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The Symposia, 1933 — 2003

1982:   Structures of DNA, Vol. XLVII

Organizer: James Watson


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Part 1
Symposium Participants    vForeword    xiiiIntroductionRight-handed and Left-handed DNA: Conformational Information in Genetic Material A. Rich    1The Handedness of DNAHelix Geometry and Hydration in A-DNA, B-DNA, and Z-DNA R. E. Dickerson, H. R. Drew, B. N. Conner, M. L. Kopka, and P. E. Pjura    13Structural Diversity in DNA: From Monomer Structures to Oligonucleotides M. A. Viswamitra    25Right-handed and Left-handed Double-helical DNA: Structural Studies A. H.-J. Wang, S. Fujii, J. H. van Boom, and A. Rich    33Left-handed DNA Duplexes V. Sasisekharan    45DNA Secondary Structures: Helices, Wrinkles, and Junctions S. Arnott, R. Chandra- sekaran, I. H. Hall, L C. Puigjaner, J. K. Walker, and M Wan    53DNA Structures and Transitions: X-Ray Diffraction Studies of Solvated Fibers S. B. Zim- merman and B. H. Pheiffer    67Left-handed DNA Helices, Supercoiling, and the B-Z Junction R. D. Wells, R. Brennan, K. A. Chapman, T. C. Goodman, P. A. Hart, W. Hillen, D. R. Kellogg, M. W. Kilpatrick, R.. D. Klein, J. Klysik, P. F. Lambert, J. E. Larson, J. J. Miglietta, S. K. Neuendorf, T. R.. O'Connor, C. K. Singleton, S. M. Stirdivant, C. M. Veneziale, R. M. Wartell, and W. Zacharias    77DNA Supercoiing and Its Effects on DNA Structure and Function J. C. Wang, L. J. Peck, and K. Becherer    85Supercoiing and Left-handed Z-DNA A. Nordheim, L. J. Peck, E. M. Lafer, B. D. Stollar, J. C. Wang, and A. Rich    93Dynamic, Sequence-dependent DNA Structures as Exemplified by Cruciform Extrusion from Inverted Repeats in Negatively Supercoiled DNA D. M. J. Lilley    101Salt-induced Transition between Two Double-helical Forms of Oligo(dC-dG) F. M. Pohl    113DNA Formed by Reassociation of Complementary Single-stranded Circles from Natural DNA Is Shown to Contain Left- and Right-handed Double Helices S. Brahms, J. Vergne, J. G. Brahms, E. DiCapua, P. Bucker, and T. Koller    119Transitions Induced by Metal Complexes among Several Forms of DNA G. L. Eichhorn, Y. A. Shin, and J. J. Butzow    125Alternative Description of the Transition between B-DNA and Z-DNA R. C. Hopkins    129Electron Microscopy of "Z-DNA" H. Castleman and B. F. Erlanger    133Generation of Left-handed Z-DNA in Solution and Visualization in Polytene Chromosomes by Immunofluorescence T. M. Jovin, J. H. van de Sande, D. A. Zarling, D. J. Arndt- Jovin, F. Eckstein, H. H. Füldner, C. Greider, I. Grieger, E. Hamori, B. Kalisch, L.P. McIntosh, and M. Robert-Nicoud    143Antibody Recognition of Z-DNA E. M. Lafer, A. Möller, R. P. C. Valle, A. Nordheim, A. Rich, and B. D. Stollar    155Interactions between Nucleic Acids and Antibodies to Z-DNA M. Leng, B. Hartmann, B. Malfoy, J. Pilet, J. Ramstein, and E. Sage    163Z-DNA and the Polytene Chromosome M. L. Pardue, A. Nordheim, E. M. Lafer, B. D. Stollar, and A. Rich    171 Conformational AnalysisDynamic Behaviors of DNA Molecules in Solution Studied by Fluorescence Microscopy M. Yanagida, Y Hiraoka, and I. Katsura    177New Techniques for Purifying Large DNAs and Studying Their Properties and Packaging D. C. Schwartz, W Saffran, J. Welsh, R. Haas, M. Goldenberg, and C. R. Cantor    189NMR Studies of DNA Conformation and Dynamics in Solution D. J. Patel, S. A.. Kozlowski, S. Ikuta, K. Itakura, R. Bhatt, and