Download or read book Spectroscopical Investigations to Determine RNA ligand Interactions and RNA dynamics written by Jan Ferner and published by . This book was released on 2009 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 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 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 RNA Ligand Interactions Part B Molecular Biology Methods written by and published by Elsevier. This book was released on 2000-06-26 with total page 579 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 RNA Spectroscopy written by Véronique Arluison and published by Humana. This book was released on 2020-02-01 with total page 0 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 Structural and Dynamic Approaches to Investigate RNA ligand Interactions in the BtuB Riboswitch and an Octameric RNA Duplex written by and published by . This book was released on 2015 with total page 265 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 RNA ligand Interactions Structural biology methods Semisynthetic methodologies RNA structure determination Techniques for monitoring RNA conformation and dynamics Modeling tertiary structure written by Daniel Walter Celander and published by . This book was released on 2000 with total page 602 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Investigating the Conformational Dynamics of RNA Molecules and Their Interaction Modes written by Niyati Jain and published by . This book was released on 2010 with total page 248 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA is a structurally flexible and dynamic molecule, and rapidly interconverts between multiple conformations. Despite the significant advances in traditional biophysical techniques like NMR spectroscopy and X-ray crystallography it is difficult to resolve the structures of dynamically inter-converting states as these methods measure the average property of an ensemble of molecules. It is necessary to resolve and get detailed descriptions of the multiple conformational structures, their quantitative distribution and their related dynamics in order to understand the ruggedness of the energy landscape. The present study attempts to link the conformational dynamics of RNA to its structure and biological function. Ultrafast time-resolved fluorescence spectroscopy is used to probe the distribution of multiple conformations and their dynamics that occur on a very fast timescales. This tool uses the resolution of time domain behavior of 2-aminopurine fluorescence decay on the ultrafast timescale to capture the characteristics of different structures. The RNAs are labeled with the fluorescent base analog 2-aminopurine to probe the base stacking patterns in RNA. Base stacking interactions is a unique feature that defines nucleic acid structures compared to proteins and are the major stabilizing force in RNA. Chapter 1 discusses the RNA folding mechanism and the relationships between sequence, structure, dynamics and function and explains the advantage of using ultrafast time resolved spectroscopy in defining structure-function relationships in RNA. Chapter 2 discusses the conformational heterogeneity and dynamics in purine-sensing riboswitches. We observed multiple conformations where the ligand is significantly stacked with the bases of the binding pocket and shows a dynamic balance between base stacking interactions and hydrogen bonding to achieve specificity and high affinity by the aptamer domain. Chapter 3 explores the conformational heterogeneity of GAAA tetraloop receptor and the impacts of the tertiary interactions between the receptor and the GAAA tetraloop, where we probe the isolated and GAAA-tetraloop bound receptor. The presence of any bound conformation in the free receptor state leads us to propose the conformational capture mechanism in tetraloop-receptor recognition. Chapter 4 summarizes findings of employing the ultrafast spectroscopy approach in studying riboswitches and the GAAA tetraloop-receptor. Overall our research is an effort to understand the role of conformational dynamics in RNA folding, tertiary interactions, recognition and functions.
Download or read book Spectroscopic Investigation of Metal RNA Interactions written by Matthew John Vogt and published by . This book was released on 2005 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Metal-RNA interactions are important to neutralize the negative charge and aid in correctly folding the RNA. Spectroscopically active metal ions, especially Mn2, have been used to probe the type of interaction the metal has with RNA. In previous studies, the hammerhead ribozyme, an RNA motif that catalyzes a site-specific phosphodiester bond cleavage reaction, was determined by room temperature EPR (electron paramagnetic resonance) studies to have a set of tightly and weakly bound metal ions. Under high salt concentrations, the hammerhead was found to bind a single Mn2 ion with high affinity and with a characteristic low temperature EPR signal. Using site specific 15N labeling of a guanine residue in conjunction with ESEEM (electron spin echo envelope modulation) spectroscopy, the high affinity Mn2+ ion was conclusively determined coordinated to G10.1 of the proposed A9/G10.1 site with four water molecules coordinated to the Mn2+ ion. EPR power saturation studies determined that under low salt conditions the hammerhead coordinates up to four Mn2+ ions in relatively close proximity compared to an RNA duplex. EXAFS (extended X-ray absorption fine structure) spectroscopy was used to determine that a Cd2+ ion coordinates to both the Rp and Sp sulfur atoms of a phosphorothioate modification at the A9 phosphate of the hammerhead. Previous EXAFS results for the Mn2+ substituted A9 phosphorothioate suggested that the Mn2+ ion coordinates to the oxygen atom for both isomers. Molecular modeling suggested that the A9/G10.1 metal site will twist the phosphate group in order to accommodate this coordination. A Mn-GMP and Mn-phosphate model complexes were prepared and characterized by EXAFS to assign the origin of the features observed for the hammerhead sample. A series of RNA sequences with internal loops containing the sheared G-A metal ion binding motif showed greater thermal stabilization of the RNA structure in the presence of Mn2+ ions compared to sequences without the motif. The EPR binding isotherms also showed a set of moderately tight metal ion interaction while circular dichroism spectroscopy was used to investigate structural differences between the sequences. These results suggest a mostly electrostatic, not structural role, for the Mn2+ ion interactions with these sequences.
