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ویرایش: [2 ed.] سری: ISBN (شابک) : 9781138312869, 113831286X ناشر: CRC PRESS سال نشر: 2022 تعداد صفحات: [644] زبان: English فرمت فایل : PDF (درصورت درخواست کاربر به PDF، EPUB یا AZW3 تبدیل می شود) حجم فایل: 126 Mb
در صورت تبدیل فایل کتاب RNA NANOTECHNOLOGY AND THERAPEUTICS. به فرمت های PDF، EPUB، AZW3، MOBI و یا DJVU می توانید به پشتیبان اطلاع دهید تا فایل مورد نظر را تبدیل نمایند.
توجه داشته باشید کتاب نانوتکنولوژی و درمان RNA. نسخه زبان اصلی می باشد و کتاب ترجمه شده به فارسی نمی باشد. وبسایت اینترنشنال لایبرری ارائه دهنده کتاب های زبان اصلی می باشد و هیچ گونه کتاب ترجمه شده یا نوشته شده به فارسی را ارائه نمی دهد.
Cover Half Title Title Page Copyright Page Table of Contents Preface Acknowledgments Introduction Contributors Part I: Concepts and Definitions in RNA Nanotechnology Chapter 1: RNA Structure and Folding RNA Chemistry RNA Structure RNA Modification Chapter 2: RNA Regulation and Function in Nature RNA Production and Function for Protein Production Noncoding RNAs and Their Function: MicroRNAs and Gene Regulation MicroRNAs and Gene Regulation Conclusions References Chapter 3: Principles and Fundamentals of RNA Nanotechnology Phylogenetic Analysis of RNAs Features of Nucleic Acids Promoting RNA Nanotechnology RNA Motifs Used in RNA Nanotechnology Stoichiometry Determination by Binomial Distribution, by Log/Log Plot with a Serial Dilution; by Finding the Common Multiple of 2 and 3 History and Evolution of RNA Nanotechnology References Chapter 4: Computation and Folding Predictions Resources for RNA Structure Computation 2D/3D Modeling/Prediction of Desired RNA Nanoparticles Folding Predictions vs. Structural Building Blocks Sequence Search and Alignment of RNA References Chapter 5: Enzymatic Synthesis and Modification of RNA Nanoparticles Construction of DNA Templates In Vitro Transcription of RNA Oligo Strands Inclusion of Chemical Modifications into Enzymatic Synthesis of RNA Oligos Rolling Circle Transcription for Large-Scale Production of RNA Conclusions References Chapter 6: Synthetic and Enzymatic Methods for RNA Labeling and Modifications RNA Synthesis Synthetic Methods for RNA Labeling Synthetic Methods for Ligation Enzymatic Methods for RNA Labeling Artificial Enzymes for Ligation Conclusions References Chapter 7: Methods and Assembly of RNA Nanotechnology Methods for the Construction of RNA Nanoparticles In Vitro Nanoparticle Assembly In Vivo Nanoparticle Assembly Conclusions References Chapter 8: Purification, Characterization, and Structure Determination of RNA Nanoparticles Purification of the RNA Nanoparticles Physical Characterization of RNA Nanoparticles Structure Determination of RNA Nanoparticles Conclusion References Chapter 9: SELEX Chapter 10: Uniqueness, Advantages, Challenges, Solutions, and Perspectives in Therapeutics Applying RNA Nanotechnology Introduction Historical Evolution of RNA Nanotechnology Uniqueness of RNA Nanotechnology Techniques for the Construction of Therapeutic RNA Nanoparticles Hand-in-Hand (Loop–Loop) Interactions Robust RNA Motif as a Scaffold to Build Multivalent Nanoparticles Palindrome Sequence Mediated Formation of RNA Dimers RNA Junctions as LEGO Pieces to Build Quaternary Structures RNA Binding Proteins to Serve as Junctions for the Formation of Arrays Combination of Rolling Circle Transcription of RNA and Self-assembly to Produce Giant Spherical RNA Particles Construction of RNA-Based Nanoparticles for Therapeutic Applications siRNA miRNA Ribozymes Riboswitches Aptamers Advantages of RNA Nanotechnology for In Vivo Applications Polyvalent Delivery for Generating