Contributors to Volume 212 elcitrA srebmun era ni sesehtnerap gniwollof the seman of .srotubirtnoc snoitailiffA listed era .tnerruc D2'IERAF ABOUL-ELA (5), Department of -DiB ROBERT W. HOEPENER (13), Department of chemistry, The University, Dundee 1DD Molecular Genetics, Biochemistry and 4HN, Scotland Microbiology, University of Cincinnati EZRA S. ABRAMS (4), Department of Biol- College of Medicine, Cincinnati, Ohio ~ygo Massachusetts Institute of Technol- 76254 ogy, Cambridge, Massachusetts 93120 HAN HTUN (15), Division of Chemistry, Cal- JACQUEEINE K. BARTON (12), Department ifornia Institute of Technology, Pasa- of Chemistry, California Institute of Tech- dena, California 52119 nology, Pasadena, California 52119 BRIAN H. JOHNSTON (10, 15), Cell and Mo- MICHAEL M. BECKER (14), Institute of lecular Biology Laboratory, SRI Interna- Biosciences and Technology, Texas A&M tional, Menlo Park, California 52049 University, Houston, Texas 03077 JASON D. KAHN (1), Department of Chemis- RICHARD BOWATER (5), Department of -DiB try, Yale University, New Haven, Con- chemistry, ehT University, Dundee 1DD necticut 11560 4HN, Scotland Y. KOHWl (9), Cancer Research Center, La CHRISTINE S. CHOW (12), Department of Jolla Cancer Research Foundation, La Chemistry, California Institute of Tech- Jolla, California 73029 nology, Pasadena, California 52119 T. KOHwI-SHIGEMATSU (9), Cancer Re- NICHOLAS R. COZZARELLI (6), Department search Center, La Jolla Cancer Research of Molecular and Cell Biology, University Foundation, La Jolla, California 73029 of California, Berkeley, Berkeley, Califor- nia 02749 STEPHEN D, LEVENE (1), Department of Molecular and Cell Biology, University of DONALD M. CROTHERS (1, 3), Department California, Berkeley, Berkeley, California of Chemistry, Yale University, New Ha- 02749 ven, Connecticut 11560 STEPHAN DIEKMANN (2), Abteilung Mole- DAVID M. J. LILLEY (5, 7), Department of kulare Biologie, Max-Planck-lnstitut fiir Biochemistry, ehT University, Dundee 1DD 4HN, Scotland Biophysikalische Chemie am Fassberg, 0043-D G6ttingen, Germany LEROY F. LIU (20), Department of Biologi- ,FUQCAJ LINE DRAK (1, 3), Department of cal Chemistry, The Johns Hopkins School Molecular Biology and Biochemistry, of Medicine, Baltimore, Maryland 50212 Harvard University, Cambridge, Massa- TIMOTHY M. LOHMAN (24, 25), Department chusetts 93120 of Biochemistry and Molecular Biophys- PETER DROGE (6, 22), Department of Biol- ics, Washington University School of ogy, University of Konstanz, D-7750 Kon- Medicine, St. Louis, Missouri 01136 stanz, Germany DAVID P. MASCOTTI (24, 25), Department of YROGERG GROSSMANN (14), Department of Biochemistry and Molecular Biophysics, Biochemistry, Case Western Reserve Uni- Washington University School of Medi- versity, Cleveland, Ohio 60144 cine, St. Louis, Missouri 01136 ix X CONTRIBUTORS TO VOLUME 212 ALFRED NORDHEIM (22), Institute for Mo- ANDREW A. SREVART (23), MRC Labora- lecular Biology, Hannover Medical tory of Molecular Biology, Cambridge School, D-3000 Hannover 61, Germany 2BC 2QH, England EMIL KEZ(ELAP (8, 17), Institute of Biophys- SAMOHT D. TULLIUS (11), Department of ics, Czechoslovak Academy of Sciences, Chemistry, The Johns Hopkins Univer- 216 56 Brno, Czechoslovakia sity, Baltimore, Maryland 81212 MARY ANN PRICE (ll), Department of WILLIAM G. TURNELL (23), MRC Labora- Chemistry, The Johns Hopkins Univer- tory of Molecular Biology, Cambridge sity, Baltimore, Maryland 21218 2BC 2QH, England DAVID G. SANFORD (21), Department of DAVID W. USSERY (13, 18), Institute of Biochemistry, Tufts University School of Biosciences and Technology, Texas A&M Medicine, Boston, Massachusetts 11120 University, Houston, Texas 03077 DRAHCIR R. SINDEN (13, 18), Institute of FRANZ BARLHOW (16), Department of -DiB Biosciences and Technology, Texas A&M chemistry, University of Alabama at Bir- University, Houston, Texas 03077 mingham, Birmingham, Alabama 35294 VINCENT P. STANTON, JR. (4), Center for HAI-YOUNG WU (20), Department of Phar- Cancer Research, Massachusetts Insti- macology, Wayne State University tute of Technology, Cambridge, Massa- School of Medicine, Detroit, Michigan chusetts 02139 10284 B. DAVID RALLOTS (2 l), Department of -DiB W. ZACHARIAS (19), Department of -DiB chemistry, Tufts University School of chemistry, University of Alabama at Bir- Medicine, Boston, Massachusetts 11120 