Introduction To Protein Dna Interactions

Author : Gary Stormo
Publisher :
ISBN 13 : 9781936113491
Total Pages : 198 pages
Book Rating : 4.9X/5 ( download)

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Download or read book Introduction to Protein-DNA Interactions written by Gary Stormo and published by . This book was released on 2013 with total page 198 pages. Available in PDF, EPUB and Kindle. Book excerpt: One of the foundations of molecular biology is how the interactions of proteins with DNA control many aspects of gene expression. Since the mid-20th century discoveries of the lac repressor and operator and the competition between the cI and cro proteins for the same segment of DNA, we have learned an enormous amount about the interactions of proteins with DNA and their control of fundamental processes in the cell. Introduction to Protein-DNA Interactions: Structure, Thermodynamics, and Bioinformatics describes what we know about protein-DNA interactions from the complementary perspectives of molecular and structural biology and bioinformatics and how each perspective informs the others. A particular emphasis is on how insights from experimental work can be translated into specific computational approaches to create unified view of the field and a fuller understanding of protein-DNA interactions.

Author : Gary Stormo
Publisher :
ISBN 13 : 9781936113507
Total Pages : 0 pages
Book Rating : 4.03/5 ( download)

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Download or read book Introduction to Protein-DNA Interactions written by Gary Stormo and published by . This book was released on 2013 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: One of the foundations of molecular biology is how the interactions of proteins with DNA control many aspects of gene expression. Since the mid-20th century discoveries of the lac repressor and operator and the competition between the cI and cro proteins for the same segment of DNA, we have learned an enormous amount about the interactions of proteins with DNA and their control of fundamental processes in the cell. Introduction to Protein-DNA Interactions: Structure, Thermodynamics, and Bioinformatics describes what we know about protein-DNA interactions from the complementary perspectives of molecular and structural biology and bioinformatics and how each perspective informs the others. A particular emphasis is on how insights from experimental work can be translated into specific computational approaches to create unified view of the field and a fuller understanding of protein-DNA interactions.

Author : Jost
Publisher : Birkhäuser
ISBN 13 : 3034875614
Total Pages : 319 pages
Book Rating : 4.15/5 ( download)

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Download or read book A Laboratory Guide to In Vitro Studies of Protein-DNA Interactions written by Jost and published by Birkhäuser. This book was released on 2013-03-13 with total page 319 pages. Available in PDF, EPUB and Kindle. Book excerpt: A Safety Considerations Many techniques described here involve a number of hazards, such as high electrical current and voltage, radioactivity and highly toxic chemicals. It is absolutely essential that the instructions of equipment manufacturers be followed, and that particular attention be paid to the local and federal safety regulations. B Introduction The expression of prokaryotic and eukaryotic genes has been shown most often to be regulated at the level of mRNA synthesis. Thanks to the rapid development of methods for dissecting DNA sequences, cis-acting regulatory elements such as promoters and enhancers have been recognised. More recently, the widely expressed intuition that discrete sequences within these elements constitute binding sites for sequence-specific binding proteins has been confirmed, especially through the use of "footprinting" assays (for examples, Galas and Schmitz, 1978). This and similar assays have already resulted in the recognition, isolation and analysis of DNA-bind ing proteins for several genes. Excellent reviews exist of the structural studies on these transcription regulatory proteins and related DNA elements (for example, Glover, 1989 and Johnson and McKnight, 1989), to which the reader is referred for detailed information. To set the scene for applications of the techniques described in this volume, only the barest outline of previous studies is presented here. Protein-DNA interactions are dependent on very specific tertiary configurations of the binding protein which allow the closest contact with the DNA helix.

Author : Tom Moss
Publisher : Springer Science & Business Media
ISBN 13 : 1592592082
Total Pages : 633 pages
Book Rating : 4.81/5 ( download)

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Download or read book DNA'Protein Interactions written by Tom Moss and published by Springer Science & Business Media. This book was released on 2008-02-02 with total page 633 pages. Available in PDF, EPUB and Kindle. Book excerpt: Dr. Tom Moss assembles the new standard collection of cutting-edge techniques to identify key protein-DNA interactions and define their components, their manner of interaction, and their manner of function, both in the cell and in the test tube. The techniques span a wide range, from factor identification to atomic detail, and include multiple DNA footprinting analyses, including in vivo strategies, gel shift (EMSA) optimization, SELEX, surface plasmon resonance, site-specific DNA-protein crosslinking, and UV laser crosslinking. Comprehensive and broad ranging, DNA-Protein Interactions: Principles and Protocols, 2nd Edition, offers a stellar array of over 100 up-to-date and readily reproducible techniques that biochemists and molecular, cellular, and developmental biologists can use successfully today to understand DNA-protein interactions.

