide Conjugates at the 5′-End of Oligonucleotide by SPFC
Synthesis of Oligonucleotide-Peptide Conjugates Using Modified Base Amino Modifier C2dT
Syntheses of Oligonucleotide-Peptide Conjugates Using 2′-OH Group of Ribose
Hybridization Properties of Oligonucleotide-Peptide Conjugates
Resistance of Oligonucleotide-Peptide Conjugates Against Nuclease Digestion
Activation of RNase H
Cytotoxicity
Control of Intracellular Trafficking by Oligonucleotide-Signal Peptide Conjugate
Inhibition of Telomerase and Telomere Attrition by sASO-NLS Conjugates Targeting hTERC
Silencing of BCR/ABL Chimeric Gene by siRNA-NES Conjugates
Silencing of BCR/ABL Chimeric Gene by siRNAs Bearing 5′-Amino Modifier 5
Silencing of BCR/ABL Chimeric Gene by siRNA-NES Conjugates
Nontoxic Transfection of siRNA-NES Conjugates by Designed Peptides
Conclusions
References
69 First- and Second-Generation Nucleoside Triphosphate Prodrugs: TriPPPro-Compounds for Antiviral Chemotherapy
Introduction
Earlier Nucleoside Triphosphate Prodrugs Bearing One Masking Group
Nucleoside Triphosphate Prodrugs Bearing Two Biodegradable Masking Groups First Generation Compounds
Application of the TriPPPro-Concept to Various Nucleoside Analogues
γ-Nonsymmetrically Modified TriPPPro-Prodrugs Bearing One Biodegradable Group (Second Generation Triphosphate Delivery Systems)
Primer Extension Assays
Summary and Conclusion
References
70 New Molecular Technologies for Oligonucleotide Therapeutics-1: Properties and Synthesis of Boranophosphate DNAs
Introduction
Properties of PB Oligodeoxyribonucleotides
Chemical Stability
Duplex Stability
Nuclease Resistance
RNase H Activity
Syntheses of PB Oligodeoxynucleotides
Challenges of PB Oligonucleotide Syntheses
Synthesis of PB Oligonucleotides from the Phosphoramidite Monomer Bearing Amino-Protecting Groups is Compatible with a Boronat...
Synthesis of PB Oligonucleotides Employing a Nucleoside 3′-O-H-Phosphonate
Synthesis with a P-Boronated Monomer
Stereoselective Synthesis of PB Oligonucleotides Employing an Oxazaphospholidine Monomer Bearing an Acid-Labile Chiral Auxilia...
Conclusion
References
71 Extracellular Vesicle-Mediated CRISPR/Cas Delivery: Their Applications in Molecular Imaging and Precision Biomedicine
Introduction
Extracellular Vesicle Platforms for Targeted CRISPR/Cas Delivery
Endogenous Extracellular Vesicles for CRISPR/Cas Delivery
Engineered Extracellular Vesicles for CRISPR/Cas Delivery
Hybridized Extracellular Vesicles for Targeted CRISPR/Cas Delivery
Delivery of CRISPR/Cas with Various Genome Editing Modes via Extracellular Vesicles
Extracellular Exosome Cargo Systems for CRISPR/Cas Plasmid DNA Delivery
Extracellular Exosomes for Targeted Delivery of CRISPR/Cas RNA
Extracellular Exosome Cargo Systems for Targeted Delivery of CRISPR/Cas Ribonucleoprotein (RNP)
Biomedical Applications via Extracellular Vesicle-Mediated CRISPR/Cas Delivery
Extracellular Exosome-Mediated CRISPR/Cas Delivery in Precise Gene Therapy
Extracellular Vesicle Delivery Systems of CRISPR/Cas for Precise Diagnosis
Machine Learning-Assisted EV-Based CRISPR System as Next-Generation Gene Editing Tool for Personalized Precise Medicine and Di...
Conclusion and Future Perspectives
References
72 Advancing XNAzymes as Nucleic Acid Therapeutics
Introduction
Xeno Nucleic Acids
XNA-Modified DNAzyme 10-23
RNA-Cleaving XNAzymes Isolated by SELEX
Conclusion
References
73 New Molecular Technologies for Oligonucleotide Therapeutics-2: A-Type Nucleic Acid Duplex-Specific Binding Oligocationic Mo...