mingham, Birmingham, Alabama 35294 Preface The structure of DNA has been known in general terms for about forty years now. Yet in the last decade we have become much more attuned to its subtleties and how they depend on the interplay of local base se- quence, environmental conditions, covalent modification, and topology. For this reason the use of the plural form for structure in the titles of Volumes 112 and 212 is significant. Structural alterations of DNA may be relatively subtle--essentially small (though very important, nevertheless) modifications to the standard B-DNA structure--or they may be very great. Until the late 1970s DNA was regarded as an invariant, straight, right-handed B-form double helix. In the intervening period DNA structures have been described that depart from virtually all the conventional patterns. DNA can be left-handed (Z- DNA), and base pairing can be rearranged (cruciform) or remodeled (H- triplex). The axis can be bent or kinked, and triple and quadruple helices are possible. This has changed our perspective of DNA structure to one of a highly polymorphic molecule. Not all of the structures that are possible may be biologically relevant, but some undoubtedly are. Some structures may even be conformational traps that must be avoided. But it is clear that if we are to understand the structures and dynamics of DNA and its interactions with ligands, a complete analysis of its conformational flexi- bility is required. Progress in a number of areas had led to our current view of DNA as a more, structurally adventurous molecule. Initially it was the advent of new methods for the synthesis of oligonucleotides of defined sequence and high purity and the consequent crystallographic analysis of a number of DNA structures at near atomic resolution that revealed the sequence dependence of DNA structure. This also gave us the first major surprise-- left-handed Z-DNA. Short, well-defined DNA fragments may also be studied by many other physical techniques, and nuclear magnetic reso- nance spectroscopy has been particularly useful. But in parallel with these general methods, a number of powerful techniques that are more specific to DNA have emerged, including the ability to synthesize any DNA sequence of interest, the facility to clone these sequences into plasmids, and the opportunity to manipulate DNA as a closed circle. Many of the perturbed structures that DNA can adopt are stabilized by negative supercoiling, and this can be exploited to analyze DNA structure and energetics. Thus band-shift methods and two-dimen- sional gel electrophoresis are now important methods for the study of xi xii PREFACE DNA structure. In addition, probing methods have become vital to the analysis of local structure in DNA, and an armory of chemical and en- zyme probes are available for this task. Chemical probes are now being extended to the analysis of DNA inside the cell, an important aspect of their use if we are to assess the biological role of DNA structural polymor- phism. In view of the amount of activity in this area in the last decade and the new methods developed, we felt it was time to collect all the methods and approaches in one place, and these volumes are the result. Originally it was our intention to produce a single volume, which, thanks to the hard work of all our authors, eventually became two. We are most grateful to all the authors for their efforts, and we hope that their reward will be the existence of these books that should be a valuable resource for all of us in the field. We also thank the staff of Academic Press for their assistance in the preparation of these volumes. DAVID M. J. LILLEY JAMES E. DAHLBERG METHODS IN ENZYMOLOGY EMULOV I. Preparation and Assay of Enzymes Edited by SIDNEY P. KCIWOLOC DNA NAHTAN O. NALPAK EMULOV II. Preparation and Assay of Enzymes Edited by YENDIS P. KCIWOLOC DNA NAHTAN O. NALPAK EMULOV III. Preparation and Assay of Substrates Edited by YENDIS P. KClWOLOC DNA NAHTAN O. NALPAK EMULOV IV. Special Techniques for the Enzymologist Edited by YENDIS P. KCIWOLOC DNA NAHTAN O. NALPAK EMULOV V. Preparation and Assay of Enzymes Edited by YENDIS P. KCIWOLOC DNA NAHTAN O. NALPAK EMULOV VI. Preparation and Assay of Enzymes )deunitnoC( Preparation and Assay of Substrates Special Techniques Edited by YENDIS P. KCIWOLOC DNA NAHTAN O. NALPAK EMULOV