Synergistic Effects Defined Size, Structure, and Stoichiometry Nanoscale Size for Enhanced Permeability and Retention Effects Targeted Delivery to Cancer Cells Non-Induction of an Antibody Response to Ensure Repeated Treatments Challenges, Solutions, and Perspectives in RNA Nanotechnology Chemical Instability Thermodynamic Instability Short In Vivo Half-Life Low Yield and High Production Costs Toxicity, In Vivo Safety, and Side Effects Specific Delivery and Targeting Problems Endosome Trapping Conclusions Acknowledgments Author Disclosure Statement References Part II: Design, Synthesis, and Characterization Methods in RNA Nanotechnology Chapter 11: The Natural Versatility of RNA Structural Elements of RNA The Anatomy of Nucleotides Sugar Pucker of RNA The Need for Thymine in DNA Physicochemical Properties of RNA and DNA Base-Pair Geometries and Stabilizing Interactions Ribozymes Riboswitches Conclusion Acknowledgments References Chapter 12: Nucleic Acids as a Building Material in Nanotechnology Rational Design and Computer-Assisted Strategies Acknowledgments References Chapter 13: Multiple Functionalities for RNA Nanoparticles Introduction The Assembly of RNA Nanoparticles Tools for Real-Time Assembly Visualization Multifunctional RNA NANPs Conclusion and Perspective References Chapter 14: From Computational RNA Structure Prediction to the Design of Biologically Active RNA-Based Nanostructures Acknowledgments References Chapter 15: Application of RNA Tertiary Structure Prediction Tool iFoldRNA in RNA Nanotechnology Introduction RNA 3D Structure Prediction Using iFoldRNA The Outline of iFoldRNA iFoldRNA Webserver RNA Modeling Accuracy Using iFoldRNA Applications of iFoldRNA in RNA Nanotechnology Tertiary Structure Construction and Comparison of Thermodynamic Stability of RNA Triangle and Rectangle Thermodynamics Analysis of RNA Cube and Ring Conclusion Acknowledgments References Chapter 16: HyperFold: A Web Server for Predicting Nucleic Acid Complexes Introduction Algorithm Entropy Estimation Partition Function Web Page Usage Limitations Conclusions Acknowledgments References Chapter 17: RNA Switches: Towards Conditional Dynamic RNA-Based Constructs for Therapeutics and Bioassays Acknowledgments References Chapter 18: RNA Multiway Junction Motifs as Lego for the Construction of Multifunctional RNA Nanoparticles Introduction 3WJ Motifs Classifications and Occurrences Application of 3WJ in Nanotechnology The Construction of 3WJ-Based RNA Nanoparticles Harboring Functional Modules Evaluation of the Functional Modules Incorporated in 3WJ RNA Nanoparticles The Construction of 3WJ-Based Square-Shaped and Triangular RNA Nanoparticles 4WJ Motifs Classifications and Occurrences Application of 4WJ Motifs in Nanotechnology Future Outlook and Perspectives Mutations to Increase Thermodynamic Stability Chemical Modifications to Increase Serum Stability Computational Approaches to Guide Nanoparticle Assembly Evaluation of Functionality of Modules Incorporated into 3WJ or 4WJ Scaffold Acknowledgments References Chapter 19: Fabrication Methods for RNA Nanoparticle Assembly Based on Bacteriophage Phi29 pRNA Structural Features RNA Nanotechnology Principles and Tools for RNA Nanoparticle Fabrication Assembly of pRNA-Based RNA Nanoparticles The Biological Function of pRNA on Phi29 DNA Packaging Motor Structure Features of Bacteriophage phi29 pRNA Bottom-Up Assembly of pRNA Nanoparticles Construction of pRNA Nanoparticles with Biological and Pharmaceutical Functionalities Incorporation of Small Interfering RNA (siRNA) into pRNA Nanoparticles Incorporation of Ribozyme into pRNA Nanoparticles