Protein 3- DNA Interactions

Content: 
Contributors to volume 208
Pages ix-xii

Preface
Page xiii
Robert T. Sauer

Volumes in series
Pages xv-xxxi

[1] Use of polyethyleneimine in purification of DNA-binding proteins Original Research Article
Pages 3-10
Richard R. Burgess

[2] Purification of sequence-specific binding proteins by DNA affinity chromatography Original Research Article
Pages 10-23
James T. Kadonaga

[3] Using protein affinity chromatography to probe structure of protein machines Original Research Article
Pages 24-45
Tim Formosa, Jack Barry, Bruce M. Alberts, Jack Greenblatt

[4] Metal requirements for nucleic acid binding proteins Original Research Article
Pages 46-54
Denise L. Merkle, Jeremy M. Berg

[5] Large-scale preparation of dna fragments for physical studies of protein binding Original Research Article
Pages 54-63
Karlheinz Tovar, Wolfgang Hillen

[6] Multidimensional nuclear magnetic resonance spectroscopy of DNA-binding proteins Original Research Article
Pages 63-82
Grace Parraga, Rachel E. Klevit

[7] Crystallization of protein-DNA complexes Original Research Article
Pages 82-99
Andrzej Joachimiak, Paul B. Sigler

[8] Gel retardation Original Research Article
Pages 103-117
Jannette Carey

[9] DNA bending in protein-DNA complexes Original Research Article
Pages 118-146
Donald M. Crothers, Marl R. Gartenberg, Thomas E. Shrader

[10] Footprinting protein-DNA complexes in Vivo Original Research Article
Pages 146-168
Selina Sasse-Dwight, Jay D. Gralla

[11] Electron microscopy of protein-DNA complexes Original Research Article
Pages 168-196
Mark Dodson, Harrison Echols

[12] Analysis of DNA-protein interactions by affinity coelectrophoresis Original Research Article
Pages 196-210
Wendell A. Lim, Robert T. Sauer, Arthur D. Lander

[13] Laser cross-linking of protein-nucleic acid complexes Original Research Article
Pages 211-236
Joel W. Hockensmith, William L. Kubasek, William R. Vorachek, Elisabeth M. Evertsz, Peter H. von Hippel

[14] Kinetic studies on promoter-RNA polymerase complexes Original Research Article
Pages 236-258
Malcolm Buckle, Alexandre Fritsch, Pascal Roux, Johannes Geiselmann, Henri Buc

[15] Thermodynamic methods for model-independent determination of equilibrium binding isotherms for protein-DNA interactions: Spectroscopic approaches to monitor binding Original Research Article
Pages 258-290
Timothy M. Lohman, Wlodzimierz Bujalowski

[16] 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 Original Research Article
Pages 291-343
M.Thomas Record Jr., Jeung-Hoi Ha, Matthew A. Fisher

[17] Detecting cooperative protein-DNA interactions and DNA loop formation by footprinting Original Research Article
Pages 343-361
Ann Hochschild

[18] DNA contacts probed by modification protection and interference studies Original Research Article
Pages 365-379
Andreas Wissmann, Wolfgang Hillen

[19] Hydroxyl radical footprinting Original Research Article
Pages 380-413
Wendy J. Dixon, Jeffrey J. Hayes, Judith R. Levin, Margaret F. Weidner, Beth A. Dombroski, Thomas D. Tullius

[20] Nuclease activity of 1,10-phenanthroline-copper in study of protein—DNA interactions Original Research Article
Pages 414-433
David S. Sigman, Michio D. Kuwabara, Ching-Hong B. Chen, Thomas W. Bruice

[21] Base analogs in study of restriction enzyme-DNA interactions Original Research Article
Pages 433-457
Christopher Raiken, Richard I. Gumport

[22] Probing information content of DNA-binding sites Original Research Article
Pages 458-468
Gary D. Stormo

[23] Protein chemical modification as probe of structure-function relationships Original Research Article
Pages 468-496
Kathleen S. Matthews, Artemis E. Chakerian, Joseph A. Gardner

[24] Characterization of protein—DNA complexes by affinity cleaving Original Research Article
Pages 497-515
Peter B. Dervan

[25] Identification of amino acid residues at interface of protein—Nucleic acid complexes by photochemical cross-linking Original Research Article
Pages 516-539
Kenneth R. Williams, William H. Konigsberg

[26] Use of nonsense suppression to generate altered proteins Original Research Article
Pages 543-563
Jeffrey H. Miller

[27] Random mutagenesis of protein sequences using oligonucleotide cassettes Original Research Article
Pages 564-586
John F. Reidhaar-Olson, James U. Bowie, Richard M. Breyer, James C. Hu, Kendall L. Knight, Wendell A. Lim, Michael C. Mossing, Dawn A. Parsell, Kevin R. Shoemaker, Robert T. Sauer

[28] Linker insertion mutagenesis as probe of structure-function relationships Original Research Article
Pages 586-603
Stephen P. Goff, Vinayaka R. Prasad

[29] A streptomycin selection for DNA-binding activity Original Research Article
Pages 604-619
Michael C. Mossing, James U. Bowie, Robert T. Sauer

[30] Identification of amino acid—base pair contacts by genetic methods Original Research Article
Pages 620-640
Richard H. Ebright

[31] Second-site reversion as means of enhancing DNA-binding affinity Original Research Article
Pages 641-651
Dale L. Oxender, Amy L. Gibson

Author index
Pages 653-676

Subject index
Pages 677-700