Methods widely used in the study of DNA binding proteins are presented in this volume. These include purification and protein characterization, assays of protein-DNA binding and protein-induced bending, and biochemical and genetic methods for probing the structure, energy, and specificity of protein-DNA interactions.
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DNA Binding and Bending:J. Carey, Gel Retardation.D.M. Crothers, M.R. Gartenberg, and T.E. Shrader, DNA Bending in Protein-DNA Complexes.S. Sasse-Dwight and J.D. Gralla, Footprinting Protein-DNA Complexes in Vivo.M. Dodson and H. Echols, Electron Microscopy of Protein-DNA Complexes.W.A. Lim, R.T. Sauer, and A.D. Lander, Analysis of DNA-Protein Interactions by Affinity Coelectrophoresis.J.W. Hockensmith, W.L. Kubasek, W.R. Vorachek, E.M. Evertsz, and P.H. von Hippel, Laser Cross-Linking Protein-Nucleic Acid Complexes.M. Buckle, A. Fritsch, P. Roux, J. Geiselmann, and H. Buc, Kinetic Studies on Promoter-RNA Polymerase Complexes.T.M. Lohman and W. Bujalowski, Thermodynamic Methods for Model-Independent Determination of Equilibrium Binding Isotherms for Protein-DNA Interactions: Spectroscopic Approaches to Monitor Binding.M.T. Record, Jr., J.-H. Ha, and M.A. Fisher, Analysis of Equilibrium and Kinetic Measurements to Determine Thermodynamic Origins of Stability and Specificity and Mechanism of Formation of Site-Specific Complexes between Proteins and Helical DNA.A. Hochschild, Detecting Cooperative Protein-DNA Interactions and DNA Loop Formation by Footprinting.
Biochemical Analysis of Protein-Nucleic DNA Interactions:A. Wissmann and W. Hillen, DNA Contacts Probed by Modification Protection and Interference Studies.W.J. Dixon, J.J. Hayes, J.R. Levin, M.F. Weidner, B.A. Dombroski, and T.D. Tullius, Hydroxyl Radical Footprinting.D.S. Sigman, M.D. Kuwabara, C.-H.B. Chen, and T.W. Brucie, Nuclease Activity of 1,10-Phenanthroline-Copper in Study of Protein-DNA Interactions.C.R. Aiken and R.I. Gumport, Base Analogs in the Study of Restriction Enzyme-DNA Interactions.G.D. Stormo, Probing Information Content of DNA-Binding Sites.K.S. Matthews, A.E. Chakerian, and J.A. Gardner, Protein Chemical Modification as Probe of Structure-Function Relationships.P.B. Dervan, Characterization of Protein-DNA Complexes by Affinity Cleaving.K.R. Williams and W.H. Konigsberg, Identification of Amino Acid Residues at Interface of Protein-Nucleic Acid Complexes by Photochemical Cross-Linking.
Genetic Analysis of Structure-Function Relationships:J.H. Miller, Use of Nonsense Suppression to Generate Altered Proteins.J.F. Reidhaar-Olson, J.U. Bowie, R.M. Breyer, J.C. Hu, K.L. Knight, W.A. Lim, M.C. Mossing, D.A. Parsell, K.R. Shoemaker, and R.T. Sauer, Random Mutagenesis of Protein Sequences Using Oligonucleotide Cassettes.S.P. Goff and V.R. Prasad, Linker Insertion Mutagenesis as Probe of Structure-Function Relationships.M.C. Mossing, J.U. Bowie, and R.T. Sauer, A Streptomycin Selection for DNA-Binding Activity.R.H. Ebright, Identification of Amino Acid-Base Pair Contacts by Genetic Methods.D.L. Oxender and A.L. Gibson, Second-Site Reversion as Means of Enhancing DNA-Binding Affinity.