protein - dna interactions

Preface DNA binding proteins are involved in a number of basic cellular pro- cesses including transcription, DNA replication, transposition, restric- tion, recombination, and DNA repair. The chapters in this volume cover a number of important methods, some old and some new, that are now widely used in the study of DNA binding proteins. These include purifica- tion and protein characterization, assays of protein-DNA binding and protein-induced DNA bending which can be used in vitro and in vivo, and biochemical and genetic methods for probing the structure, energy, and specificity of protein-DNA interactions. Previous volumes of this series that contain related methods include 65, 100, 130, 154, 155, and 170. ROBERT T. SAUER xiii Contributors to Volume 208 Article numbers are in parentheses following the names of contributors. Affiliations listed are current. CHRISTOPHER R. AIKEN (21), Infectious Diseases Laboratory, The Salk Institute, San Diego, California 92186 BRUCE M. ALBERTS (3), Department of Biochemistry and Biophysics, University of California, San Francisco, San Fran- cisco, California 94143 JACK BARRY (3), Department of Biochemis- try and Biophysics, University of Cali- fornia, San Francisco, San Francisco, California 94143 JEREMY M. BERG (4), Department of Bio- physics and Biophysical Chemistry, The Johns Hopkins University, Baltimore, Maryland 21205 JAMES U. BOWIE (27, 29), Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90024 RICHARD M. BREYER (27), Laboratoire d'lmmuno-Pharmacologie Moleculaire, Institut Cochin de Genetique Molecu- laire, Paris, France THOMAS W. BRUC1E (20), Department of Biological Chemistry and Department of Chemistry and Biochemistry and Molec- ular Biology Institute, University of Cali- fornia, Los Angeles, Los Angeles, Cali- fornia 90024 HENRI BUC (14), Unitg de Physicochimie des Macromoldcules Biologiques, Institut Pasteur, 75724 Paris Cedex 15, France MALCOLM BUCKLE (14), Unitd de Physico- chimie des Macromoldcules Biologiques, lnstitut Pasteur, 75724 Paris Cedex 15, France WLODZIMIERZ BUJALOWSKI (15), Depart- ment of Human Biological Chemistry and Genetics, University of Texas Medical Branch, Galveston, Texas 77550 RICHARD R. BURGESS (1), McArdle Labora- tory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin 53706 JANNETTE CAREY (8), Department of Chemistry, Princeton University, Prince- ton, New Jersey 08544 ARTEMIS E. CHAKERIAN (23), Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77251 CH1NG-HONG B. CHEN (20), Department of Biological Chemistry and Department tff" Chemistry and Biochemistry and Molec- ular Biology Institute, University of Cali- fornia, Los Angeles, Los Angeles, Cali- fornia 90024 DONALD M. CROTHERS (9), Department ¢ff~ Chemistry, Yale University, New Haven. Connecticut 06511 PETER B. DERVAN (24), Arnold and Mable Beckman Laboratories of Chemical Syn- thesis, California Institute of Technology, Pasadena, California 91125 WENDY J. DIXON (19), Department of Biol- ogy, The Johns Hopkins University, Balti- more, Maryland 21218 MARK DODSON (11), Department of BiD- chemistry, Stanford University School cff Medicine, Stanford, California 94305 BETH A. DOMaROSKI (19), Center for Medi- cal Genetics, The Johns Hopkins Medical Institutions, Baltimore, Maryland 21205 RICHARD n. EBRIGHT (30), Department of Chemistry and Waksman Institute, Rutgers University, New Brunswick, New Jersey 08855 HARRISON ECHOLS (11), Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720 