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RNA Interference (Life Science Research Fundamentals)
by WileyThe 2006 Nobel Prize in Physiology or Medicine was awarded to Andrew Z. Fire and Craig C. Mello for their discovery of RNA interference (RNAi). RNAi is a biological process in which RNA molecules can silence (inhibit) or up- or down-regulate gene expression, typically by causing the destruction of specific messenger RNA (mRNA) molecules. This collection of articles begins with an introduction to RNAi, and proceeds to describe uses of this technology in various approaches to disease treatment, including gene therapy. Several laboratory protocols for silencing genes via RNAi are also provided, as are protocols for down-regulating and then rescuing those down-regulated genes, which demonstrates specificity of the approach. This e-book — a curated collection from eLS, WIREs, and Current Protocols — offers a fantastic introduction to the field of RNA interference for students or interdisciplinary collaborators.
RNA Interference and CRISPR Technologies: Technical Advances and New Therapeutic Opportunities (Methods in Molecular Biology #2115)
by Mouldy SioudThis volume explores the uses of RNAi and CRISPR interferences as a general method for inhibiting gene expression, with focus on their biological functions, design, chemical modifications, delivery, and preclinical/clinical applications. In addition to relevant backgrounds, the chapters in this book discuss simple and accurate protocols dealing with the latest advances in RNAi and CRISPR applications and look at how these methods differ from one another. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.Comprehensive and cutting-edge, RNA Interference and CRISPR Technologies: Technical Advances and New Therapeutic Opportunities is a valuable resource for any scientist, teachers, graduate student, postdoc, and clinician interested in this field. This book also benefits anyone in research and development in biotech and pharmaceutical companies who want to understand more about these technologies, and their applications in biology and medicine.
RNA Interference, Editing, and Modification
by Jonatha M. GottA comprehensive collection of cutting-edge methods for elucidating the function of new genes and altering gene expression. These readily reproducible techniques can be used either in transient and stable gene splicing applied to worms, flies, trypanosomes, mammals, and plants, or in studying RNA editing mechanisms in a wide range of organisms, including systems that involve the conversion of one base to another and insertion/deletion editing. Topics of interest include stable and transient RNA interference, gene silencing, RNA editing, bioinformatics, small noncoding RNAs, and RNomics. Special attention is given to methods for the identification and characterization of small RNAs involved in RNA interference or modification.
RNA Isolation and Characterization Protocols
by Ralph Rapley David L. ManningInnovative biological investigators offer a powerful and highly useful collection of up-to-date methods for the isolation of RNA from a variety of sources, including bacterial, plant, and mammalian cells. These fine-tuned protocols take both the experienced and inexperienced investigator through the nuances of RNA manipulation, from extraction to in vitro translation. The book also includes protocols for the analysis and characterization of isolated RNA species and extensive troubleshooting hints and tips to ensure easy reproducibility. RNA Isolation and Characterization Protocols is the single best collection of easily reproducible, step-by-step RNA techniques now available for today's bench scientists.
RNA Mapping
by M. Lucrecia Alvarez Mahtab NourbakhshIn RNA Mapping- Methods and Protocols expert researchers in the field detail many of the methods which are now commonly used to study RNA. These include protocols for the consequence of the emerging interest in the characterization of cellular RNAs urged by their potential use as diagnostic biomarkers or therapeutic targets. In particular, the biological relevance of microRNAs in human physiology and disease development is highlighted in the 16 chapters focused on methods for their physical and functional mapping. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, RNA Mapping- Methods and Protocols provides instruction and inspiration for scientists who are facing the challenges of the discovery and/or functional characterization of RNA molecules for a wide variety of applications ranging from novel biomedical diagnostics to therapeutics and biomaterials.
RNA Metabolism and Gene Expression in Archaea (Nucleic Acids and Molecular Biology #32)
by Béatrice Clouet-D'OrvalThis book focuses on the regulation of transcription and translation in Archaea and arising insights into the evolution of RNA processing pathways. From synthesis to degradation and the implications of gene expression, it presents the current state of knowledge on archaeal RNA biology in 13 chapters. Topics covered include the modification and maturation of RNAs, the function of small non-coding RNAs and the CRISPR-Cas defense system. While Archaea have long been considered exotic microbial extremophiles, they are now increasingly being recognized as important model microorganisms for the study of molecular mechanisms conserved across the three domains of life, and with regard to the relevance of similarities and differences to eukaryotes and bacteria. This unique book offers a valuable resource for all readers interested in the regulation of gene expression in Archaea and RNA metabolism in general.
