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Nucleic acid structure and recognition
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ISBN: 019850635X Year: 2002 Publisher: Oxford ; New York : Oxford University Press,

Zinc-finger proteins in oncogenesis: DNA-binding and gene regulation
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ISBN: 0897667832 0897667840 9780897667845 Year: 1993 Volume: 684 Publisher: New York (N.Y.): New York Academy of Sciences,

DNA-protein interactions : principles and protocols
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ISBN: 0896032566 1592595170 9780896032569 Year: 1994 Volume: 30 Publisher: Totowa (N.J.) : Humana press,

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Abstract

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.


Book
DNA Helicases and DNA Motor Proteins
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ISBN: 1461450365 1461450373 128386505X 1489998519 Year: 2013 Publisher: New York, NY : Springer New York : Imprint: Springer,

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In recent years, a number of groundbreaking structural and mechanistic studies deepened our understanding of helicase mechanisms and established new approaches for their analyses. Many fundamental mechanistic questions ranging from the mechanism of force generation, mechanochemical coupling to distinct mechanisms by which the same enzyme translocates on DNA removing obstacles, unwinds DNA and/or remodels nucleoprotein complexes, however, remain to be answered. It is even less understood how the helicase motors are incorporated into a wide range of genome maintenance and repair machines. The field has reached a stage when the studies of molecular mechanisms and basic biology of helicases can and shall be integrated with the studies of development, cancer and longevity. The objective of this book is to provide the first systematic overview of structure, function and regulation of DNA helicases and related molecular motors. By integrating the knowledge obtained through the diverse technical approaches ranging from single-molecule biophysics to cellular and molecular biological studies the editors aim to provide a unified view on how helicases function in the cell, are regulated in response to different cellular stresses and are integrated into large macromolecular assemblies to form a complex and adaptive living system.

Foundations of structural biology
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ISBN: 1281020389 9786611020385 0080521843 0120777002 9780120777006 9780080521848 9781281020383 Year: 2000 Publisher: San Diego ; London : Academic,

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Imagine trying to understand an engine without visualizing its moving parts. Biological processes involve far more complex chemical reactions and components than any engine. Furthermore, the parts work together to do many more functions than an engine which sole task is to turn a shaft. Understanding the implications of the three-dimensional coordinates for a molecule with several thousand atoms requires an understanding of, and practice with, 3D imaging. For many biologists, this means acquiring a whole new set of skills. Foundations of Structural Biology is aimed at helping the re


Book
Biophysics of DNA-protein interactions : from single molecules to biological systems
Authors: ---
ISBN: 0387928073 9786612973840 1282973843 0387928081 Year: 2011 Publisher: New York : Springer,

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This book presents a concise overview of current research on the biophysics of DNA-protein interactions. A wide range of new and classical methods are presented by authors investigating physical mechanisms by which proteins interact with DNA. For example, several chapters address the mechanisms by which proteins search for and recognize specific binding sites on DNA, a process critical for cellular function. Single molecule methods such as force spectroscopy as well as fluorescence imaging and tracking are described in these chapters as well as other parts of the book that address the dynamics of protein-DNA interactions. Other important topics include the mechanisms by which proteins engage DNA sequences and/or alter DNA structure. These simple but important model interactions are then placed in the broader biological context with discussion of larger protein-DNA complexes . Topics include replication forks, recombination complexes, DNA repair interactions, and ultimately, methods to understand the chromatin context of the cell nucleus. This book will be of interest to readers who wish to explore current biophysical approaches to DNA-protein interactions across multiple levels of biological complexity.

Keywords

DNA-protein interactions. --- DNA-protein interactions --- Molecular biology --- Physical Phenomena --- Proteins --- Phenomena and Processes --- Amino Acids, Peptides, and Proteins --- DNA-Binding Proteins --- Biophysical Phenomena --- Chemicals and Drugs --- Human Anatomy & Physiology --- Biology --- Health & Biological Sciences --- Animal Biochemistry --- Biophysics --- Molecular biology. --- Molecular biochemistry --- Molecular biophysics --- DNA-protein binding --- Interactions, DNA-protein --- Protein-DNA interactions --- Physics. --- Biochemistry. --- Proteins. --- Cell biology. --- Biophysics. --- Biological physics. --- Biomedical engineering. --- Biophysics and Biological Physics. --- Molecular Medicine. --- Cell Biology. --- Biomedical Engineering. --- Biochemistry, general. --- Protein Structure. --- Biochemistry --- Biomolecules --- Systems biology --- DNA-ligand interactions --- Protein binding --- Medicine. --- Cytology. --- Biological and Medical Physics, Biophysics. --- Biomedical Engineering and Bioengineering. --- Biological chemistry --- Chemical composition of organisms --- Organisms --- Physiological chemistry --- Chemistry --- Medical sciences --- Clinical engineering --- Medical engineering --- Bioengineering --- Engineering --- Medicine --- Cell biology --- Cellular biology --- Cells --- Cytologists --- Clinical sciences --- Medical profession --- Human biology --- Life sciences --- Pathology --- Physicians --- Composition --- Health Workforce --- Proteins . --- Proteids --- Polypeptides --- Proteomics --- Biological physics --- Physics

