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 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 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 Biophysics of RNA Folding written by Rick Russell and published by Springer Science & Business Media. This book was released on 2012-12-09 with total page 238 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume, written by experts in the field, discusses the current understanding of the biophysical principles that govern RNA folding, with featured RNAs including the ribosomal RNAs, viral RNAs, and self-splicing introns. In addition to the fundamental features of RNA folding, the central experimental and computational approaches in the field are presented with an emphasis on their individual strengths and limitations, and how they can be combined to be more powerful than any method alone; these approaches include NMR, single molecule fluorescence, site-directed spin labeling, structure mapping, comparative sequence analysis, graph theory, course-grained 3D modeling, and more. This volume will be of interest to professional researchers and advanced students entering the field of RNA folding.
Download or read book RNA Folding written by Ronny Lorenz and published by Springer Nature. This book was released on with total page 407 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Biophysical Approaches to RNA Structure and Folding written by Daniel Herschlag and published by . This book was released on 2009 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides laboratory techniques that aim to predict the structure of a protein which can have implications ranging from drug design, to cellular pathways and their dynamics, to viral entry into cells.
Download or read book RNA 3D Structure Analysis and Prediction written by Neocles Leontis and published by Springer Science & Business Media. This book was released on 2012-06-05 with total page 402 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the dramatic increase in RNA 3D structure determination in recent years, we now know that RNA molecules are highly structured. Moreover, knowledge of RNA 3D structures has proven crucial for understanding in atomic detail how they carry out their biological functions. Because of the huge number of potentially important RNA molecules in biology, many more than can be studied experimentally, we need theoretical approaches for predicting 3D structures on the basis of sequences alone. This volume provides a comprehensive overview of current progress in the field by leading practitioners employing a variety of methods to model RNA 3D structures by homology, by fragment assembly, and by de novo energy and knowledge-based approaches.
Download or read book RNA Structure Prediction written by Risa Karakida Kawaguchi and published by Springer Nature. This book was released on 2023-01-27 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book explores recent progress in RNA secondary, tertiary structure prediction, and its application from an expansive point of view. Because of advancements in experimental protocols and devices, the integration of new types of data as well as new analysis techniques is necessary, and this volume discusses additional topics that are closely related to RNA structure prediction, such as the detection of structure-disrupting mutations, high-throughput structure analysis, and 3D structure design. Written for the highly successful Methods in Molecular Biology series, chapters feature the kind of detailed implementation advice that leads to quality research results. Authoritative and practical, RNA Structure Prediction serves as a valuable guide for both experimental and computational RNA researchers.
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 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 written by D. Söll and published by Elsevier. This book was released on 2001-12-03 with total page 355 pages. Available in PDF, EPUB and Kindle. Book excerpt: This publication summarizes the current status of our understanding of RNA, with particular emphasis on the chemistry of this key biological molecule. The various RNAs covered are messenger RNA, ribosomal RNA, transfer RNA and RNA enzymes (ribozymes). The different chapters detail biophysical and chemical methods to investigate RNA structure and function, the synthesis of native and modified RNAs and the latest advances in our understanding of the vast array of biological processes in which RNA is involved.
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 0 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 Riboswitch Discovery Structure and Function written by and published by Academic Press. This book was released on 2014-11-21 with total page 595 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 riboswitch discovery and validation, synthesis and sample prep methods for large RNAs, riboswitch structure and function methods, folding pathways and dynamics, and ligand interactions and thermodynamics. Continues the legacy of this premier serial with quality chapters authored by leaders in the field Covers research methods in riboswitch discovery, structure and function Contains sections on such topics as riboswitch discovery and validation, synthesis and sample prep methods for large RNAs, riboswitch structure and function methods, folding pathways and dynamics, ligand interactions and thermodynamics
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 RNA Ligand Interactions Part A Structural Biology Methods written by and published by Elsevier. This book was released on 2000-05-30 with total page 583 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA-Ligand Interactions, Part A focuses on structural biology methods. Major topics covered include semisynthetic methodologies (RNA synthetic methods and derivatization of RNA); RNA structure determination (X-ray crystallography, NMR, EM); techniques for monitoring RNA conformation and dynamics (solution methods and electrophoretic and spectroscopic methods); and modeling tertiary structure: Part B, its companion Volume 318 of Methods in Enzymology, focuses on molecular 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 Non Protein Coding RNAs written by Nils Walter and published by Springer Science & Business Media. This book was released on 2008-11-18 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: The 2006 Nobel Prize in Physiology or Medicine was awarded to the discoverers of RNA interference, Andrew Fire and Craig Mello. This prize, which follows “RNA” Nobels for splicing and RNA catalysis, highlights just one class of recently discovered non-protein coding RNAs. Remarkably, non-coding RNAs are thought to outnumber protein coding genes in mammals by perhaps as much as four-fold. In fact, it appears that the complexity of an organism correlates with the fraction of its genome devoted to non-protein coding RNAs. Essential biological processes as diverse as cell differentiation, suppression of infecting viruses and parasitic tra- posons, higher-level organization of eukaryotic chromosomes, and gene expression are found to be largely directed by non-protein coding RNAs. Currently, bioinformatic, high-throughput sequencing, and biochemical approaches are identifying an increasing number of these RNAs. Unfortunately, our ability to characterize the molecular details of these RNAs is significantly lacking. The biophysical study of these RNAs is an emergent field that is unraveling the molecular underpinnings of how RNA fulfills its multitude of roles in sustaining cellular life. The resulting understanding of the physical and chemical processes at the molecular level is critical to our ability to harness RNA for use in biotechnology and human therapy, a prospect that has recently spawned a multi-billion dollar industry.
Download or read book Thermodynamic Corrections to RNA Folding Models in Cells written by Jacob Sieg and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA performs numerous functions in cells owing to its capacity to adopt complex, diverse, and functional structures. Genome-wide structure-probing techniques have provided insight into RNA structure and function in vivo. However, most biophysical techniques are not readily amenable to the cellular environment. This has caused a gap in the detailed understanding of RNA thermodynamics artificial buffer conditions in vitro and understanding of RNA thermodynamics inside organisms (in vivo). In vitro studies of RNA in artificial cytoplasm that mimic a cell, so called in vivo-like conditions, provide a link between mechanistically tractable insight in vitro and understanding of RNA structure in vivo. This thesis describes the development and application of a realistic artificial cytoplasm for detailed mechanistic studies of RNA and determines thermodynamic corrections to RNA secondary structure models used in structure prediction algorithms. Chapter 2 examines the biological network of metabolites and metal ions in diverse organisms, using absolute metabolite concentrations and metal ion-binding constants in a multi-component model. This information is applied in Chapter 3 to develop the Eco80 artificial cytoplasm, which contains 80% of Escherichia coli metabolites, and demonstrates that the metabolome weakens RNA helix stability and strengthens RNA chemical stability. Chapter 4 describes folding free energies determined for an expanded helix set in Eco80 and applies in vivo-like thermodynamic corrections to improve RNA secondary structure prediction in E. coli. Chapter 5 provides unique experimental considerations for measuring the thermodynamics of RNA helix formation in artificial cytoplasm and presents the facile data-processing software MeltR. Lastly, Chapter 6 applies LC-MS/MS to RNA studies in biological systems and describes theoretical approaches to combining sequencing-based RNA structure probing with complementary LC-MS/MS analysis, as applied to measuring tRNA structure in cells. Additionally, Chapter 6 also describes unique methods of preparing cell lysates for RNA measurements and the use of LC-MS/MS based metabolite profiling to identify ligands that bind to RNA.
