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Principles Of Nucleic Acid Structure

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Principles of Nucleic Acid Structure

Principles of Nucleic Acid Structure Book
Author : Stephen Neidle
Publisher : Elsevier
Release : 2010-07-26
ISBN : 9780080553528
Language : En, Es, Fr & De

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Book Description :

This unique and practical resource provides the most complete and concise summary of underlying principles and approaches to studying nucleic acid structure, including discussion of x-ray crystallography, NMR, molecular modelling, and databases. Its focus is on a survey of structures especially important for biomedical research and pharmacological applications. To aid novices, Principles of Nucleic Acid Structure includes an introduction to technical lingo used to describe nucleic acid structure and conformations (roll, slide, twist, buckle, etc.). This completely updated edition features expanded coverage of the latest advances relevant to recognition of DNA and RNA by small molecules and proteins. In particular, the reader will find extensive new discussions on: RNA folding, ribosome structure and antibiotic interactions, DNA quadruplexes, DNA and RNA protein complexes, and short interfering RNA (siRNA). This handy guide ends with a complete list of resources, including relevant online databases and software. Completely updated with expanded discussion of topics such as RNA folding, ribosome structure and antibiotic interactions, DNA quadruplexes, DNA and RNA protein complexes, and short interfering RNA (siRNA) Includes a complete list of resources, including relevant online databases and software Defines technical lingo for novices

Principles of Nucleic Acid Structure

Principles of Nucleic Acid Structure Book
Author : Wolfram Saenger
Publisher : Springer Science & Business Media
Release : 2013-12-01
ISBN : 1461251907
Language : En, Es, Fr & De

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Book Description :

New textbooks at all levels of chemistry appear with great regularity. Some fields like basic biochemistry, organic reaction mechanisms, and chemical ther modynamics are well represented by many excellent texts, and new or revised editions are published sufficiently often to keep up with progress in research. However, some areas of chemistry, especially many of those taught at the grad uate level, suffer from a real lack of up-to-date textbooks. The most serious needs occur in fields that are rapidly changing. Textbooks in these subjects usually have to be written by scientists actually involved in the research which is advancing the field. It is not often easy to persuade such individuals to set time aside to help spread the knowledge they have accumulated. Our goal, in this series, is to pinpoint areas of chemistry where recent progress has outpaced what is covered in any available textbooks, and then seek out and persuade experts in these fields to produce relatively concise but instructive introductions to their fields. These should serve the needs of one semester or one quarter graduate courses in chemistry and biochemistry. In some cases the availability of texts in active research areas should help stimulate the creation of new courses. CHARLES R. CANTOR New York Preface This monograph is based on a review on polynucleotide structures written for a book series in 1976.

Nucleic Acid Structure and Recognition

Nucleic Acid Structure and Recognition Book
Author : Cancer Research Campaign Biomolecular Structure Unit Stephen Neidle,Stephen Neidle
Publisher : Oxford University Press, USA
Release : 2002
ISBN : 9780198506355
Language : En, Es, Fr & De

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Book Description :

This book provides a detailed view of the molecular structures of DNA and RNA and how they are recognised by small molecules and proteins. Extensive source material is provided, including information on relevant web sites and computer programmes. The major methods of structural investigationfor nucleic acids: X-ray crystallography, NMR, and molecular modelling are reviewed and their scope and limitations (in the context of nucleic acids) discussed. Also covered are the conformational features of nucleic acid building blocks, including a description of how base-pair morphologies areanalysed; the structures of DNA double helices and helical oligonucleotides, emphasising current ideas on sequence-dependent structure; and DNA-DNA interactions, including triplexes and quadruplexes. The principles of RNA folding, ribosome, and ribozyme structure are also surveyed. Both covalent andnon-covalent nucleic acid interactions with small molecules are described, with the emphasis on recognition principles and sequence specific gene recognition. The principles of protein - nucleic acid are covered, focussing on regulatory proteins.Nucleic Acid Structure and Recognition will therefore equip readers with a good understanding of all the important aspects of this major field.The Nucleic Acid Database (NDB) crystallographic and NMR structures for the nucleic acid structures described in the book are freely available through the Nucleic Acid Structure and Recognition website.