ix X CONTRIBUTORS TO VOLUME 208 ELISABETH M. EVERTSZ (13), Institute of Molecular Biology, and Departments of Chemistry and Biology, University of Oregon, Eugene, Oregon 97403 MATTHEW A. FISHER (16), Department of Chemistry, Randolph-Macon College, Ashland, Virginia 23005 TIM FORMOSA (3), Department of Biochem- istry, University of Utah, Salt Lake City, U~ah 84132 ALEXANDRE FRITSCH (14), Unit( de Phy- sicochimie des Macromol~cules Biologi- ques, lnstitut Pasteur, 75724 Paris Cedex 15, France JOSEPH A. GARDNER (23), Department of Biochemistry and Cell Biology, Rice Uni- versity, Houston, Texas 77251 MARC R. GARTENBERG (9), Department of Molecular Biology and Biophysics, Har- vard University, Cambridge, Massachu- setts 02138 JOHANNES GEISELMANN (14), Unit~ de Phy- sicochimie des Macromol~cules Biologi- ques, Institut Pasteur, 75724 Paris Cedex 15, France AMY L. GIaSON (31), Department of Biolog- ical Chemistry, The University of Michi- gan, Ann Arbor, Michigan 48109 STEPHEN P. GOFF (28), Department of Bio- chemistry and Molecular Biophysics, Co- lumbia University College of Physicians and Surgeons, New York, New York 10032 JAY D. GRALLA (10), Department of Chem- istry and Biochemistry, and the Molecular Biology Institute, University of Califor- nia, Los Angeles, Los Angeles, California 90024 JACK GREENBLATT (3), Banting and Best Department of Medical Research, Uni- versity of Toronto, Toronto, Ontario, Canada RICHARD I. GUMPORT (21), Department of Biochemistry, University of Illinois, Col- lege of Medicine, Urbana, Illinois 61801 JEUNG-HoI HA (16), Department of Bio- chemistry, University of Wisconsin Madison, Madison, Wisconsin 53706 JEFFREY J. HAYES (19), Laboratory of Molecular Biology, National Institutes of Health, Bethesda, Maryland 20892 WOLFGANG HILLEN (5, 18), lnstitut ffir Mikrobiolgie und Biochemie, Friedrich- Alexander Universitiit Erlangen-Nfirn- berg, D-8520 Erlangen, Germany ANN HOCHSCHILD (17), Department of Mi- crobiology and Molecular Genetics, Har- vard Medical School, Boston, Massachu- setts 02115 JOEL W. HOCKENSMITH (13), Department of Biochemistry, University of Virginia School of Medicine, Charlottesville, Vir- ginia 22908 JAMES C. Hu (27), Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 ANDRZEJ JOACHIMIAK (7), Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecti- cut 06511 JAMES T. KADONAGA (2), Department of Bi- ology and Center for Molecular Genet- ics, University of California, San Diego, La Jolla, California 92093 RACHEL E. KLEVIT (6), Department of Bio- chemistry, University of Washington, Seattle, Washington 98195 KENDALL L. KNIGHT (27), Department of Biochemistry and Molecular Biology, University of Massachusetts Medical Center, Worcester, Massachusetts 01655 WILLIAM H. KONIGSBERG (25), Department of Molecular Biophysics and Biochemis- try, Yale University School of Medicine, New Haven, Connecticut 06510 WILLIAM L. KUBASEK (13), Department of Molecular Biology, Massachusetts Gen- eral Hospital, Boston, Massachusetts 02114 MICHIO D. KUWABARA (20), Department of Biological Chemistry and Department of Chemistry and Biochemistry and Molec- ular Biology Institute, University of Cali- fornia, Los Angeles, Los Angeles, Cali- fornia 90024 CONTRIBUTORS TO VOLUME 208 xi ARTHUR D. LANDER (12), Department of Biology and Department of Brain and Cognitive Sciences, Massachusetts In- stitute of Technology, Cambridge, Massachusetts 02139 JUDITH R. LEVIN (19), Department of Chemistry, The