Download or read book Probing RNA Structure and RNA protein Interactions Using Nanopore Force Spectroscopy written by Jianxun Lin and published by . This book was released on 2012 with total page 236 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Biophysical Chemical and Functional Probes of RNA Structure Interactions and Folding Part B written by Daniel Herschlag and published by Academic Press. This book was released on 2009-11-16 with total page 567 pages. Available in PDF, EPUB and Kindle. Book excerpt: This MIE volume provides laboratory techniques that aim to predict the structure of a protein which can have tremendous implications ranging from drug design, to cellular pathways and their dynamics, to viral entry into cells. - Expert researchers introduce the most advanced technologies and techniques in protein structure and folding - Includes techniques on tiling assays
Download or read book RNA Protein Interactions A Practical Approach written by Christopher W.J. Smith and published by Oxford University Press, UK. This book was released on 1998-07-09 with total page 370 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA-protein interactions play a fundamental role in gene expression and protein synthesis. Recent research into the role of RNA in cells has elucidated many more vital interactions with proteins. This book provides an up-to-date and comprehensive guide to a wide range of laboratory procedures to investigate the interactions between RNA and proteins. - ;RNA-protein interactions play a vital role in gene transcription and protein expression. Interactions such as the synthesis of mRNA by RNA polymerases, to the essential modification of RNA by the proteins of the spliceosome complex, and the highly catalytic action of the ribosome in protein synthesis, are established as being fundamental to the function of RNA. Recent research into, for example, the role of RNA as a catalyst, has elucidated many more interactions with proteins that are vital to cell function. RNA - Protein Interactions: A Practical Approach provides a clear and comprehensive guide to the experimental procedures used in studying RNA - protein interactions. The approaches covered range from those initially used to detect a novel RNA-protein interaction, various biochemical and genetic approaches to purifying and cloning RNA binding proteins, through to methods for an in depth analysis of the structural basis of the interaction. The volume includes a number of procedures that have not previously been covered in this type of manual. These include the production of site-specifically modified RNAs by enzymatic and chemical methods and in vivo screening for novel RNA - protein interactions in yeast and E. coli . This is the first volume to gather in one place this wide array of approaches for studying RNA - protein interactions. As is customary for the Practical Approach series, the writing is characterized by a clear explanatory style with many detailed protocols. This informative book will be a valuable aid to laboratory workers in biochemistry and molecular biology - graduate students, postdoctoral and senior scientists - whose research encompasses this field. -
Download or read book Biophysics of RNA Protein Interactions written by Chirlmin Joo and published by Springer Nature. This book was released on 2019-09-19 with total page 249 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA molecules play key roles in all aspects of cellular life, but to do so efficiently, they must work in synergism with proteins. This book addresses how proteins and RNA interact to carry out biological functions such as protein synthesis, regulation of gene expression, genome defense, liquid phase separation and more. The topics addressed in this volume will appeal to researchers in biophysics, biochemistry and structural biology. The book is a useful resource for anybody interested in elucidating the molecular mechanisms and discrete properties of RNA-protein complexes. Included are reviews of key systems such as microRNA and CRISPR/Cas that exemplify how RNA and proteins work together to perform their biological function. Also covered are techniques ranging from single molecule fluorescence and force spectroscopy to crystallography, cryo-EM microscopy, and kinetic modeling.
