Protein - DNA Interactions

710 Pages·1991·11.885 MB·English

by  Abelson J.N., Simon M.I., Sauer R.T.

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.
TREBOR T. REUAS
iiix
Contributors to Volume 208
Article numbers are ni parentheses following the names of contributors.
Affiliations listed are current.
REHPOTSIRHC R. AIKEN (21), Infectious DRAHCIR R. SSEGRUB (1), McArdle Labora-
Diseases Laboratory, ehT Salk Institute, tory for Cancer Research, University of
San Diego, California 68129 Wisconsin-Madison, Madison, Wisconsin
BRUCE M. ALBERTS (3), Department of 60735
Biochemistry and Biophysics, University JANNETTE CAREY (8), Department of
of California, San Francisco, San Fran- Chemistry, Princeton University, Prince-
cisco, California 34149 ton, New Jersey 44580
KCAJ BARRY (3), Department of Biochemis- SIMETRA E. CHAKERIAN (23), Department
try and Biophysics, University of Cali- of Biochemistry and Cell Biology, Rice
fornia, San Francisco, San Francisco, University, Houston, Texas 15277
California 34149 GNOH-GN1HC B. CHEN (20), Department of
YMEREJ M. BERG (4), Department of Bio- Biological Chemistry and Department "fft
physics and Biophysical Chemistry, ehT Chemistry and Biochemistry and Molec-
Johns Hopkins University, Baltimore, ular Biology Institute, University of -ilaC
Maryland 50212 fornia, Los Angeles, Los Angeles, Cali-
fornia 42009
JAMES U. BOWIE (27, 29), Department of
Chemistry and Biochemistry, University DONALD M. SREHTORC (9), Department ~ff¢
of California, Los Angeles, Los Angeles, Chemistry, Yale University, New Haven.
California 42009 Connecticut 11560
RICHARD M. BREYER (27), Laboratoire PETER B. DERVAN (24), Arnold and Mable
d'lmmuno-Pharmacologie Moleculaire, Beckman Laboratories of Chemical Syn-
Institut Cochin de Genetique Molecu- thesis, California Institute of Technology,
laire, Paris, France Pasadena, California 52119
SAMOHT W. BRUC1E (20), Department of WENDY J. DIXON (19), Department of Biol-
Biological Chemistry and Department of ogy, The Johns Hopkins University, Balti-
Chemistry and Biochemistry and Molec- more, Maryland 81212
ular Biology Institute, University of -ilaC MARK DODSON (11), Department of -DiB
fornia, Los Angeles, Los Angeles, Cali- chemistry, Stanford University School cff
fornia 42009 Medicine, Stanford, California 50349
HENRI CUB (14), Unitg de Physicochimie BETH A. IKSORaMOD (19), Center for Medi-
des Macromoldcules Biologiques, Institut cal Genetics, The Johns Hopkins Medical
Pasteur, 75724 Paris Cedex ,51 France Institutions, Baltimore, Maryland 50212
MLOCLAM BUCKLE (14), Unitd de Physico- DRAHCIR n. EBRIGHT (30), Department
chimie des Macromoldcules Biologiques, of Chemistry and Waksman Institute,
lnstitut Pasteur, 75724 Paris Cedex ,51 Rutgers University, New Brunswick, New
France Jersey 55880
WLODZIMIERZ BUJALOWSKI (15), Depart- NOSIRRAH ECHOLS (11), Department of
ment of Human Biological Chemistry and Molecular and Cell Biology, University of
Genetics, University of Texas Medical California, Berkeley, Berkeley, California
Branch, Galveston, Texas 05577 02749
ix
X CONTRIBUTORS TO VOLUME 208