Johns Hopkins Univer- sity, Baltimore, Maryland 21218 WENDELL A. LIM (12, 27), Department of Biology, Massachusetts Institute of Tech- nology, Cambridge, Massachusetts 02139 TIMOTHY M, LOHMAN (15), Department of Biochemistry and Molecular Biophysics, Washington University School of Medi- cine, St. Louis, Missouri 63110 KATHLEEN S. MATTHEWS (23), Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77251 DENISE L. MERKLE (4), Department of Chemistry, University of Florida, Gaines- ville, Florida 32611 JEFFREY H. MILLER (26), Department of Microbiology and Molecular Genetics, and the Molecular Biology Institute, Uni- versity of California, Los Angeles, Los Angeles, California 90024 MICHAEL C. MOSSING (27, 29), Department of Biological Sciences, University of Notre Dame, South Bend, Indiana 46556 DALE L. OXENDER (31), Department of Biotechnology, Park-Davis Research Di- vision of Warner-Lambert, Ann Arbor, Michigan 48106 GRACE PARRAGA (6), Department of Bio- chemistry, Biocenter of the University of Basel, Basel CH-4056, Switzerland DAWN A. PARSELL (27), Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois 60637 VINAYAKA R, PRASAD (28), Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461 M. THOMAS RECORD, JR. (16), Department of Chemistry and Biochemistry, Univer- sity of Wisconsin Madison, Madison, Wisconsin 53706 JOHN F. REIDHAAR-OLsoN (27), Depart- ment of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94143 PASCAL ROUX (14), Unitd de Physicochimie des Macromoldcules Biologiques, lnstitut Pasteur, 75724 Paris Cedex 15, France SELINA SASSE-DWIGHT (10), Department of Genetics, Star, ford University School of Medicine, Stanford, California 94305 ROaERT T. SAUER (12, 27, 29), Department of Biology, Massachusetts Institute ~f Technology, Cambridge, Massachusetts 02139 KEVIN R. SHOEMAKER (27), Department of Biology, Massachusetts Institute of Tech- nology, Cambridge, Massachusetts 02139 THOMAS E. SHRADER (9), Department of Bi- ology, Massachusetts Institute of Tech- nology, CamOridge, Massachusetts 02139 PAUL B. SIGLER (7), Department of Molecu- lar Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale Univer- sity, New Haven, Connecticut 06511 DAVID S. SIGMAN (20), Department of Bio- logical Chemistry, Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90024 GARY D. STORMO (22), Department of Mo- lecular, Cellular and Developmental Biol- ogy, University of Colorado, Boulder, Colorado 80309 KARLHEINZ TOVAR (5), lnstitut fiir Mikro- biologie und Biochemie, Friedrich-Alex- ander Universitiit Erlangen-Niirnberg, D- 6382 Erlangen, Germany THOMAS D. TULLIUS (19), Department of Chemistry, The Johns Hopkins Univer- sity, Baltimore, Maryland 21218 PETER H. YON HIPPEL (13), Institute of Molecular Biology, and Departments of Chemistry and Biology, University of Oregon, Eugene, Oregon 97403 WILLIAM R. VORACHEK (13), Department of Biochemistry, University of Virginia School of Medicine, Charlottesville, Vir- ginia 22908 xii CONTRIBUTORS TO VOLUME 208 MARGARET F. WEIDNER (19), Seattle, Washington 98109 KENNETH R. WILLIAMS (25), Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06510 ANDREAS WISSMANN (18), BASF Biore- search Corp., Cambridge, Massachusetts 02139 METHODS IN ENZYMOLOGY VOLUME I. Preparation and Assay of Enzymes Edited by SIDNEY P. COLOWICK AND NATHAN O. KAPLAN VOLUME II. Preparation and Assay of Enzymes Edited by SIDNEY P. COLOWICK AND NATHAN O. KAPLAN VOLUME III. Preparation and Assay of Substrates Edited by SIDNEY