Incorporation of RNA Aptamer into pRNA Nanoparticles Incorporation of Chemical Targeting Ligand such as Folate into pRNA Nanoparticles Incorporation of Fluorescent Marker into pRNA Nanoparticles Concluding Remarks Acknowledgments References Chapter 20: Purification of RNA, Modified Oligos, and RNA Nanoparticles Introduction Liquid Chromatography Principles of Oligonucleotide Purification Anion Exchange HPLC (IP)-RP HPLC IPRP Info Combined Continuous Elution Gel-Electrophoresis (CEGE) CEGE Purification of Transcription Products CEGE Purification of RNA Nanoparticles Ultracentrifugation CsCl Density Gradient Ultracentrifugation for the Purification of Transcription Products Sucrose Gradient Rate Zonal Ultracentrifugation for the Purification of RNA Nanoparticles Choosing the Best Method for Your Application Acknowledgments References Chapter 21: Physicochemical Characterization of Nucleic Acid Nanoparticles Introduction Electrophoretic Mobility Shift Assays (EMSA) to Test Assembly Efficiency Evaluation Thermodynamic Stability by UV-Thermal Denaturation (UV-Melt) and Temperature Gradient Gel Electrophoresis (TGGE) Nuclease Resistance Properties of NANP Can Be Assessed by Serum Stability Assay Hydrodynamic Diameter Assessment by DLS NANP 2D Imaging by Atomic Force Microscopy and 3D Structure Determination by Cryo-Electron Microscopy and X-ray Crystallography Acknowledgment References Chapter 22: Light Scattering Techniques for Characterization of NANPs and Their Formulations Dynamic Light Scattering Phase-Analysis Light Scattering Multi-Angle Light Scattering Small-Angle Scattering References Chapter 23: Electron Microscopy of Nucleic Acid Nanoparticles Acknowledgments References Chapter 24: A Single-Molecule FRET Approach for Investigating the Binding Mechanisms of Anti-Viral Aptamers Introduction Hepatitis C Virus Biology Nucleic Acid Aptamer Therapies Single-Molecule Fluorescence Spectroscopy Experimental Approach Bioconjugation Techniques Fluorescence Excitation Scheme Fluorescence Emission and Detection Data Analysis Molecular Dimension of Free HCV Core Protein Dependence on Solution Conditions Molecular Dimension of Aptamer-Bound HCV Core Protein Compaction of HCV Core Protein Binding Affinity Binding Specificity Discussion and Conclusions Model for Inhibition Future Perspectives Materials and Methods Acknowledgments References Chapter 25: Entropy and Enthalpy in RNA Nanoparticle Assembly and Thermodynamic Stability for Medical Application Using RNA Nanotechnology Introduction Energetics in the Formation of RNA Nanoparticles Gibbs Free Energy Enthalpy in Nanoparticle Assembly Entropy in Nanoparticle Assembly Prediction and Calculation of Thermodynamic Parameters of RNAs Thermodynamic Stability of 3WJ RNA Nanoparticles Stability of the pRNA-3WJ Effects of Chemical Modifications on the Stability of RNA and 3WJ Nanoparticles Assemblies of RNA Three-Way Junction (3WJs) Driven by Entropy and Enthalpy Applications of Stable 3WJ Nanoparticles Conclusions Acknowledgments References Part III: Immunorecognition of RNA Nanoparticles Chapter 26: Immunorecognition of Nucleic Acid Nanoparticles PRR Recognition of Nucleic Acids Engineering NANP Immunorecognition References Chapter 27: Viral Noncoding RNAs in Modulating Cellular Defense and Their Potential for RNA Nanotechnology Cell Defense Against Viruses Viral RNAs in Evasion of Cell Defense NANPs and Modulation of Immune Restrictions Acknowledgments References Chapter 28: RIG-I as a Therapeutic Target for Nucleic Acid Nanoparticles (NANPs) References Chapter 29: Driving Dynamic Functions with Programmable RNA Nanostructures