HTEBASILE M. EVERTSZ (13), Institute of YERFFEJ J. HAYES (19), Laboratory of
Molecular Biology, and Departments of Molecular Biology, National Institutes of
Chemistry and Biology, University of Health, Bethesda, Maryland 29802
Oregon, Eugene, Oregon 30479
GNAGFLOW HILLEN (5, 18), lnstitut ffir
MATTHEW A. FISHER (16), Department of Mikrobiolgie und Biochemie, Friedrich-
Chemistry, Randolph-Macon College, Alexander Universitiit Erlangen-Nfirn-
Ashland, Virginia 23005 berg, D-8520 Erlangen, Germany
TIM ASOMROF (3), Department of Biochem- ANN DLIHCSHCOH (17), Department of Mi-
istry, University of Utah, Salt Lake City, crobiology and Molecular Genetics, Har-
ha~U 84132 vard Medical School, Boston, Massachu-
ERDNAXELA FRITSCH (14), Unit( de Phy- setts 51120
sicochimie des Macromol~cules Biologi- JOEL W. HTIMSNEKCOH (13), Department
ques, lnstitut Pasteur, 75724 Paris Cedex of Biochemistry, University of Virginia
,51 France School of Medicine, Charlottesville, Vir-
HPESOJ A. GARDNER (23), Department of ginia 22908
Biochemistry and Cell Biology, Rice Uni-
SEMAJ C. Hu (27), Department of Biology,
versity, Houston, Texas 15277
Massachusetts Institute of Technology,
MARC R. GREBNETRAG (9), Department of Cambridge, Massachusetts 02139
Molecular Biology and Biophysics, Har-
ANDRZEJ JOACHIMIAK (7), Department of
vard University, Cambridge, Massachu-
Molecular Biophysics and Biochemistry,
setts 02138
Yale University, New Haven, Connecti-
SENNAHOJ NNAMLESIEG (14), Unit~ de Phy- cut 11560
sicochimie des Macromol~cules Biologi-
ques, Institut Pasteur, 75724 Paris Cedex SEMAJ T. AGANODAK (2), Department of Bi-
ology and Center for Molecular Genet-
,51 France
ics, University of California, San Diego,
YMA L. GIaSON (31), Department of Biolog-
La Jolla, California 39029
ical Chemistry, The University of Michi-
gan, Ann Arbor, Michigan 48109 LEHCAR E. KLEVIT (6), Department of Bio-
chemistry, University of Washington,
NEHPETS P. GOFF (28), Department of Bio-
Seattle, Washington 59189
chemistry and Molecular Biophysics, Co-
lumbia University College of Physicians KENDALL L. KNIGHT (27), Department of
and Surgeons, New York, New York Biochemistry and Molecular Biology,
23001 University of Massachusetts Medical
YAJ D. GRALLA (10), Department of Chem- Center, Worcester, Massachusetts 55610
istry and Biochemistry, and the Molecular WILLIAM H. GREBSGINOK (25), Department
Biology Institute, University of Califor- of Molecular Biophysics and Biochemis-
nia, Los Angeles, Los Angeles, California try, Yale University School of Medicine,
42009 New Haven, Connecticut 06510
JACK GREENBLATT (3), Banting and Best WILLIAM L. KUBASEK (13), Department of
Department of Medical Research, Uni- Molecular Biology, Massachusetts Gen-
versity of Toronto, Toronto, Ontario, eral Hospital, Boston, Massachusetts
Canada 41120
DRAHCIR I. GUMPORT (21), Department of MICHIO D. ARABAWUK (20), Department of
Biochemistry, University of Illinois, Col- Biological Chemistry and Department of
lege of Medicine, Urbana, Illinois 10816 Chemistry and Biochemistry and Molec-
JEUNG-HoI HA (16), Department of Bio- ular Biology Institute, University of Cali-