P. COLOWICK AND NATHAN O. KAPLAN VOLUME IV. Special Techniques for the Enzymologist Edited by SIDNEY P. COLOWICK AND NATHAN O. KAPLAN VOLUME V. Preparation and Assay of Enzymes Edited by SIDNEY P. COLOWICK AND NATHAN O. KAPLAN VOLUME VI. Preparation and Assay of Enzymes (Continued) Preparation and Assay of Substrates Special Techniques Edited by SIDNEY P. COLOWICK AND NATHAN O. KAPLAN VOLUME VII. Cumulative Subject Index Edited by SIDNEY P. COLOWICK AND NATHAN O. KAPLAN VOLUME VIII. Complex Carbohydrates Edited by ELIZABETH F. NEUFELD AND VICTOR GINSBURG VOLUME IX. Carbohydrate Metabolism Edited by WILLIS A. WOOD VOLUME X. Oxidation and Phosphorylation Edited by RONALD W. ESTABROOK AND MAYNARD E. PULLMAN VOLUME XI. Enzyme Structure Edited by C. H. W. HIRS VOLUME XII. Nucleic Acids (Parts A and B) Edited by LAWRENCE GROSSMAN AND KIVIE MOLDAVE xv xvi METHODS IN ENZYMOLOGY VOLUME XlII. Citric Acid Cycle Edited by J. M. LOWENSTEIN VOLUME XIV. Lipids Edited by J. M. LOWENSTEIN VOLUME XV. Steroids and Terpenoids Edited by RAYMOND B. CLAYTON VOLUME XVI. Fast Reactions Edited by KENNETH KUSTIN VOLUME XVII. Metabolism of Amino Acids and Amines (Parts A and B) Edited by HERBERT TABOR AND CELIA WHITE TABOR VOLUME XVIII. Vitamins and Coenzymes (Parts A, B, and C) Edited by DONALD B. MCCORMICK AND LEMUEL D. WRIGHT VOLUME XIX. Proteolytic Enzymes Edited by GERTRUDE E. PERLMANN AND LASZLO LORAND VOLUME XX. Nucleic Acids and Protein Synthesis (Part C) Edited by KIVIE MOLDAVE AND LAWRENCE GROSSMAN VOLUME XXI. Nucleic Acids (Part D) Edited by LAWRENCE GROSSMAN AND KIVIE MOLDAVE VOLUME XXlI. Enzyme Purification and Related Techniques Edited by WILLIAM B. JAKOBY VOLUME XXIII. Photosynthesis (Part A) Edited by ANTHONY SAN PIETRO VOLUME XXIV. Photosynthesis and Nitrogen Fixation (Part B) Edited by ANTHONY SAN PIETRO VOLUME XXV. Enzyme Structure (Part B) Edited by C. H. W. HIRS AND SERGE N. TIMASHEFF VOLUME XXVI. Enzyme Structure (Part C) Edited by C. H. W. HIRS AND SERGE N. TIMASHEFF METHODS IN ENZYMOLOGY xvii VOLUME XXVII. Enzyme Structure (Part D) Edited by C. H. W. HIRS AND SERGE N. TIMASHEFF VOLUME XXVIII. Complex Carbohydrates (Part B) Edited by VICTOR GINSBURG VOLUME XXIX. Nucleic Acids and Protein Synthesis (Part E) Edited by LAWRENCE GROSSMAN AND KIVIE MOLDAVE VOLUME XXX. Nucleic Acids and Protein Synthesis (Part F) Edited by KIVIE MOLDAVE AND LAWRENCE GROSSMAN VOLUME XXXI. Biomembranes (Part A) Edited by SIDNEY FLEISCHER AND LESTER PACKER VOLUME XXXII. Biomembranes (Part B) Edited by SIDNEY FLEISCHER AND LESTER PACKER VOLUME XXXIII. Cumulative Subject Index Volumes I-XXX Edited by MARTHA G. DENNIS AND EDWARD A. DENNIS VOLUME XXXIV. Affinity Techniques (Enzyme Purification: Part B) Edited by W1LLIAM B. JAKOBY AND MEIR WILCHEK VOLUME XXXV. Lipids (Part B) Edited by JOHN M. LOWENSTEIN VOLUME XXXVI. Hormone Action (Part A: Steroid Hormones) Edited by BERT W. O'MALLEY AND JOEL G. HARDMAN VOLUME XXXVII. Hormone Action (Part B: Peptide Hormones) Edited by BERT W. O'MALLEY AND JOEL G. HARDMAN VOLUME XXXVIII. Hormone Action (Part C: Cyclic Nucleotides) Edited by JOEL G. HARDMAN AND BERT W. O'MALLEY VOLUME XXXIX. Hormone Action (Part D: Isolated Cells, Tissues, and Organ Systems) Edited by JOEL G. HARDMAN AND BERT W. O'MALLEY VOLUME XL. Hormone Action (Part E: Nuclear Structure and Function) Edited by BERT W. O'MALLEY AND JOEL G. HARDMAN xviii METHODS IN ENZYMOLOGY VOLUME XLI. Carbohydrate Metabolism (Part B) Edited by W. A. WOOD VOLUME XLII. Carbohydrate