Download or read book Biophysical Chemical and Functional Probes of RNA Structure Interactions and Folding Part A written by Daniel Herschlag and published by Academic Press. This book was released on 2009-11-16 with total page 491 pages. Available in PDF, EPUB and Kindle. Book excerpt: This MIE volume provides laboratory techniques that aim to predict the structure of a protein which can have tremendous implications ranging from drug design, to cellular pathways and their dynamics, to viral entry into cells. - Expert researchers introduce the most advanced technologies and techniques in protein structure and folding - Includes techniques on tiling assays
Download or read book RNA Protein Interaction Protocols written by Susan R. Haynes and published by Springer Science & Business Media. This book was released on 2008-02-03 with total page 485 pages. Available in PDF, EPUB and Kindle. Book excerpt: The molecular characterization of RNA and its interactions with proteins is an important and exciting area of current research. Organisms utilize a variety of RNA–protein interactions to regulate the expression of their genes. This is particularly true for eukaryotes, since newly synthesized messenger RNA must be extensively modified and transported to the cytoplasm before it can be used for protein synthesis. The realization that posttranscriptional processes are critical components of gene regulation has sparked an explosion of interest in both stable ribonucleoprotein (RNP) complexes and transient RNA–protein interactions. RNA is conformationally flexible and can adopt complex structures that provide diverse surfaces for interactions with proteins. The fact that short RNA molecules (aptamers; see Chapter 16) can be selected to bind many different types of molecules is evidence of the structural variability of RNA. RNA molecules are rarely entirely single- or double-stranded, but usually contain multiple short duplexes interrupted by single-stranded loops and bulges; in some RNAs, such as tRNAs, the short duplexes stack on each other. Further variability is generated by the presence of non-Watson-Crick base pairs, modified nucleotides, and more complex structures, such as pseudoknots and triple-strand interactions.
Download or read book Structures of Large RNA Molecules and Their Complexes written by and published by Academic Press. This book was released on 2015-06-06 with total page 675 pages. Available in PDF, EPUB and Kindle. Book excerpt: This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods in RNA folding and dynamics, RNA-protein interactions and large RNPs. Continues the legacy of this premier serial with quality chapters on structures of large RNA molecules and their complexes
Download or read book RNA Protein Complexes and Interactions written by Ren-Jang Lin and published by Springer Nature. This book was released on 2023-05-11 with total page 349 pages. Available in PDF, EPUB and Kindle. Book excerpt: This second edition updates, complements, and expands upon the first edition by providing a collection of cutting-edge techniques developed or refined in the past few years along with tried-and-true methods. Chapters explore the isolation and characterization of RNA-protein complexes, the analysis and measurement of RNA-protein interaction, and related novel techniques and strategies. Written in the highly successful Methods in Molecular Biology series format, the chapters include brief introductions to the material, lists of necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and a Notes section which highlights tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, RNA-Protein Complexes and Interactions: Methods and Protocols, Second Edition aims to be comprehensive guide for researchers in the field.
Download or read book Computational Analysis of the Interplay Between RNA Structure and Function written by Elan A. Shatoff and published by . This book was released on 2021 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA is ubiquitous in the cellular environment, and it can function in innumerable ways with a variety of interaction partners. A RNA molecule's structure, in particular the set of base pairing interactions between the nucleotides of the molecule known as secondary structure, can help determine its function. Since most proteins can only bind to either single stranded or double stranded RNA, RNA secondary structure can also help determine where and how RNA-protein binding interactions occur. In this work I investigate computational models for RNA-protein interactions in a variety of different contexts. In Chapter 2 I probe the effect of single nucleotide variations on RNA-protein binding as mediated by RNA secondary structure. Single nucleotide variations are single nucleotide changes in an organism's genome that can often cause disease, and may do so through a number of different mechanisms. In this work we propose that sequence changes can affect accessibility to protein binding sites through changes in secondary structure, even when these sequence changes occur tens of nucleotides outside of protein binding sites. We find that single nucleotide variations can have a many fold effect on the binding affinity of proteins for RNA, and characterize the genome-wide effect of single nucleotide variations on HuR binding. HuR is a single-stranded RNA binding protein that