RNA Metabolism in Mitochondria (Nucleic Acids and Molecular Biology #34)
by Jorge Cruz-Reyes Michael W. GrayThis volume focuses on mitochondrial RNA metabolism, emphasizing recent discoveries and technological advances in this fast moving area that increase our understanding of mitochondrial gene function. Topics addressed include the interplay of mitochondria with the nucleus and cytosol, structure-function connections, and relevance to human disease. Mitochondria are the powerhouses of the cell, and a great deal is known about mitochondrial energy metabolism. Less well known is the plethora of amazing mechanisms that have evolved to control expression of mitochondrial genomes. Several RNA processes and machineries in protozoa, plants, flies and humans are discussed, including: transcription and RNA polymerase mechanism; tRNA processing of 5′ and 3′ ends; mRNA maturation by nucleotide insertion/deletion editing and by RNA splicing; mRNA stability; and RNA import. Specialized factors and ribonucleoproteins (RNPs) examined include pentatricopeptide repeat (PPR) proteins, RNase P, polymerases, helicases, nucleases, editing and repair enzymes. Remarkable features of these processes and factors are either not found outside mitochondria, differ substantially among eukaryotic lineages, or are unique in biology.
RNA Metabolism in Trypanosomes
by Albrecht BindereifTrypanosomes are unicellular protozoa of ancient evolutionary origin that are responsible for several tropical diseases, such as African sleeping sickness. Over the last few decades, research in trypanosome biology has revealed many unique and fascinating features, many of which have helped to establish new paradigms in other biological systems. This applies in particular to studies in gene expression and regulation, which benefit enormously from the trypanosome genome projects and from the new genome-wide approaches recently introduced in trypanosome research. This volume covers the most important aspects of biosynthesis, processing, and functions of RNA in trypanosomes, ranging from transcription to RNA editing, mRNA splicing/translation/turnover, processing of transfer and ribosomal RNA, RNA interference, and current transcriptome-wide analyses. Recent progress in RNA-focused research in trypanosomatids promises to yield novel insights into trypanosome-specific features, as well as to reveal in the process new potential therapeutic strategies for combating these parasitic diseases.
RNA Methylation
by Alexandra LusserThis volume provides a comprehensive collection of current methods and protocols to study posttranscriptional base modifications in RNA with special focus on methylation. The protocols in this book discuss state-of-the-art methods for investigating aspects of RNA methylation on different types of RNA. The protocols cover topics such as wet-lab techniques for the detection of methylation, instructions for bioinformatics analyses of transcriptome-scale data, and protocols for the functional examination of RNA modifications and enzymes. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, RNA Methylation: Methods and Protocols is a valuable resource for biochemists and molecular biologists, from various fields, who wish to investigate different types of RNA methylations.
RNA Modifications: Methods and Protocols (Methods in Molecular Biology #2298)
by Mary McMahonThis detailed book describes some of the most recent advances and up-to-date methodologies to detect, quantify, analyze, and elucidate the biological function of different types of RNA modifications. Importantly, the methodologies and tools described herein can be applied to a wide variety of organisms and can be used to address biological and clinical questions. Beginning with a section on bioinformatics tools, the collection continues with sections on detecting RNA modifications using Nanopore direct RNA sequencing, next-generation sequencing approaches, qPCR- and molecular biology-based methods, mass spectrometry- and NMR-based methods, as well as approaches to assess kinetics, determinants, and functions of RNA modifications. Written for the highly successful Methods in Molecular Biology series style, chapters include introduction to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, RNA Modifications: Methods and Protocols serves as an ideal guide for those working directly in the fields of epitranscriptomics and post-transcriptional gene regulation, as well as for scientists and clinicians interested in bioinformatic tools to study RNA modifications and techniques to dissect their roles in physiology and disease.Chapter 20 is available open access under a CC BY 4.0 license.
RNA Nanostructures: Design, Characterization, and Applications (Methods in Molecular Biology #2709)
by Kirill A. AfoninThis volume details protocols for computer-assisted design and experimental characterization of RNA nanostructures. Chapters guide readers through RNA nanotechnology, design and characterization of RNA nanostructures, assessment of immunology of nanomaterials, biosensing and drug delivery, various biomedical applications, and delivery approaches for therapeutic RNA nanoparticles. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, RNA Nanostructures: Design, Characterization, and Applications aims to address essential topics and concerns in the growing field of RNA nanotechnology.
RNA Nanostructures
by Eckart Bindewald Bruce A. ShapiroThis volume presents a collection of computational and experimental protocols pertaining to the creation, characterization, and utilization of RNA nanostructures. The chapters in this book cover topics such as ion effects in RNA folding; design and crystallography of self-assembling RNA nanostructures; x-aptamer selection and validation; RNAi in HIV-infected cells; and preparation of a conditional RNA switch. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, RNA Nanostructures: Methods and Protocols is a valuable resource for the design and production of RNA nanostructures. Researchers and scientists sharing these detailed protocols is important for sustained progress in the field.