Author : Mark C. Williams
Publisher : Springer Science & Business Media
ISBN 13 : 0387928081
Total Pages : 354 pages
Book Rating : 4.81/5 ( download)

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Download or read book Biophysics of DNA-Protein Interactions written by Mark C. Williams and published by Springer Science & Business Media. This book was released on 2010-10-05 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt: Depite the rapid expansion of the field of biophysics, there are very few books that comprehensively treat specific topics in this area. Recently, the field of single molecule biophysics has developed very quickly, and a few books specifically treating single molecule methods are beginning to appear. However, the promise of single molecule biophysics is to contribute to the understanding of specific fields of biology using new methods. This book would focus on the specific topic of the biophysics of DNA-protein interactions, and would include the use of new approaches, including both bulk methods as well as single molecule methods. This would make the book attractive to anyone working in the general area of DNA-protein interactions, which is of course a much wider market than just single molecule biophysicists or even biophysicists. The subject of the book will be the biophysics of DNA-protein interactions, and will include new methods and results that describe the physical mechanism by which proteins interact with DNA. For example, there has been much recent work on the mechanism by which proteins search for specific binding sites on DNA. A few chapters will be devoted to experiments and theory that shed light on this important problem. We will also cover proteins that alter DNA properties to facilitate interactions important for transcription or replication. Another section of the book will cover the biophysical mechanism by which motor proteins interact with DNA. Finally, we will cover larger protein-DNA complexes, such as replication forks, recombination complexes, DNA repair interactions, and their chromatin context.

Author : Biman Bagchi
Publisher : Cambridge University Press
ISBN 13 : 1107037298
Total Pages : 383 pages
Book Rating : 4.98/5 ( download)

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Download or read book Water in Biological and Chemical Processes written by Biman Bagchi and published by Cambridge University Press. This book was released on 2013-11-14 with total page 383 pages. Available in PDF, EPUB and Kindle. Book excerpt: A unified overview of the dynamical properties of water and its unique and diverse role in biological and chemical processes.

Author : Phoebe A. Rice
Publisher : Royal Society of Chemistry
ISBN 13 : 0854042725
Total Pages : 417 pages
Book Rating : 4.22/5 ( download)

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Download or read book Protein-Nucleic Acid Interactions written by Phoebe A. Rice and published by Royal Society of Chemistry. This book was released on 2008-05-22 with total page 417 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides both in-depth background and up-to-date information in this area. The chapters are organized by general themes and principles, written by experts who illustrate topics with current findings. Topics covered include: - the role of ions and hydration in protein-nucleic acid interactions - transcription factors and combinatorial specificity - indirect readout of DNA sequence - single-stranded nucleic acid binding proteins - nucleic acid junctions and proteins, - RNA protein recognition - recognition of DNA damage. It will be a key reference for both advanced students and established scientists wishing to broaden their horizons.

Author : Phoebe A Rice
Publisher : Royal Society of Chemistry
ISBN 13 : 1847558267
Total Pages : 416 pages
Book Rating : 4.68/5 ( download)

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Download or read book Protein-Nucleic Acid Interactions written by Phoebe A Rice and published by Royal Society of Chemistry. This book was released on 2008-04-22 with total page 416 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Author : Harald Seitz
Publisher : Springer Science & Business Media
ISBN 13 : 3540481478
Total Pages : 212 pages
Book Rating : 4.78/5 ( download)

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Download or read book Analytics of Protein-DNA Interactions written by Harald Seitz and published by Springer Science & Business Media. This book was released on 2007-01-16 with total page 212 pages. Available in PDF, EPUB and Kindle. Book excerpt: With contributions by numerous experts

Author : Altuna Akalin
Publisher : CRC Press
ISBN 13 : 1498781861
Total Pages : 462 pages
Book Rating : 4.62/5 ( download)

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Download or read book Computational Genomics with R written by Altuna Akalin and published by CRC Press. This book was released on 2020-12-16 with total page 462 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015.