Analytics of protein–DNA interactions
Authors: ---
ISSN: 07246145 ISBN: 9783540481478 3540481478 3540481508 9786610727575 1280727578 Year: 2007 Volume: 104 Publisher: Berlin: Springer,

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Keywords

DNA-protein interactions --- DNA-Binding Proteins --- DNA Footprinting --- genetics --- methods --- chemistry --- Biochemistry --- Biotechnology --- Human genetics --- Medicine --- Microbiology --- Interactions ADN-protéine --- Biology. --- DNA-protein interactions. --- Electronic books. -- local. --- Proteins --- Nuclease Protection Assays --- Genetic Techniques --- Investigative Techniques --- Amino Acids, Peptides, and Proteins --- Chemicals and Drugs --- Analytical, Diagnostic and Therapeutic Techniques and Equipment --- Human Anatomy & Physiology --- Health & Biological Sciences --- Mechanical Engineering --- Engineering & Applied Sciences --- Animal Biochemistry --- Bioengineering --- Biomedical Engineering --- DNA-protein binding --- Interactions, DNA-protein --- Protein-DNA interactions --- Chemistry. --- Medical microbiology. --- Analytical chemistry. --- Biotechnology. --- Genetic engineering. --- Medicinal chemistry. --- Biochemistry. --- Genetic Engineering. --- Biochemistry, general. --- Analytical Chemistry. --- Medical Microbiology. --- Medicinal Chemistry. --- Biological chemistry --- Chemical composition of organisms --- Organisms --- Physiological chemistry --- Biology --- Chemistry --- Medical sciences --- Chemistry, Medical and pharmaceutical --- Chemistry, Pharmaceutical --- Drug chemistry --- Drugs --- Medical chemistry --- Medicinal chemistry --- Pharmacochemistry --- Designed genetic change --- Engineering, Genetic --- Gene splicing --- Genetic intervention --- Genetic surgery --- Genetic recombination --- Transgenic organisms --- Chemical engineering --- Genetic engineering --- Analysis, Chemical --- Analytical chemistry --- Chemical analysis --- Metallurgical analysis --- Mineralogy, Determinative --- Physical sciences --- Composition --- Life sciences --- Biomass --- Life (Biology) --- Natural history --- DNA-ligand interactions --- Protein binding --- Analytical biochemistry. --- Microbiology. --- Microbial biology --- Microorganisms --- Analytic biochemistry --- Chemistry, Analytic --- Bioanalytic chemistry --- Bioanalytical chemistry --- Analytic chemistry


Book
The biophysical chemistry of nucleic acids & proteins
Author:
ISBN: 9780956478115 0956478115 Year: 2010 Publisher: [Place of publication not identified] Helvetian Press

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Keywords

Nucleic acids --- Proteins --- Enzymes --- Physical biochemistry --- Macromolecules --- Ligand binding (Biochemistry) --- Protein folding --- Polypeptides --- Nucleic acid hybridization --- Catalysis --- DNA --- DNA-protein interactions --- RNA --- RNA-protein interactions --- Nucleic Acids --- 577.122 --- Gene Products, Protein --- Gene Proteins --- Protein --- Protein Gene Products --- Proteins, Gene --- Molecular Mechanisms of Pharmacological Action --- 577.122 Protein metabolism --- Protein metabolism --- Nucleic Acid --- Acid, Nucleic --- Acids, Nucleic --- Interactions, RNA-protein --- Protein-RNA interactions --- RNA-protein binding --- Protein binding --- Ribonucleic acid --- Ribose nucleic acid --- Ribose --- DNA-protein binding --- Interactions, DNA-protein --- Protein-DNA interactions --- DNA-ligand interactions --- Deoxyribonucleic acid --- Desoxyribonucleic acid --- Thymonucleic acid --- TNA (Nucleic acid) --- Deoxyribose --- Genes --- Activation (Chemistry) --- Chemistry, Physical and theoretical --- Surface chemistry --- Enzyme regulation --- Regulation of enzyme activity --- Biological control systems --- Cytogenetics --- Cytology --- Hybridization --- Polynucleotides --- Biomolecules --- Biopolymers --- Peptides --- Denaturation of proteins --- Protein denaturation --- Protein unfolding --- Unfolding of proteins --- Coagulation --- Folding of proteins --- Protein conformation --- Biocatalysts --- Ferments --- Soluble ferments --- Catalysts --- Enzymology --- Binding, Ligand (Biochemistry) --- Biochemistry --- Dye-ligand affinity chromatography --- Radioligand assay --- Molecules --- Supramolecular chemistry --- Biophysical chemistry --- Physical organic chemistry --- Proteids --- Proteomics --- Conformation --- Denaturation --- Structure --- Regulation --- Technique --- Unfolding --- Folding

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