DNA'Protein Interactions Principles and Protocols
Kneale, G. Geoff.
DNA'Protein Interactions Principles and Protocols by G. Geoff Kneale. - 1st edition 1994 - 1 recurso en línea (XV, 427 páginas) - Methods in Molecular Biology 30 1940-6029 .
DNase I Footprinting -- Footprinting with Exonuclease III -- Hydroxyl Radical Footprinting -- Hydroxyl Radical Interference -- 1,10-Phenanthroline-Copper Ion Nuclease Footprinting of DNA-Protein Complexes in Situ Following Mobility-Shift Electrophoresis Assays -- Identification of Protein-DNA Contacts with Dimethyl Sulfate -- Diethyl Pyrocarbonate as a Probe of Protein-DNA Interactions -- Osmium Tetroxide Modification and the Study of DNA-Protein Interactions -- Diffusible Singlet Oxygen as a Probe of DNA Deformation -- Ethylation Interference -- Uranyl Photofootprinting of DNA-Protein Complexes -- Nitration of Tyrosine Residues in Protein-Nucleic Acid Complexes -- Limited Proteolysis of Protein-Nucleic Acid Complexes -- Cloning and Expression of DNA Binding Domains Using PCR -- Overexpression and Purification of Eukaryotic Transcription Factors as Glutathione-S-Transferase Fusions in E. coli -- Site-Directed Mutagenesis by the Cassette Method -- Site-Directed and Site-Saturation Mutagenesis Using Oligonucleotide Primers -- UV Laser-Induced Protein-DNA Crosslinking -- Ultraviolet Crosslinking of DNA-Protein Complexes via 8-Azidoadenine -- Filter-Binding Assays -- The Gel Shift Assay for the Analysis of DNA-Protein Interactions -- Improved Plasmid Vectors for the Analysis of Protein-Induced DNA Bending -- Determination of Sequence Preferences of DNA Binding Proteins Using Pooled Solid-Phase Sequencing of Low Degeneracy Oligonucleotide Mixtures -- Analysis of DNA-Protein Interactions by Intrinsic Fluorescence -- A Competition Assay for DNA Binding Using the Fluorescent Probe ANS -- Circular Dichroism for the Analysis of Protein-DNA Interactions -- Electron Microscopy of Protein-Nucleic Acid Complexes -- Reconstitution of Protein-DNA Complexes for Crystallization -- Assay of Restriction Endonucleases Using Oligonucleotides -- Assays for Restriction Endonucleases Using Plasmid Substrates -- Assays for Transcription Factor Activity -- An Assay for In Vitro Recombination Between Duplex DNA Molecules.
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.
9781592595174
10.1385/0896032566 doi
DNA'Protein Interactions Principles and Protocols by G. Geoff Kneale. - 1st edition 1994 - 1 recurso en línea (XV, 427 páginas) - Methods in Molecular Biology 30 1940-6029 .
DNase I Footprinting -- Footprinting with Exonuclease III -- Hydroxyl Radical Footprinting -- Hydroxyl Radical Interference -- 1,10-Phenanthroline-Copper Ion Nuclease Footprinting of DNA-Protein Complexes in Situ Following Mobility-Shift Electrophoresis Assays -- Identification of Protein-DNA Contacts with Dimethyl Sulfate -- Diethyl Pyrocarbonate as a Probe of Protein-DNA Interactions -- Osmium Tetroxide Modification and the Study of DNA-Protein Interactions -- Diffusible Singlet Oxygen as a Probe of DNA Deformation -- Ethylation Interference -- Uranyl Photofootprinting of DNA-Protein Complexes -- Nitration of Tyrosine Residues in Protein-Nucleic Acid Complexes -- Limited Proteolysis of Protein-Nucleic Acid Complexes -- Cloning and Expression of DNA Binding Domains Using PCR -- Overexpression and Purification of Eukaryotic Transcription Factors as Glutathione-S-Transferase Fusions in E. coli -- Site-Directed Mutagenesis by the Cassette Method -- Site-Directed and Site-Saturation Mutagenesis Using Oligonucleotide Primers -- UV Laser-Induced Protein-DNA Crosslinking -- Ultraviolet Crosslinking of DNA-Protein Complexes via 8-Azidoadenine -- Filter-Binding Assays -- The Gel Shift Assay for the Analysis of DNA-Protein Interactions -- Improved Plasmid Vectors for the Analysis of Protein-Induced DNA Bending -- Determination of Sequence Preferences of DNA Binding Proteins Using Pooled Solid-Phase Sequencing of Low Degeneracy Oligonucleotide Mixtures -- Analysis of DNA-Protein Interactions by Intrinsic Fluorescence -- A Competition Assay for DNA Binding Using the Fluorescent Probe ANS -- Circular Dichroism for the Analysis of Protein-DNA Interactions -- Electron Microscopy of Protein-Nucleic Acid Complexes -- Reconstitution of Protein-DNA Complexes for Crystallization -- Assay of Restriction Endonucleases Using Oligonucleotides -- Assays for Restriction Endonucleases Using Plasmid Substrates -- Assays for Transcription Factor Activity -- An Assay for In Vitro Recombination Between Duplex DNA Molecules.
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.
9781592595174
10.1385/0896032566 doi