Download or read book Investigation of Conformational Dynamics in Regulatory RNA written by Jia Lu and published by . This book was released on 2012 with total page 208 pages. Available in PDF, EPUB and Kindle. Book excerpt: It has been hypothesized that the ground state conformational dynamics of RNA can significantly enhance its functional capacity beyond its static structure modeled by traditional biophysical techniques. Therefore, understanding the dynamic aspects of RNA structures is fundamentally important for fully elucidating the sequence-structure-dynamics-function relationship. Time-resolved fluorescence up-conversion spectroscopy allowed us to resolve the heterogeneous nature of RNA molecules and capture the conformational changes upon ligand binding to advance our understanding of detailed mechanism of conformational dynamics for different RNA molecules. The non-specific base stacking interaction makes a major contribution to the RNA ground state rugged energy landscape and is also the main stabilizing force in RNA. The fluorescent base 2-aminopurine, which is an analog to adenine, was used to characterize the heterogeneity of base stacking patterns in RNA, and get a quantitative description of inter-converting states in the ensemble.
Download or read book RNA Dynamics and Interactions Investigated by Photocrosslinking written by and published by . This book was released on 2004 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: A complete understanding of protein synthesis requires description of the cyclical motions and interactions that occur in ribosomal RNA and transfer RNA during translation. The purpose of the following research was to gain understanding of the nature of these motions and interactions, and to develop new tools to measure how ligands alter the conformational flexibility of RNA during the steps of initiation, elongation and termination. Different tRNA substrates were bound to the E. coli 70S to simulate the arrangement of the tRNA-ribosomal complex before and after peptide bond formation, and different UV-induced 16S rRNA-tRNA photocrosslinks were produced in these complexes, illustrating that the 16S rRNA P-site undergoes local deformations during elongation. A statistical study was undertaken to understand the nature of conformational states in the 30S ribosomal subunit. Using the lists of observed UVB/C- and UVA-s4U-induced crosslinks and the T. thermophilus 30S X-ray crystal structure, frequencies were compared to a number of geometrical parameters demonstrating that crosslink formation requires substantial RNA motions. In addition, the results show that the restricted pattern of crosslink formation in E. coli 16S rRNA is due to the overall rigidity of the 30S subunit outside of the active site. One consequence of these conclusions is that potocrosslinking rates depend on the ease of inter-nucleotide conformational movements. This was exploited in a study that used the temperature response of the rate constant for the UVA-induced photo-crosslink between s4U8 X C13 in E. coli tRNA to determine tRNA geometry and internal energy. The rate constants followed Arrhenius behavior in their dependence on temperature, and this allowed calculation of the activation energy associated with the conformational rearrangement necessary to bring the photoreactive bonds together. The experiments show that changes in the tRNA on ribosomes can be uncovered by photocrosslinking, that RN.
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 Methods for Studying Nucleic Acid Drug Interactions written by Meni Wanunu and published by CRC Press. This book was released on 2016-04-19 with total page 397 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since most therapeutic efforts have been predominantly focused on pharmaceuticals that target proteins, there is an unmet need to develop drugs that intercept cellular pathways that critically involve nucleic acids. Progress in the discovery of nucleic acid binding drugs naturally relies on the availability of analytical methods that assess the eff
Download or read book Encyclopedia of Spectroscopy and Spectrometry written by and published by Academic Press. This book was released on 2010-04-09 with total page 7207 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Second Edition of the Encyclopedia of Spectroscopy and Spectrometry pulls key information into a single source for quick access to answers and/or in-depth examination of topics. "SPEC-2" covers theory, methods, and applications for researchers, students, and professionals—combining proven techniques and new insights for comprehensive coverage of the field. The content is available in print and online via ScienceDirect, the latter of which offers optimal flexibility, accessibility, and usability through anytime, anywhere access for multiple users and superior search functionality. No other work gives analytical and physical (bio)chemists such unprecedented access to the literature. With 30% new content, SPEC-2 maintains the "authoritative, balanced coverage" of the original work while also breaking new ground in spectroscopic research. Incorporates more than 150 color figures, 5,000 references, and 300 articles (30% of which are new), for a thorough examination of the field Highlights new research and promotes innovation in applied areas ranging from food science and forensics to biomedicine and health Features a new co-editor: David Koppenaal of Pacific Northwest National Laboratory, Washington, USA, whose work in atomic mass spectrometry has been recognized internationally
Download or read book Ribozymes written by Sabine Müller and published by John Wiley & Sons. This book was released on 2021-07-09 with total page 81 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ribozymes Provides comprehensive coverage of a core field in the molecular biosciences, bringing together decades of knowledge from the world’s top professionals in the field Timely and unique in its breadth of content, this all-encompassing and authoritative reference on ribozymes documents the great diversity of nucleic acid-based catalysis. It integrates the knowledge gained over the past 35 years in the field and features contributions from virtually every leading expert on the subject. Ribozymes is organized into six major parts. It starts by describing general principles and strategies of nucleic acid catalysis. It then introduces naturally occurring ribozymes and includes the search for new catalytic motifs or novel genomic locations of known motifs. Next, it covers the development and design of engineered ribozymes, before moving on to DNAzymes as a close relative of ribozymes. The next part examines the use of ribozymes for medicinal and environmental diagnostics, as well as for therapeutic tools. It finishes with a look at the tools and methods in ribozyme research, including the techniques and assays for structural and functional characterization of nucleic acid catalysts. The first reference to tie together all aspects of the multi-faceted field of ribozymes Features more than 30 comprehensive chapters in two volumes Covers the chemical principles of RNA catalysis; naturally occurring ribozymes, engineered ribozymes; DNAzymes; ribozymes as tools in diagnostics and therapy, and tools and methods to study ribozymes Includes first-hand accounts of concepts, techniques, and applications by a team of top international experts from leading academic institutions Dedicates half of its content to methods and practical applications, ranging from bioanalytical tools to medical diagnostics to therapeutics Ribozymes is an unmatched resource for all biochemists, biotechnologists, molecular biologists, and bioengineers interested in the topic.