Basic Principles in Nucleic Acid Chemistry

Basic Principles in Nucleic Acid Chemistry Book
Author : Paul O.P. Ts'o
Publisher : Elsevier
Release : 2012-12-02
ISBN : 0323146899
Language : En, Es, Fr & De

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Book Description :

Basic Principles in Nuclear Acid Chemistry, Volume II presents the significant progress in nucleic acid research and its contribution and influence on various aspects of human life. This book contains five chapters and begins with the susceptibility of nucleic acids towards attack by chemical reagents whose reactions with polynucleotides have been studied. This topic is followed by a presentation of experimental techniques used to study the properties of nucleic acids. The following chapter discusses some basic features embodied in the polyribo- and poly-deoxyribonucleotide backbone chains; the possibility of rotation around backbone bonds in the ""random"" single-stranded form; and the short- and long-range interactions in idealized and real chains. This chapter also looks into the thermodynamic and polyelectrolyte aspects of nucleic acid behavior. A chapter describes the special features of the third class of DNA, namely, closed duplex DNA, in which covalent chain scissions are absent. The last chapter examines the intrinsic properties and the interaction of the dimers and oligomers, with special emphasis on the influence of the phosphodiester linkages on the conformation and interaction of these short segments of nucleic acids. This book is of great value to workers in biomedical research and to higher level biochemistry instructors.

Basic Principles in Nucleic Acid Chemistry

Basic Principles in Nucleic Acid Chemistry Book
Author : Paul O.P. Ts'o
Publisher : Elsevier
Release : 2012-12-02
ISBN : 0323144004
Language : En, Es, Fr & De

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Book Description :

Basic Principles in Nucleic Acid Chemistry, Volume I provides information pertinent to the fundamental aspects of nucleic acids. This book discusses the development of the basic principles in nucleic acid research that will serve as a foundation for further advancement in nucleic acid research. Organized into six chapters, this volume begins with an overview of the history of the scientific study of nucleic acid as a genetic material. This text then examines the utility of the analogs of the naturally occurring nucleic acid components as biochemical tools and as therapeutic agents. Other chapters consider mass spectrometry that deals with the production and chemistry of ions in the vapor phase. This book discusses as well the various aspects of the excited states of the nucleic acids. The final chapter deals with the systematic study of the physiochemical properties of the monomeric units of nucleic acid. This book is a valuable resource for molecular biologists, scientists, and research workers.

Computational studies of RNA and DNA

Computational studies of RNA and DNA Book
Author : Jirí Šponer,Filip Lankaš
Publisher : Springer Science & Business Media
Release : 2006-10-05
ISBN : 1402048513
Language : En, Es, Fr & De

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Book Description :

This book integrates modern computational studies of nucleic acids, ranging from advanced electronic structure quantum chemical calculations through explicit solvent molecular dynamics (MD) simulations up to mesoscopic modelling, with the main focus given to the MD field. It gives an equal emphasis to the leading methods and applications while successes as well as pitfalls of the computational techniques are discussed.

Principles and Practice of Experiments with Nucleic Acids

Principles and Practice of Experiments with Nucleic Acids Book
Author : John Howard Parish
Publisher :
Release : 1972
ISBN :
Language : En, Es, Fr & De

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Book Description :

Nucleic acid components; Isolation; Fractionation; Identification; Degradation; Synthesis; Chemical reactions; Primary structure of DNA and RNA; Secondary structure; Hybridization; Size and shape; Interaction between nucleic acids and small molecules; Tertiary structure; Interaction between nucleic acids and proteins.

Protein Nucleic Acid Interactions

Protein Nucleic Acid Interactions Book
Author : Phoebe A Rice,Carl C Correll
Publisher : Royal Society of Chemistry
Release : 2008-04-22
ISBN : 1847558267
Language : En, Es, Fr & De

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Book Description :