RNA Nanotechnology and Therapeutics
by Peixuan Guo Kirill A. AfoninInterest in RNA nanotechnology has increased in recent years as recognition of its potential for applications in nanomedicine has grown. Edited by the world's foremost experts in nanomedicine, this comprehensive, state-of-the-art reference details the latest research developments and challenges in the biophysical and single molecule approaches in RNA nanotechnology. In addition, the text also provides in-depth discussions of RNA structure for nanoparticle construction, RNA computation and modeling, single molecule imaging of RNA, RNA nanoparticle assembly, RNA nanoparticles in therapeutics, immunorecognition of RNA nanomaterials, RNA chemistry for nanoparticle synthesis, and conjugation and labeling. Presents the latest research and discoveries in RNA nanotechnology Features contributions from world-class experts in the field Covers RNA nanoparticles in therapeutics Describes self-assembled RNA nanoparticles
RNA Nanotechnology and Therapeutics
by Peixuan Guo Farzin HaqueInterest in RNA nanotechnology has increased in recent years as recognition of its potential for applications in nanomedicine has grown. Edited by the world's foremost experts in nanomedicine, this comprehensive, state-of-the-art reference details the latest research developments and challenges in the biophysical and single molecule approaches in RNA nanotechnology. In addition, the text also provides in-depth discussions of RNA structure for nanoparticle construction, RNA computation and modeling, single molecule imaging of RNA, RNA nanoparticle assembly, RNA nanoparticles in therapeutics, RNA chemistry for nanoparticle synthesis, and conjugation and labeling.
RNA Processing
by Gene W. W. YeoRibonucleic acid (RNA) binding proteins currently number in the thousands and defects in their function are at the heart of diseases such as cancer and neurodegeneration. RNA binding proteins have become implicated in the intricate control of surprisingly diverse biological settings, such as circadian rhythm, stem cell self-renewal, oncogenesis and germ cell development. This book surveys a range of genome-wide and systems approaches to studying RNA binding proteins, the importance of RNA binding proteins in development, cancer and circadian rhythm.
RNA Regulation
by Robert A. MeyersBased on one of the leading encyclopedic resources in cell and molecular biology worldwide, this two-volume work contains more than 75% new content, not previously published in the Encyclopedia. All the other chapters have been carefully updated.The result is a comprehensive overview of the different functions of the various forms of RNA in living organisms, with each contributor carefully selected and an internationally recognized expert on his or her field. Special focus is on the different forms of expression regulation through RNA, with medical applications in the treatment of diseases -- from cancers and immune responses to infections and aging -- covered in detail. At least 45 of the 55 articles are new content previously not published in the Encyclopedia.
RNA Remodeling Proteins
by Marc BoudvillainThis volume provides readers with current methods to study RNA remodeling proteins. The methods, ranging from basic to complex, help the scientific community understand the role and fate of RNA species in cells, and their structures and interactions with other biomolecules. The book begins with two introductory chapters, followed by chapters where readers will find procedures to identify RNA remodeling proteins and their cofactors, physiological RNA targets and biological functions, and complex molecular mechanisms of action using purified components. Written in the highly successful Methods of Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, RNA Remodeling Proteins: Methods and Protocols seeks to aid scientists in the further study of this ever evolving field of proteins and mechanisms.
RNA Remodeling Proteins: Methods and Protocols (Methods in Molecular Biology #2209)
by Marc BoudvillainThis volume provides the most current methods to study RNA remodeling proteins. Chapters detail methods, ranging from basic to complex, procedures to identify RNA remodeling proteins and their cofactors, physiological RNA targets and biological functions, and complex molecular mechanisms of action using purified components. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, application details for both the expert and non-expert reader, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, RNA Remodeling Proteins: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.
RNA Scaffolds
by Luc PonchonThis volume provides techniques on recent developments that use RNA scaffolds as molecular tools. RNA Scaffolds: Methods and Protocols guides readers through methods on various domains as molecular biology, nanotechnologies, and structural biology. Written for the Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols and tips on troubleshooting and avoiding known pitfalls. Practical and authoritative, RNA Scaffolds: Methods and Protocols will serve as an invaluable reference for those interested in further study into this fascinating field.
RNA Scaffolds: Methods and Protocols (Methods in Molecular Biology #2323)
by Luc PonchonThis second edition volume expands on the previous edition with discussions of recently developed techniques that use RNA scaffolds as molecular tools. These latest methods are used in the fields of molecular biology, cellular biology, nanotechnology, and structural biology. The chapters in this book cover topics such as RNA footprinting using small chemical reagents; using tRNA scaffolds to assist RNA crystallization; identification of RNA-binding proteins associated to RNA structural elements; and synthetic biology medicine and bacteria-based cancer therapeutics. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, RNA Scaffolds: Methods and Protocols, Second Edition is a valuable resource that explores the fascinating uses of RNA in these different areas, and will inspire experts and novice researchers to further study this developing field.
RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods
by Jan Gorodkin Walter L. RuzzoThe existence of genes for RNA molecules not coding for proteins (ncRNAs) has been recognized since the 1950's, but until recently, aside from the critically important ribosomal and transfer RNA genes, most focus has been on protein coding genes. However, a long series of striking discoveries, from RNA's ability to carry out catalytic function, to discovery of riboswitches, microRNAs and other ribo-regulators performing critical tasks in essentially all living organisms, has created a burgeoning interest in this primordial component of the biosphere. However, the structural characteristics and evolutionary constraints on RNA molecules are very different from those of proteins, necessitating development of a completely new suite of informatic tools to address these challenges. In RNA Sequence, Structure, Function: Computational and Bioinformatic Methods, expert researchers in the field describe a substantial and relevant fraction of these methodologies from both practical and computational/algorithmic perspectives. Focusing on both of these directions addresses both the biologist interested in knowing more about RNA bioinformatics as well as the bioinformaticist interested in more detailed aspects of the algorithms. Written in the highly successful Methods in Molecular Biology series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results. Thorough and intuitive, RNA Sequence, Structure, Function: Computational and Bioinformatic Methods aids scientists in continuing to study key methods and principles of RNA bioinformatics.
RNA Silencing
by Gordon CarmichaelA collection of readily reproducible methods for the design, preparation, and use of RNAs for silencing gene expression in cells and organisms. The techniques range widely and include methods addressing the biochemical aspects of the silencing machinery, RNA silencing in non-mammalian organisms, and the in vivo delivery of siRNAs and silencing vectors. There are also techniques for designing, preparing, and using RNAs to silence gene expression, for fine-tuning regulation by targeting specific isoforms of a given gene, and for the study and use of microRNAs. The protocols follow the successful Methods in Molecular BiologyTM series format, each offering step-by-step laboratory instructions, an introduction outlining the principle behind the technique, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding known pitfalls.
RNA Spectroscopy: Methods and Protocols (Methods in Molecular Biology #2113)
by Véronique Arluison Frank WienThis volume looks at the different spectroscopic and biophysical methods used by researchers to study the structure and folding of RNA, and to follow their interactions with proteins. The chapters in this book cover topics such as single-molecule spectroscopy of multiple RNA species; surface plasmon resonance, MS or microcalorimetry for investigating molecular interactions with RNA; FTIR, SAXS, SANS and SRCD spectroscopies to analyze RNA structure; use of fluorescent nucleotides to map RNA-binding sites on proteins surfaces or CryoEM; and much more. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.Cutting-edge and comprehensive, RNA Spectroscopy: Methods and Protocols is a valuable resource for anyone interested in learning more about this developing field.
RNA Structure and Dynamics (Methods in Molecular Biology #2568)
by Jienyu Ding Jason R. Stagno Yun-Xing WangThis volume provides a wide spectrum of multidisciplinary approaches for studying RNA structure and dynamics, including detailed accounts of experimental and computational procedures. Chapters guide readers through cryo-electron microscopy, crystallography, isothermal titration calorimetry, small angle X-ray scattering, single-molecule Förster Energy transfer, X-ray free electron laser, atomic force microscopy, computational simulation, and prediction. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols.Authoritative and cutting-edge, RNA Structure and Dynamics aims to be a foundation for future studies and to be a source of inspiration for new investigations in the field.
RNA Structure and Function (RNA Technologies #14)
by Jan BarciszewskiThis book focuses on the current status of our understanding of RNA, a key biological molecule. The various RNAs covered are messenger RNA, ribosomal RNA, transfer RNA, noncoding RNAs, modified nucleosides, and RNA enzymes. The different chapters detail methods to investigate RNA structure and function, the chemistry of modified RNAs, and the latest advances in our understanding of the vast array of biological processes in which RNA is involved.RNA, in one form or another, touches almost everything in a cell. RNA has both structural and catalytic properties. RNA fulfills a broad range of functions. These molecules are no longer seen as passive elements transferring the genetic information from DNA into proteins but regulate the activity of genes during development, cellular differentiation, and changing environments. RNAs are involved in various aspects of cell physiology and disease development. Discoveries of RNA with unexpected diverse functions in healthy and diseased cells, such as the role of RNA as both the source and countermeasure to cancer or severe viral infection, stimulate new trends, passion, and solutions for molecular medicine.In this book, fundamental questions about the biochemical and genetic importance of RNA, how mRNAs are generated and used to produce proteins, how noncoding and catalytic RNAs mediate key cellular processes, how to determine RNA structure and how to apply RNA in treatment of diseases.This book is an essential resource for researches in academia and industry contributing to the development of new RNA therapeutics. The book is geared toward scientists from the graduate level on up and particularly appeals to active investigators in RNA biology, molecular biology, and biochemistry.