chemistry, University of Wisconsin-- fornia, Los Angeles, Los Angeles, Cali-
Madison, Madison, Wisconsin 60735 fornia 42009
CONTRIBUTORS TO VOLUME 208 xi
ARTHUR D. LANDER (12), Department of JOHN F. REIDHAAR-OLsoN (27), Depart-
Biology and Department of Brain and ment of Biochemistry and Biophysics,
Cognitive Sciences, Massachusetts In- University of California, San Francisco,
stitute of Technology, Cambridge, San Francisco, California 34149
Massachusetts 02139
LACSAP ROUX (14), Unitd de Physicochimie
JUDITH R. LEVIN (19), Department of des Macromoldcules Biologiques, lnstitut
Chemistry, The Johns Hopkins Univer- Pasteur, 75724 Paris Cedex ,51 France
sity, Baltimore, Maryland 21218
SELINA SASSE-DWIGHT (10), Department of
WENDELL A. LIM (12, 27), Department of Genetics, Star, ford University School
Biology, Massachusetts Institute of Tech- of Medicine, Stanford, California 50349
nology, Cambridge, Massachusetts 93120 ROaERT T. SAUER (12, 27, 29), Department
YHTOMIT M, LOHMAN (15), Department of of Biology, Massachusetts Institute ~f
Biochemistry and Molecular Biophysics, Technology, Cambridge, Massachusetts
Washington University School of Medi- 93120
cine, St. Louis, Missouri 01136 KEVIN R. REKAMEOHS (27), Department of
NEELHTAK S. MATTHEWS (23), Department Biology, Massachusetts Institute of Tech-
of Biochemistry and Cell Biology, Rice nology, Cambridge, Massachusetts 93120
University, Houston, Texas 15277 SAMOHT E. REDARHS (9), Department of Bi-
ESINED L. MERKLE (4), Department of ology, Massachusetts Institute of Tech-
Chemistry, University of Florida, Gaines- nology, CamOridge, Massachusetts 93120
ville, Florida 11623 PAUL B. SIGLER (7), Department of Molecu-
JEFFREY H. MILLER (26), Department of lar Biophysics and Biochemistry, Howard
Microbiology and Molecular Genetics, Hughes Medical Institute, Yale Univer-
and the Molecular Biology Institute, Uni- sity, New Haven, Connecticut 11560
versity of California, Los Angeles, Los DAVID S. SIGMAN (20), Department of Bio-
Angeles, California 42009 logical Chemistry, Molecular Biology
LEAHCIM C. MOSSING (27, 29), Department Institute, University of California, Los
of Biological Sciences, University of Angeles, Los Angeles, California 42009
Notre Dame, South Bend, Indiana 46556 YRAG D. OMROTS (22), Department of Mo-
DALE L. OXENDER (31), Department of lecular, Cellular and Developmental Biol-
Biotechnology, Park-Davis Research Di- ogy, University of Colorado, Boulder,
vision of Warner-Lambert, Ann Arbor, Colorado 80309
Michigan 48106 KARLHEINZ TOVAR (5), lnstitut fiir Mikro-
GRACE PARRAGA (6), Department of Bio- biologie und Biochemie, Friedrich-Alex-
chemistry, Biocenter of the University of ander Universitiit Erlangen-Niirnberg, D-
Basel, Basel CH-4056, Switzerland 6382 Erlangen, Germany
DAWN A. PARSELL (27), Howard Hughes SAMOHT D. TULLIUS (19), Department of
Medical Institute, University of Chicago, Chemistry, The Johns Hopkins Univer-
Chicago, Illinois 60637 sity, Baltimore, Maryland 21218
AKAYANIV R, PRASAD (28), Department of PETER H. NOY HIPPEL (13), Institute of
Microbiology and Immunology, Albert Molecular Biology, and Departments of