The structural biology of protein-nucleic acid interactions is in some ways a mature field and in others in its infancy. High-resolution structures of protein-DNA complexes have been studied since the mid 1980s and a vast array of such structures has now been determined, but surprising and novel structures still appear quite frequently. High-resolution structures of protein-RNA complexes were relatively rare until the last decade. Propelled by advances in technology as well as the realization of RNA's importance to biology, the number of example structures has ballooned in recent years. New insights are now being gained from comparative studies only recently made possible due to the size of the database, as well as from careful biochemical and biophysical studies. As a result of the explosion of research in this area, it is no longer possible to write a comprehensive review. Instead, current review articles tend to focus on particular subtopics of interest. This makes it difficult for newcomers to the field to attain a solid understanding of the basics. One goal of this book is therefore to provide in-depth discussions of the fundamental principles of protein-nucleic acid interactions as well as to illustrate those fundamentals with up-to-date and fascinating examples for those who already possess some familiarity with the field. The book also aims to bridge the gap between the DNA- and the RNA- views of nucleic acid - protein recognition, which are often treated as separate fields. However, this is a false dichotomy because protein - DNA and protein - RNA interactions share many general principles. This book therefore includes relevant examples from both sides, and frames discussions of the fundamentals in terms that are relevant to both. The monograph approaches the study of protein-nucleic acid interactions in two distinctive ways. First, DNA-protein and RNA-protein interactions are presented together. Second, the first half of the book develops the principles of protein-nucleic acid recognition, whereas the second half applies these to more specialized topics. Both halves are illustrated with important real life examples. The first half of the book develops fundamental principles necessary to understand function. An introductory chapter by the editors reviews the basics of nucleic acid structure. Jen-Jacobsen and Jacobsen discuss how solvent interactions play an important role in recognition, illustrated with extensive thermodynamic data on restriction enzymes. Marmorstein and Hong introduce the zoology of the DNA binding domains found in transcription factors, and describe the combinational recognition strategies used by many multiprotein eukaryotic complexes. Two chapters discuss indirect readout of DNA sequence in detail: Berman and Lawson explain the basic principles and illustrate them with in-depth studies of CAP, while in their chapter on DNA bending and compaction Johnson, Stella and Heiss highlight the intrinsic connections between DNA bending and indirect readout. Horvath lays out the fundamentals of protein recognition of single stranded DNA and single stranded RNA, and describes how they apply in a detailed analysis of telomere end binding proteins. Nucleic acids adopt more complex structures - Lilley describes the conformational properties of helical junctions, and how proteins recognize and cleave them. Because RNA readily folds due to the stabilizing role of its 2'-hydroxyl groups, Li discusses how proteins recognize different RNA folds, which include duplex RNA. With the fundamentals laid out, discussion turns to more specialized examples taken from important aspects of nucleic acid metabolism. Schroeder discusses how proteins chaperone RNA by rearranging its structure into a functional form. Berger and Dong discuss how topoisomerases alter the topology of DNA and relieve the superhelical tension introduced by other processes such as replication and transcription. Dyda and Hickman show how DNA transposes mediate genetic mobility and Van Duyne discusses how site-specific recombinases "cut" and "paste" DNA. Horton presents a comprehensive review of the structural families and chemical mechanisms of DNA nucleases, whereas Li in her discussion of RNA-protein recognition also covers RNA nucleases. Lastly, FerrÚ-D'AmarÚ shows how proteins recognize and modify RNA transcripts at specific sites. The book also emphasises the impact of structural biology on understanding how proteins interact with nucleic acids and it is intended for advanced students and established scientists wishing to broaden their horizons.

Nucleic Acids Structure and Function for General Biochemistry Biology and Biotechnology

Nucleic Acids  Structure and Function for General Biochemistry  Biology and Biotechnology  Book
Author : Fidelis Manyanga,Alec Sithole
Publisher : Lulu.com
Release : 2014-08-29
ISBN : 1312460903
Language : En, Es, Fr & De

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Book Description :

The study of the structure, function, and synthesis of DNA and RNA molecules is one of the important branches of biological studies. The study of DNA and the genes that it contains is broadly known as genomics. Gene expression has distinct roles for DNA and RNA during transcription and translation. In this book, DNA structure and function, transcription, and translation are discussed in detail. The book is ideal for college level students studying general biochemistry, biotechnology, and biology. Each chapter begins with some learning objectives, followed by innovative explanations of concepts, and lastly, references for further studies. Enjoy!

Biophysics of RNA Folding

Biophysics of RNA Folding Book
Author : Rick Russell
Publisher : Springer Science & Business Media
Release : 2012-12-09
ISBN : 1461449545
Language : En, Es, Fr & De

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Book Description :

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.

Ribozymes and RNA Catalysis

Ribozymes and RNA Catalysis Book
Author : David Malcolm James Lilley,Fritz Eckstein
Publisher : Royal Society of Chemistry
Release : 2008
ISBN : 0854042539
Language : En, Es, Fr & De

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Book Description :

The emphasis of this book concerns the origins of catalysis in RNA and is well suited for undergraduates, postgraduates and researchers in catalytic chemistry.