Programmable Nanomaterials Riboswitches and Ribozymes Aptamers Implementing Functions into Dynamic Nucleic Acid Nanoparticles NANPs as Scaffolds for Functional RNAs Dynamic NANPs Future Directions Acknowledgments References Chapter 30: Defining Immunological Properties of Nucleic Acid Nanoparticles Using Human Peripheral Blood Mononuclear Cells Introduction Nucleic Acid-based Technologies Therapeutic NANPs NANPs’ Safety and Immune-mediated Efficacy Considerations Development of the Protocol Advantages Limitations Overview of the Procedure Applications Alternative Methods Experimental Design PBMCs Controls Preparation of Nucleic Acid Components NANP Design NANP Assembly Cytokine Detection Understanding the Mechanism of NANP Recognition Control Nucleic Acid Nanoparticles Biological Materials Reagents Reagent Setup Equipment Procedure Troubleshooting Anticipated Results Anticipated Results for Mechanistic Analysis (Steps 57–60) Acknowledgments References Part IV: Delivery of Functional RNA Nanoparticles Chapter 31: The Emerging Field of RNA Nanotechnology Distinct Attributes of RNA Inside the Body Techniques for Constructing RNA Nanoparticles Applications of RNA Nanotechnology Challenges and Perspectives Acknowledgements Additional Information References Chapter 32: Thermodynamically Stable RNA Three-Way Junction for Constructing Multifunctional Nanoparticles for Delivery of Therapeutics Properties of 3WJ-pRNA Properties of 3WJ-pRNA with Therapeutic Modules In Vitro and in Vivo Assessments of Multi-Module 3WJ-pRNA Comparing 3WJ-pRNA with Other Biological 3WJ Motifs Methods Synthesis and Purification of pRNA Construction and Purification of pRNA Complexes Construction of Multi-Module RNA Nanoparticles Competition Assays and Radiolabel Chasing Melting Experiments for T m Stability Assay in Serum HBV Ribozyme Activity Assay MG Aptamer Fluorescence Assay Flow Cytometry Analysis of Folate-Mediated Cell Binding Confocal Microscopy Assay for the Silencing of Genes in Cancer Cell Model AFM Imaging Stability and Systemic Pharmacokinetic Analysis in Animals Targeting Tumor Xenograft by Systemic Injection in Animals Acknowledgments Author Contributions Additional Information Note References Chapter 33: RNAi Nanotherapeutics for Localized Cancer Therapy Acknowledgments References Chapter 34: Delivery of RNA Nanoparticles Acknowledgments References Chapter 35: Recommendations for Planning In Vivo Studies for RNAi Therapeutics Acknowledgments References Chapter 36: Mesoporous Silica Nanoparticles for Efficient siRNA Delivery Engineering MSNs to Address Major Challenges in siRNA Delivery Therapeutic Applications of siRNA-Loaded MSN Platform in Human Diseases Multifunctional Applications of siRNA-Loaded MSNs for Cancer Treatment Theranostic Applications of siRNA-Loaded MSNs for Cancer Imaging and Therapy Conclusions References Chapter 37: Method of Large-Scale Exosome Purification and Its Use for Pharmaceutical Applications Introduction Current Method for Exosome Purification Differential Ultracentrifugation Cushion-Modified Ultracentrifugation Density Gradient Ultracentrifugation Size Exclusion Chromatography Large-Scale Exosomes Production and Purification Production of Exosomes Purification of Exosomes Progress on Exosome-Based Pharmaceutics Development Conclusion Acknowledgments References Chapter 38: Engineered Extracellular Vesicle-Based Therapeutics for Liver Cancer Introduction Engineered Biological Nanoparticles as Carriers of RNA-Based Therapeutics Extracellular Vesicles as Biological Nanoparticles Physicochemical Characterization of Extracellular Vesicles Engineering EVs Through