Einstein College of Medicine, Bronx, New Chemistry and Biology, University of
York 16401 Oregon, Eugene, Oregon 30479
M. THOMAS RECORD, JR. (16), Department WILLIAM R. VORACHEK (13), Department
of Chemistry and Biochemistry, Univer- of Biochemistry, University of Virginia
sity of Wisconsin--Madison, Madison, School of Medicine, Charlottesville, Vir-
Wisconsin 53706 ginia 22908
xii CONTRIBUTORS TO VOLUME 208
TERAGRAM F. WEIDNER (19), Seattle, Yale University School of Medicine, New
Washington 90189 Haven, Connecticut 06510
HTENNEK R. WILLIAMS (25), Howard ANDREAS WISSMANN (18), BASF Biore-
Hughes Medical Institute, Department of search Corp., Cambridge, Massachusetts
Molecular Biophysics and Biochemistry, 93120
METHODS IN ENZYMOLOGY
VOLUME I. Preparation and Assay of Enzymes
Edited by SIDNEY P. COLOWICK DNA NATHAN O. KAPLAN
VOLUME II. Preparation and Assay of Enzymes
Edited by SIDNEY P. COLOWICK DNA NATHAN O. KAPLAN
VOLUME III. Preparation and Assay of Substrates
Edited by SIDNEY P. COLOWICK DNA NATHAN O. KAPLAN
VOLUME IV. Special Techniques for the Enzymologist
Edited by SIDNEY P. COLOWICK DNA NATHAN O. KAPLAN
VOLUME V. Preparation and Assay of Enzymes
Edited by SIDNEY P. COLOWICK DNA NATHAN O. KAPLAN
VOLUME VI. Preparation and Assay of Enzymes (Continued)
Preparation and Assay of Substrates
Special Techniques
Edited by SIDNEY P. COLOWICK DNA NATHAN O. KAPLAN
VOLUME VII. Cumulative Subject Index
Edited by SIDNEY P. COLOWICK DNA NATHAN O. KAPLAN
VOLUME VIII. Complex Carbohydrates
Edited by ELIZABETH F. NEUFELD DNA VICTOR GRUBSNIG
VOLUME IX. Carbohydrate Metabolism
Edited by WILLIS A. WOOD
VOLUME X. Oxidation and Phosphorylation
Edited by RONALD W. KOORBATSE DNA MAYNARD E. PULLMAN
VOLUME XI. Enzyme Structure
Edited by C. H. W. HIRS
VOLUME XII. Nucleic Acids (Parts A and B)
Edited by LAWRENCE NAMSSORG DNA KIVIE EVADLOM
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. NOTYALC
VOLUME XVI. Fast Reactions
Edited yb KENNETH KUSTIN
VOLUME XVII. Metabolism of Amino Acids and Amines (Parts A and B)
Edited by HERBERT TABOR DNA CELIA WHITE ROBAT
VOLUME XVIII. Vitamins and Coenzymes (Parts A, B, and C)
Edited yb DONALD B. MCCORMICK DNA LEMUEL D. WRIGHT
VOLUME XIX. Proteolytic Enzymes
Edited by GERTRUDE E. PERLMANN DNA LASZLO LORAND
VOLUME XX. Nucleic Acids and Protein Synthesis (Part C)
Edited by KIVIE MOLDAVE DNA LAWRENCE NAMSSORG
VOLUME XXI. Nucleic Acids (Part D)
Edited by LAWRENCE NAMSSORG DNA KIVIE EVADLOM
VOLUME XXlI. Enzyme Purification and Related Techniques
Edited by WILLIAM B. YBOKAJ
VOLUME XXIII. Photosynthesis (Part A)
Edited by ANTHONY NAS PIETRO
VOLUME XXIV. Photosynthesis and Nitrogen Fixation (Part B)
Edited by ANTHONY NAS PIETRO
VOLUME XXV. Enzyme Structure (Part B)
Edited by C. H. W. HIRS DNA SERGE N. TIMASHEFF
VOLUME XXVI. Enzyme Structure (Part C)
Edited by C. H. W. HIRS DNA SERGE N. TIMASHEFF
xvii
METHODS IN ENZYMOLOGY
EMULOV XXVII. Enzyme Structure (Part D)
Edited by C. H. W. HIRS DNA EGRES N. FFEHSAMIT
EMULOV XXVIII. Complex Carbohydrates (Part B)
Edited by ROTCIV GRUBSNIG
EMULOV XXIX. Nucleic Acids and Protein Synthesis (Part E)
Edited yb ECNERWAL NAMSSORG DNA KIVIE EVADLOM