Artificial Nucleases

Artificial Nucleases Book
Author : Marina A. Zenkova
Publisher : Springer Science & Business Media
Release : 2004-01-07
ISBN : 9783540201120
Language : En, Es, Fr & De

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Book Description :

The development of agents capable of cleaving RNA and DNA has attracted considerable attention from researchers in the last few years, because of the immediate and very important applications they can find in the emerging fields of biotechnology and pharmacology. There are essentially two classes of these agents - nucleases that occur naturally inside cells and synthetically produced artificial nucleases. The first class includes protein enzyme nucle ases and catalytic RNA structured ribozymes that perform cleavage of the phosphodiester bonds in nucleic acids according to a hydrolytic pathway in the course of different biochemical processes in the cell. A different pathway is used by some antibiotics which cleave DNA via redox-based mechanisms resulting in oxidative damage of nucleotide units and breakage of the DNA backbone. The above molecules are indispensable tools for manipulating nucleic acids and processing RNA; DNA-cleaving antibiotics and cytotoxic ribonucleases have demonstrated utility as chemotherapeutic agents. The second class, artificial nucleases, are rationally designed to imitate the active centers of natural enzymes by simple structures possessing minimal sets of the most important characteristics that are essential for catalysis. A dif ferent approach, in vitro selection, was also used to create artificial RNA and DNA enzymes capable of cleaving RNA. Being less efficient and specific as compared to the natural enzymes, the primitive mimics are smaller and robust and can function in a broad range of conditions.

Antisense Drug Technology

Antisense Drug Technology Book
Author : Stanley T. Crooke
Publisher : CRC Press
Release : 2001-09-14
ISBN : 9780824705664
Language : En, Es, Fr & De

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Book Description :

This state-of-the-art reference provides comprehensive coverage of the development of antisense oligonucleotides to inhibit cancer cells as well as those involved in infectious, inflammatory, and immune-mediated diseases-highlighting new tools and technologies in medicinal chemistry, RNA biochemistry, and molecular and cellular biology to produce new therapeutic compounds. Presents previously unpublished data on the use of antisense technology to dissect pharmacological processes and confirm the roles of various genes! Showcasing the benefits of antisense drug use, including reduced toxicity and earlier disease detection, Antisense Drug Technology discusses novel formulations of antisense drugs practical methods to design effective isotype selective inhibitors molecular mechanisms of antisense drugs mRNA as a current biological template modern postreceptor binding mechanisms and more! With contributions by over 60 seasoned experts in the field and containing more than 3000 helpful references, tables, drawings, and photographs, Antisense Drug Technology is an illuminating source for organic, medicinal, and pharmaceutical chemists; biochemists; geneticists; hematologists; oncologists; molecular and cell biologists; virologists; immunologists; and medical school and graduate students in these disciplines.

Medicinal Chemistry of Nucleic Acids

Medicinal Chemistry of Nucleic Acids Book
Author : Li-He Zhang,Zhen Xi,Jyoti Chattopadhyaya
Publisher : John Wiley & Sons
Release : 2011-08-10
ISBN : 9781118092811
Language : En, Es, Fr & De

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Book Description :

Complete, up-to-date coverage of the broad area of nucleic acid chemistry and biology Assembling contributions from a collection of authors with expertise in all areas of nucleic acids, medicinal chemistry, and therapeutic applications, Medicinal Chemistry of Nucleic Acids presents a thorough overview of nucleic acid chemistry—a rapidly evolving and highly challenging discipline directly responsible for the development of antiviral and antitumor drugs. This reliable resource delves into a multitude of subject areas involving the study of nucleic acids—such as the new advances in genome sequencing, and the processes for creating RNA interference (RNAi) based drugs—to assist pharmaceutical researchers in removing roadblocks that hinder their ability to predict drug efficacy. Offering the latest cutting-edge science in this growing field, Medicinal Chemistry of Nucleic Acids includes: In-depth coverage of the development and application of modified nucleosides and nucleotides in medicinal chemistry A close look at a large range of current topics on nucleic acid chemistry and biology Essential information on the use of nucleic acid drugs to treat diseases like cancer A thorough exploration of siRNA for RNAi and the regulation of microRNA, non-coding RNA (ncRNA), a newly developing and exciting research area Thorough in its approach and promising in its message, Medicinal Chemistry of Nucleic Acids probes the new domains of pharmaceutical research—and exposes readers to a wealth of new drug discovery opportunities emerging in the dynamic field of nucleic acid chemistry.