Introduction
Artificial Cationic Oligosaccharides that Specifically Bind to A-Type Nucleic Acid Duplexes
Artificial Cationic Oligopeptides that Bind Specifically to A-Type Nucleic Acid Duplexes
Conclusion
References
Part IX: Biotechnology and Synthetic Biology of Nucleic Acids
74 Amides and Other Nonionic Backbone Modifications in RNA
Introduction
Amide-Modified DNA
Synthesis, Biophysical, and Structural Properties of Amide-Modified RNA
Biological Activity of Amide-Modified RNAs
Other Nonionic Backbones
Conclusion
References
75 Expanding the RNA- and RNP-Based Regulatory World in Mammalian Cells
Introduction
RNA Switch
Background
Protein-Responsive OFF Switch
miRNA-Responsive Switch
NMD-Mediated RNA Inverter
Alternative Splicing-Based ON Switch
Ribozyme-Based ON Switch
PERSIST
miRNA ON Switch
eToehold Switch
RNA Sensors by ADAR-Mediated Base Editing
CaVT System
CRISPR-Cas Technology
Fundamental Knowledge of CRISPR-Cas Systems
PAM-Altered Cas Proteins
Genome Editing Without DNA Double-Strand Break
Transcriptional Regulation with Engineered Cas Proteins
Epigenetic Regulation
RNA-Targeting CRISPR Technology
Conclusion and Future Perspective
References
Further Readings
76 Design and Biological Application of RTK Agonist Aptamers
Introduction
Main Text
Generation of RTK-Binding Aptamers
TrkB-Binding Aptamers
VEGFR-Binding Aptamers
Met-Binding Aptamers
FGFR-Binding Aptamers
IR-Binding Aptamers
Perspectives
Conclusion
References
77 G-Quadruplex-Based Aptamers in Therapeutic Applications
Introduction
G-Quadruplex (G4) Motifs in Oligonucleotide Aptamers
G4-Forming Aptamers in Therapeutic Applications
G4-Based Aptamers as Potential Drugs
Antiviral G4-Aptamers
Anti-SARS-CoV-2 Aptamers
Anti-HIV Aptamers
G4-Based Aptamers Against Other Viruses
Anticancer G4-Based Aptamers
Anticoagulant G4-Based Aptamers
G4-Based Aptamers as Drug Delivery Systems
AS1411-Drug Covalent/Noncovalent Conjugates
AS1411-Drug-Liposome Systems
AS1411-Drug-Nanoparticle Systems
Other G4-Forming Aptamers as Drug Delivery Systems
Conclusions and Perspectives
References
78 Nucleic Acids in Green Chemistry
Introduction
Environmentally Friendly Synthetic Chemistry with Nucleic Acids
Environmentally Friendly Nucleic Acid Synthesis
Atomically Economic Synthesis of Ribose and Its Precursors Using Hydroxyapatite
Connection of Nucleotides
Nucleic Acids that Provide Special Reaction Fields
Platform for Supporting Metal Catalysts
Asymmetric Reaction Field
Role of Ionic Liquids in Nucleic Acid Green Chemistry
Stability of Nucleic Acid Structures in Ionic Liquids
Solubility of Nucleic Acids in Ionic Liquids
Extraction of Nucleic Acids Using Ionic Liquids
Function of Nucleic Acids in Ionic Liquids
DNA Used as a New Material
DNA Fuel
DNA Cast Film
Bioplastics
Conclusions
References
79 G-Quadruplexes in Human Viruses: A Promising Route to Innovative Antiviral Therapies
Introduction
Baltimore Class I: Double-Stranded DNA
Herpesviridae
Alphaherpesviruses
Betaherpesviruses
Gammaherpesviruses
Papillomaviridae
Adenoviridae
Baltimore Class IV: (+) Single-Stranded RNA
Coronaviridae
Flaviviridae
Togaviridae
Picornaviridae
Baltimore Class V:(-) Single-Stranded RNA
Filoviridae
Orthomyxoviridae
Baltimore Class VI: (+) Single-Stranded RNA - RT
Baltimore Class VII: Double-Stranded DNA - RT
Discussion and Future Perspectives
References
80 Nonchromatographic Purification of Synthetic RNA
Introduction
Purification of Oligonucleotides by Polymerization of Target Strands
Purification of Oligonucleotides by Polymerization and Removal of Failure Strands
Fluorous Affinity Purification of Synthetic Oligonucleotides
Oligonucleotide Purification Using Photocleavable Biotinylated Handle
A ``Catch and Release´´ Strategy for Nonchromatographic Purification of Oligonucleotides
Solid-Phase-Assisted Purification via Oximation Chemistry
Purification of Synthetic RNAs Using Bond-Breaking Bio-orthogonal Chemistry
Purification of Synthetic RNAs Using Inverse Electron Demand Diels-Alder Chemistry
Conclusion
References
81 Genome Editing Using CRISPR
Introduction
Canonical Methods for Genome Editing
Restriction Enzymes
ZFN
Talen
Genome Editing Using the CRISPR-Cas System
Discovery of CRISPR Genes and Identification of Their Function
Potential of the CRISPR-Cas9 System as a Genome Editing Tool
Single RNA-Guided Endonuclease
The Mechanisms of Genome Editing Using the CRISPR-Cas9 System
Canonical Nonhomologous End Joining (c-NHEJ) Repair
Homology-Directed Repair (HDR)
Microhomology-Mediated End-Joining (MMEJ) Repair
Single-Strand Annealing (SSA)
CRISPR-Cas9-Based Genome Editing Strategies Reliant upon DSBs
Enhancing HDR
Suppression of c-NHEJ
Activating HDR Factors
Regulating the Cell Cycle
Increasing the Accessibility of Donor DNA
Using ssDNA as a Donor
Non-HDR-Based Genome Editing
Precise Integration into a Target Chromosome (PITCh)
Homology-Mediated End Joining (HMEJ)
Homology-Independent Targeted Integration (HITI)
Genome Editing Derivatives Utilizing CRISPR Without Generating DNA DSBs
Base Editors (BEs)
Cytosine Base Editor (CBE)
Adenine Base Editor (ABE)
Efforts toward Versatile Application of BEs
Prime Editors (PEs)
Development of PEs
Improvements of PEs
Transposases Associated with the CRISPR-Cas System
Insertion of Transposable Elements by Guide RNA-Assisted Targeting (INTEGRATE)
CRISPR-Associated Transposase (CAST)
Cas-Transposon (CasTn)
Cas13-Based Tool for RNA Editing
Conclusion
References
82 Biomaterials Based on DNA Conjugates and Assemblies
Introduction
DNA-Sugar Conjugates through Diazo-Coupling
DNA-Sugar and DNA-Peptide Conjugates with Spatial Arrangement
DNA-Modified Artificial Viral Capsids Self-Assembled from DNA-Peptide Conjugates
Nucleo-Spheres: Nano- and Micron-Sized Spherical DNA Assemblies
Spatiotemporal Control of Peptide Nanofiber Growth Using DNA-Peptide Conjugates
Conclusion
References
83 G-Quadruplex Resolving by Specific Helicases
Introduction
Classifications of Helicases
G4-Unwinding Helicases
G4 Helicases in DNA Replication, Transcription, and Maintenance
RecQ-Like Helicases: BLM and WRN
G4 Unwinding Helicases in mRNA Regulation
G4-Helicases in Immunity and Infection
Helicases in Viruses
Conclusion
References
84 Binding and Modulation of G-Quadruplex DNA and RNA Structures by Proteins
Introduction
RGG Domains Indicate the Potential of a Protein to Bind to G4s
Multiple Transcription Factors Bind to G4 Regions via RGG-Motif
G4-Binding Proteins and Genome Stability
Conclusion
References
Part X: Functional Nucleic Acids
85 Targeting DNA with Triplexes
Introduction
Triplets
Structures
Kinetics
Nucleotide Analogues
Base Analogues for Overcoming the pH Limitation in Parallel Triplets
Recognizing Pyrimidine Interruptions in Parallel Triplexes
Recognizing Pyrimidine Interruptions in Antiparallel Triplexes
Recognizing all Four Bases
Increasing Triplex Stability
Triplex Binding Ligands
Extended Bases
Backbones
Addition of Positive Charges
Uncharged Backbones
Triplexes in Biology
Intramolecular Triplexes
Intermolecular Triplexes in Biology
Triplexes and RNA Stability
RNA:DNA Triplexes Formed by Noncoding RNAs
Interaction of RNA with Chromatin
Triplexes and Noncoding RNA
Triplex Applications
Triplexes and DNA Nanostructures
Assembly
Triplexes for Sequence Detection
Attaching a Cargo
Conclusions
References
86 Metal Ion-Induced Changes in the Stability of DNA Duplexes
Introduction
Duplex Stabilization by Metal-Mediated Artificial Base Pairing
History of Metal-Mediated Unnatural Base Pairs
Duplex Stabilization by a Single Metal-Mediated Base Pair
Duplex Stabilization by Multiple Metal-Mediated Base Pairs
Metal-Mediated Regulation of Duplex Stability Based on the Bifacial Base Pairing of Modified Pyrimidine Bases
Effects of pH on the Duplex Stabilization by Metal-Mediated Base Pairing
Metal-Mediated Stabilization of Other DNA Structures
Metal-Mediated Stabilization of DNA Triplexes and Quadruplexes
Metal-Mediated Stabilization of DNA Three-Way Junction Structures
Recent Applications of Metal-Mediated Duplex Stabilization
Development of Metal-Responsive DNAzymes Based on the Metal-Mediated Duplex Stabilization
Development of Other Types of Metal-Responsive DNA Molecules
Conclusion
References
87 Liquid-Liquid Phase Separation and Nucleic Acids
Introduction
Structure and Stability of Nucleic Acids Depend on the Surrounding Environment
Behavior of Nucleic Acids in a Solution That Mimics the Cellular Environment Using Co-solutes
Behavior of Nucleic Acids in a Solution That Mimics the Environment Within Cellular Organelles
Behavior of Nucleic Acids in Ionic Liquids
Effects of Nucleic Acid Structure on Phase Separation
Biomolecules Contained Within Droplets
Influence of Nucleic Acid Structure on Droplet Formation and Function
Nucleic Acids in Droplets That Lead to Onset and Progression of Diseases
Nucleic Acids in Droplets Involved in Cancer
Nucleic Acid Structures of Cancer-Related Genes
Effects of Nucleic Acid Structure on Cancer-Related Gene Expression
Phase Separation Related to Cancer Progression
Nucleic Acids in Droplets Involved in Neurodegenerative Disease Mechanisms
Nucleic Acids Involved in Neurodegenerative Diseases
Noncanonical Structures of DNA and RNA in Genes Associated with Neurodegenerative Diseases
Structures of Nucleic Acids That Affect Cytotoxicity via Phase Separation in Neurodegenerative Diseases
Therapeutic Strategies Targeting Nucleic Acids That Cause Phase Separation
Nucleic Acids as Therapeutic Targets
Oligonucleotide Therapy Targeting Nucleic Acids That Cause Phase Separation
CRISPR Therapy Targeting Nucleic Acids That Cause Phase Separation
Small Molecules Targeting Nucleic Acids That Cause Phase Separation
Conclusions
References
88 Natural Riboswitches
Introduction
Natural Riboswitches as Models for RNA Structure and RNA-Small Molecule Interactions
In-Line Probing as a Method for In Vitro Riboswitch Validation
Structural Methods to Study Riboswitch-Ligand Interactions
Biophysical Methods to Study Riboswitch Dynamics
Natural Riboswitches Showcase Mechanisms of Gene Regulation at the RNA Level
Transcription Regulation
Translation Regulation
Other Mechanisms of Regulation
Sophisticated Regulation by Tandem Riboswitches
Riboswitches as Antibiotic Targets
Conclusions
References
89 External Stimulation-Responsive Artificial Nucleic Acids: Peptide Ribonucleic Acid (PRNA)-Programmed Assemblies
General Introductions
Nucleic Acid Medicines: Oligonucleotide Therapeutics
Antisense Strategies
Issues for Improving Oligonucleotide Therapeutics
Overview of Artificial/Modified Nucleic Acid Design: Nucleotide Modification for the Therapeutic Use
Stimuli-Responsive Nucleoside/Nucleotide Analogs and Oligonucleotides
Photo-Irradiation-Responsive Nucleosides/Nucleotides and Oligonucleotides
Redox-Responsive Nucleosides/Nucleotides and Oligonucleotides
Reactive Oxygen Species-Responsive Nucleosides/Nucleotides and Oligonucleotides
Enzymatic Reaction-Responsive Nucleosides/Nucleotides and Oligonucleotides
pH-Responsive Nucleosides/Nucleotides and Oligonucleotides
Development of Peptide Ribonucleic Acids (PRNAs) for the pH Change-Dependent Nucleobase Orientation Control
Conclusion
References
90 Targeting RNA with Small Molecules
Introduction
Small Molecules That Target RNA: Discovery, Design, and Modes of Action
SMIRNA Targeting of miRNAs
Traditional Methods to Identify SMIRNAs
High Throughput Screening
Identifying Chemical Matter from In Vitro Binding Assays
Phenotypic Screening
Structured-Based Drug Design to Enable Identification of SMIRNAs
General Overview of Sequence-Based Design of Structure-Specific SMIRNAs
Defining Privileged RNA Motif-SMIRNA Interactions via 2DCS and HiT-STARTS
Inforna-Enabled Sequence-Based Design of SMIRNAs that Target Human miRNAs
Design of Dimeric SMIRNAs Targeting Disease-Causing miRNAs
Neomycin-Nucleobase Conjugates Targeting Oncogenic miRNAs
Fragment-Based Approach to Identify and Optimize Bioactive SMIRNAs
Targeted Cleavage and Degradation of miRNAs
Overview of Targeted RNA Degradation by Ribonuclease Targeting Chimeras (RIBOTAC)
The Natural Activator 2′-5′ Poly(A) as the RNase L-Recruiting Module
Synthetic Small Molecule as the RNase L-Recruiting Module
SMIRNAs Targeting of mRNAs of Traditionally Undruggable Proteins
Overview of Undruggable Proteins
SMIRNAs Targeting mRNAs as Translational Inhibitors
SMIRNAs Targeting SNCA mRNA to Inhibit Translation
SMIRNAs that Modulate MAPT Splicing
Conclusion
References
Index