Surface Modifications Use of RNA Aptamers for Targeting Specificity An Illustrative Application – Developing Targeted Therapies for HCC Choice of Cellular Targets Choice of Targeted Cell Types Choice of Targeting Aptamer Generation of Targeted Biological Nanoparticles Conclusions and Future Perspectives Acknowledgments References Chapter 39: Extracellular Vesicles (EVs): An Innovative Approach to Engineering Nucleic Acid Delivery What are Extracellular Vesicles? Therapeutic Potential of EVs as a Drug Delivery Vehicle EV Loading Methods Electroporation Sonoporation/Sonication Producer Cell Engineering Small RNA/DNA Loading Kit- Exo-Fect siRNA/miRNA Transfection Kit Cellular Uptake Conclusions References Chapter 40: Extracellular Vesicles (EVs): Naturally Occurring Vehicles for RNA Nanotherapeutics Introduction The Biogenesis of EVs Exosomes Microvesicles Apoptotic Bodies Other EVs The RNA Cargo of EVs mRNA MicroRNA Other Non-Coding RNAs The (Patho)physiological Role of EVs Immune Modulation Extracellular Signaling Cargo Trafficking Nucleic Acid Trafficking Cancer Progression Biomarkers of Disease Development and Regeneration Central Nervous System Function and Disease EVs as Therapeutic Tools EV Biodistribution: Engineering for Enhanced Uptake EV Cargo-Loading Methods Preclinical Studies of EV Therapeutic Applications EVs for RNA Therapeutics EVs in Clinical Trials Conclusions References Chapter 41: Harnessing Exosomes and Bioinspired Exosome-Like Nanoparticles for siRNA Delivery Introduction Exosome Composition Loading Exosomes with siRNA Harnessing Natural Exosomes for siRNA Delivery Modified Exosome for Targeted siRNA Delivery Designing Bioinspired Exosome-Like Nanoparticles for siRNA Delivery Conclusion Acknowledgments References Part V: Application and Exploitation in RNA Nanotechnology Chapter 42: RNA Structural Modeling for Therapeutic Applications Introduction Computational Models for RNA Nanotechnology and Therapeutics miRNA, siRNA, shRNA, and sRNA Binding Site Prediction RNA Structure Prediction for Double-Stranded and Multi-Stranded RNA RNA Nanostructure Design Computationally Modeling the Structure of RNA Aptamers Conclusion Acknowledgment References Chapter 43: RNA Micelles for Therapeutics Delivery and Cancer Therapy Introduction: RNA Micelles Formation and Characterization of RNA Micelles Delivery of Therapeutics by RNA Micelles Immunogenicity Evaluation of RNA Micelles Conclusion and Perspectives Acknowledgments References Chapter 44: Bacteriophage RNA Leading the Way in RNA Nanotechnology for Targeted Cancer Therapy Introduction Packaging RNA Platform in RNA Nanotechnology Overcoming Bottlenecks in Targeted Drug Delivery Future Outlook Towards Clinical Use Acknowledgments Conflict of Interest References Chapter 45: Current State in the Development of RNAi Self-Assembled Nanostructures Introduction RNAi Mechanism Challenges of siRNA Delivery in the in vivo Environment RNA Nanoparticle Aptamer-siRNA Chimeras gp120 Aptamer–siRNA Chimeras pRNA–siRNA Chimeras pRNA/siRNAs/Aptamers Chimeras pRNA Three-Way Junction/Four-Way Junction–siRNA Chimeras Tripodal RNA Nanoparticles Self-Assembled siRNA Nanoparticles Conclusions and Future Prospects Acknowledgments References Chapter 46: RNA-Based Devices for Diagnostic and Biosensing RNA as a Material for Biosensors MicroRNA Detection Long Non-Coding RNA Detection Detection of RNAs Using RNA Biosensors Fluorescence In Situ Hybridization Molecular Beacons RNA Switches RNA Devices Which Respond to Non-Nucleic Acid Analytes and Processes Ribozymes and Riboswitches Aptamers Future Directions of RNA-Based Diagnostics Acknowledgments