Metabolism (Part C) Edited by W. A. ;WOOD VOLUME XLIII. Antibiotics Edited by JOHN H. HASH VOLUME XLIV. Immobilized Enzymes Edited by KLAUS MOSBACH VOLUME XLV. Proteolytic Enzymes (Part B) Edited by LASZLO LORAND VOLUME XLVI. Affinity Labeling Edited by WILLIAM B. JAKOBY AND MEIR WILCHEK VOLUME XLVII. Enzyme Structure (Part E) Edited by C. H. W. HIRS AND SERGE N. TIMASHEFF VOLUME XLVIII. Enzyme Structure (Part F) Edited by C. H. W. HIRS AND SERGE N. TIMASHEFF VOLUME XLIX. Enzyme Structure (Part G) Edited by C. H. W. HIRS AND SERGE N. TIMASHEFF VOLUME L. Complex Carbohydrates (Part C) Edited by VICTOR GINSBURG VOLUME LI. Purine and Pyrimidine Nucleotide Metabolism Edited by PATRICIA A. HOFFEE AND MARY ELLEN JONES VOLUME LII. Biomembranes (Part C: Biological Oxidations) Edited by SIDNEY FLEISCHER AND LESTER PACKER VOLUME LIII. Biomembranes (Part D: Biological Oxidations) Edited by SIDNEY FLEISCHER AND LESTER PACKER VOLUME LIV. Biomembranes (Part E: Biological Oxidations) Edited by SIDNEY FLEISCHER AND LESTER PACKER METHODS IN ENZYMOLOGY xix VOLUME LV. Biomembranes (Part F: Bioenergetics) Edited by SIDNEY FLEISCHER AND LESTER PACKER VOLUME LVI. Biomembranes (Part G: Bioenergetics) Edited by SIDNEY FLEISCHER AND LESTER PACKER VOLUME LVII. Bioluminescence and Chemiluminescence Edited by MARLENE A. DELUCA VOLUME LVIII. Cell Culture Edited by WILLIAM B. JAKOBY AND IRA PASTAN VOLUME LIX. Nucleic Acids and Protein Synthesis (Part G) Edited by KIVIE MOLDAVE AND LAWRENCE GROSSMAN VOLUME LX. Nucleic Acids and Protein Synthesis (Part H) Edited by KIVIE MOLDAVE AND LAWRENCE GROSSMAN VOLUME 61. Enzyme Structure (Part H) Edited by C. H. W. HIRS AND SERGE N. TIMASHEFF VOLUME 62. Vitamins and Coenzymes (Part D) Edited by DONALD B. MCCORMICK AND LEMUEL D. WRIGHT VOLUME 63. Enzyme Kinetics and Mechanism (Part A: Initial Rate and Inhibitor Methods) Edited by DANIEL L. PURICH VOLUME 64. Enzyme Kinetics and Mechanism (Part B: Isotopic Probes and Complex Enzyme Systems) Edited by DANIEL L. PURICH VOLUME 65. Nucleic Acids (Part I) Edited by LAWRENCE GROSSMAN AND KIVIE MOLDAVE VOLUME 66. Vitamins and Coenzymes (Part E) Edited by DONALD B. MCCORMICK AND LEMUEL D. WRIGHT VOLUME 67. Vitamins and Coenzymes (Part F) Edited by DONALD B. MCCORMICK AND LEMUEL D. WRIGHT [...]... and E.-L Winnacker, Biochim Biophys Acta 951, 411 (1988) 12 PURIFICATION AND CHARACTERIZATION [2] TABLE I SEQUENCE-SPECIFIC DNA- BINDING PROTEINS PURIFIED BY DNA AFFINITY TECHNIQUE Factor Mammalian Spl CTF/NFI AP-1 AP-2 NF-rB Pit- 1/GHF- 1/PUF-I /zEBP-E ATP SRF/f-EBP/CBF TEF-1 OBP UBF1 TFIIIC2 Avian COUP factor PAL Drosophila melanogaster GAGA DTF- 1 Zeste Transposase Saccharomyces cerevisiae HSE-binding/HSTF... the sequence-specific DNA- binding protein or a molecule that is closely associated with the DNA- binding protein It is important to identify nonspecific DNA- binding proteins that may contaminate the protein preparations after DNA affinity chromatography The use of a control DNA affinity resin that does not contain binding sites for the sequence-specific factor in parallel with the specific DNA affinity... resin The desired sequence-specific DNA- binding protein binds to the recognition sites in the affinity resin rather than to the competitor DNA in solution, while other proteins, including nonspecific DNAbinding proteins, flow through the resin The sequence-specific factor is then eluted from the affinity resin with a salt gradient A typical protein can be purified 50 0- to 