binds to AU-rich sequences, and has links to diseases such as cancer. We also find an asymmetry in this effect for HuR, indicating that this effect may be under selection. Following the previous work, which utilizes a model incorporating single stranded RNA binding proteins into RNA secondary structure folding, I introduce a model for incorporating double stranded RNA binding proteins (dsRBPs) into RNA secondary structure partition function calculations in Chapter 3. The dsRBPs are an important but understudied class of proteins that have uses in a wide range of processes. We implement our model in the ViennaRNA package, and validate it by calculating a number of experimental observables for transactivation response element RNA-binding protein. We find that RNA secondary structure can have a many fold effect on the effective binding affinity of dsRBPs, and show that calculated affinities for pre-miRNA-like constructs correlate with experimentally measured processing rates. Our model provides a novel method for interrogating the interplay between dsRBPs and RNA secondary structure. In Chapter 4 I study RNA-protein interactions in a different context, and investigate the role of Shine-Dalgarno (SD) sequences in translation in the Bacteroidetes. The Bacteroidetes are a phylum of bacteria known to rarely use SD sequences, but after performing a survey of SD usage in the phylum we find that certain ribosomal protein genes utilize them, particularly rpsU. A cryo-electron microscopy structure of the ribosome from Flavobacterium johnsoniae, a member of the Bacteroidetes, also shows that S21, which is encoded by the ribosomal open reading frame rpsU, sequesters the anti-Shine-Dalgarno (ASD) sequence. In our survey of SD sequences we also find covariation between the SD sequence of rpsU and the ASD sequence. These observations suggest an autoregulatory model for S21 in the Bacteroidetes.
Download or read book RNA Structure and Function written by Jan Barciszewski and published by Springer Nature. This book was released on 2023-12-05 with total page 662 pages. Available in PDF, EPUB and Kindle. Book excerpt: This 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.
Download or read book RNA Structure and Folding written by Dagmar Klostermeier and published by Walter de Gruyter. This book was released on 2013-10-14 with total page 432 pages. Available in PDF, EPUB and Kindle. Book excerpt: While structure-function relationships of proteins have been studied for a long time, structural studies of RNA face additional challenges. Nevertheless, with the continuous discovery of novel RNA molecules with key cellular functions and of novel pathways and interaction networks, the need for structural information of RNA is still increasing. This volume provides an introduction into techniques to assess structure and folding of RNA. Each chapter explains the theoretical background of one technique, and illustrates possibilities and limitations in selected application examples.
Download or read book RNA Structure and Dynamics written by Jienyu Ding and published by Springer Nature. This book was released on 2022-10-13 with total page 256 pages. Available in PDF, EPUB and Kindle. Book excerpt: This 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.
Download or read book RNA Spectroscopy written by Véronique Arluison and published by Humana. This book was released on 2021-02-15 with total page 356 pages. Available in PDF, EPUB and Kindle. Book excerpt: This 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.
Download or read book Probing RNA Dynamics and Protein ligand Interactions Using Fluorescence Spectroscopy written by Andrew Myles Parrott and published by . This book was released on 1999 with total page 460 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book RNA Ligand Interactions Part B Molecular Biology Methods written by and published by Academic Press. This book was released on 2000-06-16 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA-Ligand Interactions, Part B focuses on molecular biology methods. Major topics covered include: solution probe methods, tethered-probe methodologies, in vitro affinity selection methodologies, genetic methodologies for detecting RNA-protein interactions, protein engineering methodologies useful for RNA-protein interaction studies, and cell biology methods. RNA-Ligand Interactions, Part A, its companion, VOLUME 317 focuses on structural biology methods. The critically acclaimed laboratory standard for more than forty years, Methods in Enzymology is one of the most highly respected publications in the field of biochemistry. Since 1955, each volume has been eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with more than 300 volumes (all of them still in print), the series contains much material still relevant today--truly an essential publication for researchers in all fields of life sciences.
Download or read book Structure and Thermodynamics of RNA protein Interactions written by Carolina Moises Reyes and published by . This book was released on 2000 with total page 446 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Biophysical Chemical and Functional Probes of RNA Structure Interactions and Folding written by Daniel Herschlag and published by . This book was released on 2009 with total page 502 pages. Available in PDF, EPUB and Kindle. Book excerpt:
