Handbook of Chemical Biology of Nucleic Acids

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 Telo