Biophysics Of Dna Protein Interactions

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.

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.

The study of protein-nucleic acid interactions is currently one of the most rapidly growing areas of molecular biology. DNA binding proteins are at the very heart of the regulation and control of gene expression, replication, and recombination: Enzymes that recognize and either modify or cleave specific DNA sequences are equally important to the cell. Some of the techniques reported in this volume can be used to identify previously unknown DNA binding proteins from crude cell extracts. Virtually all are capable of giving direct information on the molecular basis of the interaction—the location of the DNA binding site; the strength and specificity of binding; the identities of individual groups on specific bases involved in binding; the specific amino acid residues of the protein that interact with the DNA; or the effects of protein binding on gross conformation and local structure of DNA. The recognition of DNA sequences by proteins is a complex phenomenon, involving specific hydrogen bonding contacts to the DNA bases ("direct readout") and/or interactions with the sugar-phos phate backbone ("indirect readout"). The latter interactions can also be highly specific because of sequence-dependent conformational changes in the DNA. In addition, intercalation of planar aromatic amino acid side-chains between the DNA bases can occur, most notably with single-stranded DNA binding proteins. Furthermore, when bound, many DNA binding proteins induce drastic structural changes in the DNA as an integral part of their function.

This important publication addresses the interactions of proteins with nonspecific binding sites on DNA as they play critical roles in fundamental cellular processes such as transcription, DNA replication, and recombination. The book presents current reviews of the biochemistry of representative nonspecific DNA-protein systems, and of their physiological functions. It includes chapters on the techniques used to characterize the complexes, on their thermodynamic properties, and on the role of nonspecific binding as gene regulatory proteins search for specific target sites on the chromosome. Systems considered include the effects of nonspecific binding in regulation of the lactose operon of Escherichia coli, the T4 bacteriophage gene 32 protein, the E. coli single strand binding (SSB) protein and recA protein, eukaryotic SSB's and histone-DNA complexes. The book presents those proteins displaying multiple modes of DNA binding as participants in more than one cellular process. This monograph combines rigorous descriptions of new findings for these important systems with provocative interpretations of the biological significance of the results. It is of great value to researchers ranging from graduate students to senior scientists in the areas of biochemistry, microbiology and molecular/cell biology.

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.

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.

Gene expression can mean the difference between a functional and non-functional genome, between health and disease, and with the development of transgenic crops, the difference between survival and starvation. In DNA-Protein Interactions: Principles and Protocols, Third Edition, this vital subject is brought up to date with protocols exploring the most cutting-edge developments in the field, including in vivo and genome-wide interaction techniques. Addressing topics such as chromatin immunoprecipitation, topological studies, photocrosslinking, FRET and imaging techniques, the volume fully updates and expands upon the successful previous editions. Written in the convenient and informative Methods in Molecular BiologyTM series format, chapters include introductions to their respective subjects, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Comprehensive and authoritative, DNA-Protein Interactions: Principles and Protocols, Third Edition serves as an ideal guide for all those exploring this dynamic, essential, and increasingly affordable area of research.

As the mysteries stored in our DNA have been more completely revealed, scientists have begun to face the extraordinary challenge of unraveling the int- cate network of protein–protein interactions established by that DNA fra- work. It is increasingly clear that proteins continuously interact with one another in a highly regulated fashion to determine cell fate, such as proliferation, diff- entiation, or death. These protein–protein interactions enable and exert str- gent control over DNA replication, RNA transcription, protein translation, macromolecular assembly and degradation, and signal transduction; essentially all cellular functions involve protein–protein interactions. Thus, protein–p- tein interactions are fundamental for normal physiology in all organisms. Alt- ation of critical protein–protein interactions is thought to be involved in the development of many diseases, such as neurodegenerative disorders, cancers, and infectious diseases. Therefore, examination of when and how protein–p- tein interactions occur and how they are controlled is essential for understa- ing diverse biological processes as well as for elucidating the molecular basis of diseases and identifying potential targets for therapeutic interventions. Over the years, many innovative biochemical, biophysical, genetic, and computational approaches have been developed to detect and analyze p- tein–protein interactions. This multitude of techniques is mandated by the diversity of physical and chemical properties of proteins and the sensitivity of protein–protein interactions to cellular conditions.