RNA 3D Structure Analysis and Prediction

RNA 3D Structure Analysis and Prediction
Author: Neocles Leontis
Publisher: Springer Science & Business Media
Total Pages: 402
Release: 2012-06-05
Genre: Science
ISBN: 3642257402

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.

RNA Structure and Dynamics

RNA Structure and Dynamics
Author: Jienyu Ding
Publisher: Springer Nature
Total Pages: 256
Release: 2022-10-13
Genre: Science
ISBN: 1071626876

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.

RNA Trafficking and Nuclear Structure Dynamics

RNA Trafficking and Nuclear Structure Dynamics
Author: Philippe Jeanteur
Publisher: Springer
Total Pages: 153
Release: 2014-10-09
Genre: Science
ISBN: 9783662312261

This volume explores nuclear structure and trafficking involving or relevant to RNA and RNPs. Topics include advances and current problems in the structural organization of different subnuclear compartments, Cajal bodies and gems, speckles containing splicing factors, and PML bodies characteristic of ProMyelocytic leukemia. The book also describes the dynamic aspects of RNA trafficking and the latest technologies for live cell imaging of mRNA.

RNA

RNA
Author: D. Söll
Publisher: Elsevier
Total Pages: 355
Release: 2001-12-03
Genre: Science
ISBN: 0080540627

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.

Innovations in Biomolecular Modeling and Simulations

Innovations in Biomolecular Modeling and Simulations
Author: Tamar Schlick
Publisher: Royal Society of Chemistry
Total Pages: 381
Release: 2012-05-24
Genre: Science
ISBN: 1849735042

The chemical and biological sciences face unprecedented opportunities in the 21st century. A confluence of factors from parallel universes - advances in experimental techniques in biomolecular structure determination, progress in theoretical modeling and simulation for large biological systems, and breakthroughs in computer technology - has opened new avenues of opportunity as never before. Now, experimental data can be interpreted and further analysed by modeling, and predictions from any approach can be tested and advanced through companion methodologies and technologies. This two volume set describes innovations in biomolecular modeling and simulation, in both the algorithmic and application fronts. With contributions from experts in the field, the books describe progress and innovation in areas including: simulation algorithms for dynamics and enhanced configurational sampling, force field development, implicit solvation models, coarse-grained models, quantum-mechanical simulations, protein folding, DNA polymerase mechanisms, nucleic acid complexes and simulations, RNA structure analysis and design and other important topics in structural biology modeling. The books are aimed at graduate students and experts in structural biology and chemistry and the emphasis is on reporting innovative new approaches rather than providing comprehensive reviews on each subject.

Handbook of RNA Biochemistry

Handbook of RNA Biochemistry
Author: Roland K. Hartmann
Publisher: John Wiley & Sons
Total Pages: 1370
Release: 2015-06-22
Genre: Science
ISBN: 3527327762

The second edition of a highly acclaimed handbook and ready reference. Unmatched in its breadth and quality, around 100 specialists from all over the world share their up-to-date expertise and experiences, including hundreds of protocols, complete with explanations, and hitherto unpublished troubleshooting hints. They cover all modern techniques for the handling, analysis and modification of RNAs and their complexes with proteins. Throughout, they bear the practising bench scientist in mind, providing quick and reliable access to a plethora of solutions for practical questions of RNA research, ranging from simple to highly complex. This broad scope allows the treatment of specialized methods side by side with basic biochemical techniques, making the book a real treasure trove for every researcher experimenting with RNA.

Nucleic Acids

Nucleic Acids
Author: Victor A. Bloomfield
Publisher: Sterling Publishing Company
Total Pages: 854
Release: 2000-04-17
Genre: Science
ISBN: 9780935702491

Providing a comprehensive account of the structures and physical chemistry properties of nucleic acids, with special emphasis on biological function, this text has been organized to meet the needs of those who have only a basic understanding of physical chemistry and molecular biology.

RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods

RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods
Author: Jan Gorodkin
Publisher: Humana
Total Pages: 0
Release: 2014-03-18
Genre: Science
ISBN: 9781627037082

The 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 Structure and Function

RNA Structure and Function
Author: Jan Barciszewski
Publisher: Springer Nature
Total Pages: 662
Release: 2023-12-05
Genre: Science
ISBN: 3031363906

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.