Table Of ContentContributors to Volume 212
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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