VII. Cumulative Subject Index Edited yb YENDIS P. KCIWOLOC DNA NAHTAN O. NALPAK EMULOV VIII. Complex Carbohydrates Edited by HTEBAZILE F. NEUFELD DNA ROTCIV GRUBSNIG EMULOV IX. Carbohydrate Metabolism Edited yb WILLIS A. DOOW EMULOV X. Oxidation and Phosphorylation Edited yb DLANOR W. KOORBATSE DNA DRANYAM E. NAMLLUP EMULOV XI. Enzyme Structure Edited by C. H. W. HIRS EMULOV XII. Nucleic Acids (Parts A and B) Edited by ECNERWAL NAMSSORG DNA KIVIE EVADLOM xiii xiv METHODS IN ENZYMOLOGY VOLUME XIII. Citric Acid Cycle Edited by J. M. LOWENSTEIN VOLUME XIV. Lipids Edited yb J. M. N1ETSNEWOL VOLUME XV. Steroids and Terpenoids Edited yb 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 by 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 KIVlE MOLDAVE DNA LAWRENCE NAMSSORG VOLUME XXI. Nucleic Acids (Part D) Edited yb LAWRENCE NAMSSORG DNA KIVIE EVADLOM VOLUME XXII. 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 SDOHTEM IN YGOLOMYZNE VX VOLUME XXVII. Enzyme Structure (Part D) Edited by C. H. W. HIRS DNA SERGE N. TIMASHEFF VOLUME XXVIII. Complex Carbohydrates (Part B) Edited by VICTOR GINSaURG VOLUME XXIX. Nucleic Acids and Protein Synthesis (Part E) Edited by LAWRENCE NAMSSORG DNA KIVIE EVADLOM 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 DNA LESTER REKCAP VOLUME XXXII. Biomembranes (Part B) Edited by SIDNEY FLEISCHER DNA LESTER REKCAP VOLUME XXXIII. Cumulative Subject Index Volumes I-XXX Edited by MARTHA G. DENNIS DNA EDWARD A. DENNIS VOLUME XXXIV. Affinity Techniques (Enzyme Purification: Part B) Edited yb WILLIAM B. YBOKAJ DNA 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 DNA JOEL G. NAMDRAH VOLUME XXXVII. Hormone Action (Part B: Peptide Hormones) Edited by BERT W. O'MALLEY DNA JOEL G. NAMDRAH VOLUME XXXVIII. Hormone Action (Part C: Cyclic Nucleotides) Edited by JOEL G. HARDMAN DNA BERT W. O'MALLEY VOLUME XXXIX. Hormone Action (Part D: Isolated Cells, Tissues, and Organ Systems) Edited by JOEL G. HARDMAN DNA BERT W. O'MALLEY VOLUME XL. Hormone Action (Part E: Nuclear Structure and Function) d.etidE by BERT W. O'MALLEY DNA JOEL G. NAMDRAH xvi METHODS IN ENZYMOLOGY VOLUME XLI. Carbohydrate Metabolism (Part B) Edited yb W. A. WOOD VOLUME XLII. Carbohydrate Metabolism (Part )C Edited by W. A. WOOD VOLUME XLIII. Antibiotics Edited yb JOHN H. HASH VOLUME XLIV. Immobilized Enzymes Edited yb KLAUS HCABSOM VOLUME XLV. Proteolytic Enzymes (Part B) Edited by LORAND LASZLO VOLUME XLVI. Affinity Labeling Edited by WILLIAM B. YBOKAJ DNA MEIR WILCHEK VOLUME XLVII. Enzyme Structure (Part E) Edited yb 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 yb C. H. W. HIRS DNA SERGE N. TIMASHEFF VOLUME L. Complex Carbohydrates (Part C) Edited by VICTOR GRUBSNIG VOLUME LI. Purine and Pyrimidine Nucleotide Metabolism Edited yb PATRICIA A. HOFFEE DNA ELLEN MARY JONES VOLUME LII. Biomembranes (Part C: Biological Oxidations) Edited by SIDNEY FLEISCHER DNA LESTER REKCAP VOLUME LIII. Biomembranes (Part D: Biological Oxidations) Edited yb SIDNEY FLEISCHER DNA LESTER REKCAP VOLUME LIV. Biomembranes (Part E: Biological Oxidations) Edited yb SIDNEY ELEISCHER AND LESTER PACKER xvii METHODS IN ENZYMOLOGY EMULOV LV. Biomembranes (Part F: Bioenergetics) Edited by YENDIS REHCSIELF DNA LESTER REKCAP EMULOV LVI. Biomembranes (Part G: Bioenergetics) Edited by YENDIS 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 xviii SDOHTEM NI YGOLOMYZNE EMULOV .86 Recombinant DNA Edited yb YAR Wu EMULOV .96 Photosynthesis and Nitrogen Fixation (Part C) Edited by YNOHTNA NAS ORTEIP EMULOV .07 Immunochemical Techniques (Part A) Edited yb NELEH NAV SIKANUV DNA NHOJ J. ENOGNAL EMULOV .17 Lipids (Part )C Edited yb NHOJ M. NIETSNEWOL EMULOV .27 Lipids (Part D) Edited yb NHOJ M. NIETSNEWOL EMULOV .37 Immunochemical Techniques (Part )B Edited by NHOJ J. ENOGNAL DNA NELEH NAV SIKANUV EMULOV .47 Immunochemical Techniques (Part )C Edited yb NHOJ J. ENOGNAL DNA NELEH NAV SIKANUV VOLUME75. Cumulative Subject Index Volumes XXXI, XXXII, XXXIV-LX Edited yb DRAWDE A. SINNED DNA AHTRAM G. SINNED EMULOV .67 Hemoglobins Edited by ODLARE ,ININOTNA IGIUL ROSSI-BERNARDI, AND EMILIA CHIANCONE EMULOV .77 Detoxication and Drug Metabolism Edited by MAILLIW B. YBOKAJ EMULOV .87 Interferons (Part A) Edited by YENDIS AKTSEP EMULOV .97 Interferons (Part B) Edited yb YENDIS AKTSEP EMULOV .08 Proteolytic Enzymes (Part )C Edited yb OLZSAL DNAROL