EMULOV XXX. Nucleic Acids and Protein Synthesis (Part F)
Edited by KIVIE EVADLOM DNA ECNERWAL NAMSSORG
EMULOV XXXI. Biomembranes (Part A)
Edited by SIDNEY REHCSIELF DNA LESTER REKCAP
EMULOV XXXII. Biomembranes (Part B)
Edited by SIDNEY REHCSIELF DNA LESTER REKCAP
EMULOV XXXIII. Cumulative Subject Index Volumes I-XXX
Edited by AHTRAM G. DENNIS DNA DRAWDE A. SINNED
EMULOV XXXIV. Affinity Techniques (Enzyme Purification: Part B)
Edited by MAILL1W B. YBOKAJ DNA MEIR KEHCLIW
EMULOV XXXV. Lipids (Part B)
Edited by JOHN M. NIETSNEWOL
EMULOV XXXVI. Hormone Action (Part A: Steroid Hormones)
Edited by BERT W. O'MALLEY DNA JOEL G. NAMDRAH
EMULOV XXXVII. Hormone Action (Part B: Peptide Hormones)
Edited yb BERT W. O'MALLEY DNA JOEL G. NAMDRAH
EMULOV XXXVIII. Hormone Action (Part C: Cyclic Nucleotides)
Edited yb JOEL G. NAMDRAH DNA BERT W. O'MALLEY
EMULOV XXXIX. Hormone Action (Part D: Isolated Cells, Tissues, and
Organ Systems)
Edited by JOEL G. NAMDRAH DNA BERT W. O'MALLEY
EMULOV XL. Hormone Action (Part E: Nuclear Structure and Function)
Edited yb BERT W. O'MALLEY DNA JOEL G. NAMDRAH
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 HCABSOM
VOLUME XLV. Proteolytic Enzymes (Part B)
Edited by LASZLO LORAND
VOLUME XLVI. Affinity Labeling
Edited by WILLIAM B. JAKOBY DNA MEIR WILCHEK
VOLUME XLVII. Enzyme Structure (Part E)
Edited by C. H. W. HIRS DNA SERGE N. TIMASHEFF
VOLUME XLVIII. Enzyme Structure (Part F)
Edited by C. H. W. HIRS DNA SERGE N. TIMASHEFF
VOLUME XLIX. Enzyme Structure (Part G)
Edited by C. H. W. HIRS DNA 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 DNA MARY ELLEN JONES
VOLUME LII. Biomembranes (Part C: Biological Oxidations)
Edited by SIDNEY FLEISCHER DNA LESTER REKCAP
VOLUME LIII. Biomembranes (Part D: Biological Oxidations)
Edited by SIDNEY FLEISCHER DNA LESTER REKCAP
VOLUME LIV. Biomembranes (Part E: Biological Oxidations)
Edited by SIDNEY FLEISCHER DNA LESTER REKCAP
xix
METHODS IN ENZYMOLOGY
EMULOV LV. Biomembranes (Part F: Bioenergetics)
Edited by SIDNEY REHCSIELF DNA LESTER REKCAP
EMULOV LVI. Biomembranes (Part G: Bioenergetics)
Edited by SIDNEY REHCSIELF DNA LESTER REKCAP
EMULOV LVII. Bioluminescence and Chemiluminescence
Edited by ENELRAM A. DELUCA
EMULOV LVIII. Cell Culture
Edited by WILLIAM B. YBOKAJ DNA ARI NATSAP
EMULOV LIX. Nucleic Acids and Protein Synthesis (Part G)
Edited by KIVIE EVADLOM DNA ECNERWAL NAMSSORG
EMULOV LX. Nucleic Acids and Protein Synthesis (Part H)
Edited by KIVIE EVADLOM DNA ECNERWAL NAMSSORG
EMULOV 61. Enzyme Structure (Part H)
Edited by C. H. W. HIRS DNA EGRES N. FFEHSAMIT
EMULOV 62. Vitamins and Coenzymes (Part )D
Edited by DLANOD B. KCIMROCCM DNA LEMUEL D. THGIRW
EMULOV 63. Enzyme Kinetics and Mechanism (Part A: Initial Rate and
Inhibitor Methods)
Edited by DANIEL L. HCIRUP
EMULOV 64. Enzyme Kinetics and Mechanism (Part B: Isotopic Probes
and Complex Enzyme Systems)
Edited by DANIEL L. HCIRUP
EMULOV 65. Nucleic Acids (Part I)
Edited by ECNERWAL NAMSSORG DNA KIVIE EVADLOM
EMULOV 66. Vitamins and Coenzymes (Part E)
Edited by DLANOD B. KCIMROCCM DNA LEMUEL D. THGIRW
EMULOV 67. Vitamins and Coenzymes (Part F)
Edited by DLANOD B. KCIMROCCM DNA LEMUEL D. THGIRW