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.
Biochemists, geneticists, molecular biologists, cell biologists, microbiologists, genetic engineers, analytical chemists, biophysicists, and industrial researchers working on protein products.
Protein-DNA Interactions, 1st Edition
Purification and Characterization:R.R. Burgess
, Use of Polyethyleneimine in Purification of DNA Binding Proteins.J.T. Kadonaga
, Purification of Sequence-Specific Binding Proteins by DNA Affinity Chromatography.T. Formosa, J. Barry, B.M. Alberts, and J. Greenblatt
, Using Protein Affinity Chromatography to Probe Structure of Protein Machines.D.L. Merkle and J.M. Berg
, Metal Requirements for Nucleic Acid Binding Proteins.K. Tovar and W. Hillen
, Large-Scale Preparation of DNA Fragments for Physical Studies of Protein Binding.G. P~aaarraga and R.E. Klevit
, Multidimensional Nuclear Magnetic Resonance Spectroscopy DNA-Binding Proteins.A. Joachimiak and P.B. Sigler
, Crystallization of Protein-DNA Complexes.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.
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