References Chapter 47: MicroRNAs: Biology and Role in RNA Nanotechnology The Biogenesis of miRNAs The Mechanism of Action of miRNAs The Role of miRNAs in Disease and Therapy Cancer Cardiovascular Diseases Neurological Diseases Delivery of miRNAs as Therapeutics Acknowledgment References Chapter 48: Conjugation of RNA Aptamer to RNA Nanoparticles for Targeted Drug Delivery Introduction Structure of RNA Nanoparticles RNA Nanoparticles Formed by Dimerization of phi29 pRNA RNA Nanoparticle Composed of pRNA Multimer and Higher Order Structures as Scaffold Multivalent RNA Nanoparticles Based on the Three-Way Junction Motif RNA Polygon Nanoparticles Based on the Three-Way Junction Motif Conjugation of RNA Aptamers to RNA Nanoparticles for Targeted Drug Delivery RNA Aptamers and SELEX Approaches to Conjugate Aptamer to RNA Nanoparticles Key Factors for Conjugating Aptamer to RNA Nanoparticles Application Status of RNA Aptamer-Conjugated pRNA Nanoparticles Conclusions and Future Perspective Acknowledgments References Chapter 49: MicroRNAs in Human Cancers and Therapeutic Applications Introduction Biogenesis and Working Mechanism of miRNA miRNAs in Human Cancers miRNA Modulation for Cancer Therapy Chemically Modified Nucleotide Analogs Viral Delivery of miRNAs Non-Viral Delivery of miRNAs RNA Nanoparticles for Tissue-Specific Targeted miRNA Perspectives Acknowledgment References Chapter 50: Tuning the Size, Shape, and Structure of RNA Nanoparticles for Favorable Cancer Targeting and Immunostimulation Introduction Definition of RNA Nanotechnology Advantages of RNA Nanotechnology for Cancer Targeting and Immunomodulation RNA Nanoparticles Are Distinct from Traditional Therapeutic RNAs RNA Nanoparticles Show Favorable Cancer Targeting and Minimal Organ Accumulation RNA Nanoparticles Intrinsically Display Immunologically Inert Property and Non-Toxicity Physicochemical Properties of RNA Nanoparticles Affect In Vivo Biodistribution and Immune Response Nanoparticle Size Nanoparticle Shape Sequence Signature and Modular Stoichiometry Surface Chemistry Other Factors Perspectives RNA Nanotechnology for Potential Immunotherapy Understanding the Interactions of RNA Nanoparticles at the Nano-Bio Interface Conclusion Acknowledgments Conflict of Interest Note References Chapter 51: RNA Nanotechnology and Extracellular Vesicles (EVs) for Gene Therapy Background of EVs and Potential Application in Cancer Therapy RNA Nanotechnology for EVs Ligand Displaying and Delivering siRNA Arrow-Head or Arrow-Tail for RNA Loading or Membrane Display RNA-Displaying EVs Can Target Tumors and Silence Genes in Cancer Cell Inhibition of Tumor Growth by Ligand-3WJ-Displaying EVs Challenge of EVs Production and Alternative Source of EVs Displaying of Ligands on GDENs Using Arrow-Tail RNA Nanoparticles for Specific Cancer Targeting Therapeutic RNA Delivery and Tumor Suppression by Ligand-Displaying GDENs EVs Avoid Endosome Trapping and Facilitate Cytosol Delivery by Direct Fusion Mechanism Confirmation of Cytosol Delivery with Folate-Exosome Mechanism of Direct Fusion or Back Fusion After Entering Endosome Comparison of Gene-Silencing Efficiency and Tumor Inhibition Potency between Folate-Displaying Exosome and Folate-Conjugated siRNA References Chapter 52: Application of RNA Aptamers in Nanotechnology and Therapeutics Introduction Generation of Aptamers by In Vitro Selection Individual Aptamers as Reagents and Therapeutics Multivalent Aptamers and Aptamer-containing Nanoparticles Aptamer-Articulated Nanoscale Systems Prospects for Aptamer-Enabled Dynamic Structures Conclusion Acknowledgments References Index