1000-fold with 30% yield by... VOLUME 208 Protein- DNA Interactions Edited by ROBERT T SAUER VOLUME 209 Phospholipid Biosynthesis (in preparation) Edited by EDWARD A DENNIS AND DENNIS E VANCE [1] USE OF POLYETHYLENEIMINE 3 [1] U s e o f P o l y e t h y l e n e i m i n e in P u r i f i c a t i o n of DNA- Binding Proteins By RICHARD R BURGESS One of the important early steps in purifying a DNA- binding protein is to separate the protein. .. the total protein precipitated by PEI will depend on the pH (at higher pH, more proteins will carry a negative charge and be precipitated) and on the ionic strength (increasing ionic strength will weaken PEI -protein interactions) At low ionic strength ( 0-0 .1 M NaCI), DNA and all acidic proteins will be precipitated At higher ionic strength (0. 1-1 M NaC1), only DNA and highly negatively charged proteins... suitable for affinity chromatography General Approach to Purification of Sequence-Specific DNA- Binding Proteins A strategy for the purification of sequence-specific DNA- binding proteins is as follows First, the DNA sequence to which the factor binds is determined by techniques such as DNase I footprinting, ~4methidiumpropyl EDTA-Fe(II) footprinting,~5 and dimethyl sulfate methylation protection 16 If possible,... thymus DNA, attached to cellulose I and agarose 2 supports More recently, a variety of procedures have been described for DNA affinity purification of sequence-specific DNA- binding proteins The different DNA affinity resins that have been employed include plasmid DNA adsorbed to cellulose, 3 biotinylated DNA fragments attached to agarose, cellulose, or magnetic beads by biotin-avidin or biotin-streptavi1... encoding the proteins It has generally been difficult, however, to isolate these DNAbinding factors by conventional chromatography because they typically constitute less than 0.01% of the total cellular protein Fortunately, it is now possible to purify sequence-specific DNA- binding proteins by DNA affinity chromatography DNA affinity chromatography was originally developed with nonspecific DNAs, such... of extracts with DEAE-cellulose,4 and treatment with DNase 1.5 Perhaps the most effective method involves precipitation with polyethyleneimine. 6-8 This chapter will focus on the use of polyethyleneimine in early stages of the purification of DNA- binding proteins It should be noted, however, that the use of polyethyleneimine in protein purification is not restricted to DNA- binding proteins and has been... 2095 (1987) [2] SEQUENCE-SPECIFIC D N A AFFINITY CHROMATOGRAPHY 15 columns (using the same protein fraction as the starting material) should minimize misidentification of a nonspecific DNA- binding protein for the desired factor In addition, the polypeptide that is responsible for the sequence-specific DNA- binding activity can be identified by recovery of protein from an S D S - P A G E gel and renaturation . widely used in the study of DNA binding proteins. These include purifica- tion and protein characterization, assays of protein- DNA binding and protein- induced DNA bending which can be used. Preface DNA binding proteins are involved in a number of basic cellular pro- cesses including transcription, DNA replication, transposition, restric- tion, recombination, and DNA repair Biochemie, Friedrich- Alexander Universitiit Erlangen-Nfirn- berg, D-8520 Erlangen, Germany ANN HOCHSCHILD (17), Department of Mi- crobiology and Molecular Genetics, Har- vard Medical School,