Prokaryotic Gene Expression

Prokaryotic Gene Expression Book
Author : Simon Baumberg
Publisher : OUP Oxford
Release : 1999-05-27
ISBN : 0191565571
Language : En, Es, Fr & De

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Book Description :

Prokaryotic gene expression is not only of theoretical interest but also of highly practical significance. It has implications for other biological problems, such as developmental biology and cancer, brings insights into genetic engineering and expression systems, and has consequences for important aspects of applied research. For example, the molecular basis of bacterial pathogenicity has implications for new antibiotics and in crop development. Prokaryotic Gene Expression is a major review of the subject, providing up-to-date coverage as well as numerous insights by the prestigious authors. Topics covered include operons; protein recognition of sequence specific DNA- and RNA-binding sites; promoters; sigma factors, and variant tRNA polymerases; repressors and activators; post-transcriptional control and attenuation; ribonuclease activity, mRNA stability, and translational repression; prokaryotic DNA topology, topoisomerases, and gene expression; regulatory networks, regulatory cascades and signal transduction; phosphotransfer reactions; switch systems, transcriptional and translational modulation, methylation, and recombination mechanisms; pathogenicity, toxin regulation and virulence determinants; sporulation and genetic regulation of antibiotic production; origins of regulatory molecules, selective pressures and evolution of prokaryotic regulatory mechanisms systems. Over 1100 references to the primary literature are cited. Prokaryotic Gene Expression is a comprehensive and authoritative review of current knowledge and research in the area. It is essential reading for postgraduates and researchers in the field. Advanced undergraduates in biochemistry, molecular biology, and microbiology will also find this book useful.

Principles and Techniques of Practical Biochemistry

Principles and Techniques of Practical Biochemistry Book
Author : PH D Keith Wilson,Keith Wilson,John Walker,Professor John M Walker
Publisher : Cambridge University Press
Release : 2000-03-16
ISBN : 9780521658737
Language : En, Es, Fr & De

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Book Description :

New edition of biochemistry textbook which introduces principles and techniques used in undergraduate practical classes.

Small Molecule DNA and RNA Binders

Small Molecule DNA and RNA Binders Book
Author : Martine Demeunynck,Christian Bailly,W. David Wilson
Publisher : John Wiley & Sons
Release : 2006-03-06
ISBN : 3527605665
Language : En, Es, Fr & De

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Book Description :

The development of molecules that selectively bind to nucleic acids has provided many details about DNA and RNA recognition. The range of such substances, such as metal complexes, peptides, oligonucleotides and a wide array of synthetic organic compounds, is as manifold as the functions of nucleic acids. Nucleic acid recognition sequences are often found in the major or minor groove of a double strand, while other typical interactions include intercalation between base pairs or the formation of triple or quadruple helices. One example of a binding mode that has recently been proposed is end stacking on such complex structures as the telomere tetraplex. In this comprehensive book, internationally recognized experts describe in detail the important aspects of nucleic acid binding, and in so doing present impressive approaches to drug design. Since typical substances may be created naturally or synthetically, emphasis is placed on natural products, chemical synthesis, the use of combinatorial libraries, and structural characterization. The whole is rounded off by contributions on molecular modeling, as well as investigations into the way in which any given drug interacts with its nucleic acid recognition site.

Principles of Molecular Biology

Principles of Molecular Biology Book
Author : Burton E. Tropp
Publisher : Jones & Bartlett Publishers
Release : 2012-12-14
ISBN : 144964791X
Language : En, Es, Fr & De

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Book Description :

Includes access to the Student Companion Website with every print copy of the text. Written for the more concise course, Principles of Molecular Biology is modeled after Burton Tropp's successful Molecular Biology: Genes to Proteins and is appropriate for the sophomore level course. The author begins with an introduction to molecular biology, discussing what it is and how it relates to applications in "real life" with examples pulled from medicine and industry. An overview of protein structure and function follows, and from there the text covers the various roles of technology in elucidating the central concepts of molecular biology, from both a historical and contemporary perspective. Tropp then delves into the heart of the book with chapters focused on chromosomes, genetics, replication, DNA damage and repair, recombination, transposition, transcription, and wraps up with translation. Key Features: - Presents molecular biology from a biochemical perspective, utilizing model systems, as they best describe the processes being discussed -Special Topic boxes throughout focus on applications in medicine and technology -Presents "real world" applications of molecular biology that are necessary for students continuing on to medical school or the biotech industry -An end-of-chapter study guide includes questions for review and discussion -Difficult or complicated concepts are called-out in boxes to further explain and simplify