D. R. Hare    197Application of Multiple-pulse ¹H-NMR Techniques to the Study of Two Synthetic DNA Decamers J. Feigon, J. M. Wright, W. A. Denny, W. Leupin, and D. R. Kearns    207Statistical Mechanical Analysis of Competing Conformational Transitions in Superhelical DNA C. J. Benham    219Theoretical Probes of DNA Conformation Examining the B?Z Conformational Transition W. K. Olson, A. R. Srinivasan, N. L. Marky, and V. N. Balaji    229Cooperative Transitions in DNA with No Separation of Strands V. I. Ivanov, L. E. Minchenkova, F. E. Minyat, and A. K. Schyolkina    243Computer Simulation of DNA Double-helix Dynamics M. Levitt    251Transmission of Long-range Effects in DNA D. M. Crothers and M. Fried    263Sequence-dependent Variations of B-DNA Structure and Protein-DNA Recognition E. N. Trifonov    271A Bent Helix in Kinetoplast DNA J. C. Marini, S. D. Levene, D. M. Crothers, and P. T. Englund    279Helical Periodicity of DNA On and Off the Nucleosome as Probed by Nucleases A. Klug, L. C. Lutter, and D. Rhodes    285Chemically Modified DNAb-Kinked DNA-a Structure That Gives Rise to Drug Intercalation and DNA Breathing-andIts Wider Significance in Determining the Premelting and Melting Behavior of DNAH. M. Sobell, T. D. Sakore, S. C. Jam, A. Banerjee, K. K. Bhandary, B. S. Reddy, and E. D. Lozansky    293Some New Aspects of Actinomycin D-Nucleic Acid Binding F. Takusagawa and H. M. Berman    315Netropsin Increases the Linking Number of DNA A. D. B. Malcolm and G. Snounou    323Interactions of Aflatoxin B, and Alkylating Agents with DNA: Structural and Functional Studies J. M. Essigmann, C. L Green, R. G. Croy, K.. W. Fowler, G. H. Büchi, and G. N. Wogan    327Carcinogens Can Induce Alternate Conformations in Nucleic Acid Structure R.M. Santella, D. Grunberger, and I. B. Weinstein    339Footprinting with MPE·Fe(II). Complementary-strand Analyses of Distamycin- and Actinomycin-binding Sites on Heterogeneous DNA M. W. Van Dyke and P. B. Dervan    347Ethidium Bromide Alters the Binding Mode of cis-Diamminedichloroplatinum(II) to pBR322 DNA C. M. Merkel and S. J. Lippard    355Sharp Kink of DNA at Psoralen-cross-link Site Deduced from Crystal Structure of Psoralen- Thymine Monoadduct S.-H. Kim, S. Peckler, B. Graves, D. Kanne, H. Rapoport, and J. E. Hearst    361Synthetic Sequence-specific Ligands G. V. Gursky, A. S. Zasedateley, A. L. Zhuze, A. A. Khorlin, S. L. Grokhovsky, S. A. Streltsov, A. N. Surovaya, S. M. Nikitin, A. S. Krylov, V. O. Retchinsky, M. V. Mikhailov, R. S. Beabealashvili, and B. P. Gottikh    367Altered Structure of Ultraviolet-irradiated DNA: Evidence for Unwinding H. J. Edenberg    379Chemical Synthesis of DNASolid-phase Synthesis of Polynucleotides. VIII. A Simplified Synthesis of Oligodeoxy- ribonucleotides Z -K. Tan, S. Ikuta, T. Haung, A. Dugaiczyk, and K. Itakura    383Continuous-flow Phosphotriester Method for Solid-phase Synthesis of Oligodeoxyribonucleo- tides M. J. Gait, H. W. D. Matthes, M. Singh, B. S. Sproat, and R. Titmas    393Synthesis and Conformational Analysis of Synthetic DNA Fragments J. H. van Boom, G. A. van der Marel, H. Westerink, C. A. A. van Boeckel, J. -R. Mellema, C. Altona, C. W. Hilbers, C. A. G. Haasnoot, S. H. de Bruin, and R. G. Berendsen    403Chemical Synthesis and Biological Studies on Mutated Gene-control Regions M. H. Caruthers, S. I. Beaucage, J. W. Efcavitch, E. F. Fisher, R.. A.. Goldman, P. L. deHaseth, W. Mandecki, M. D. Matteucci, M. S. Rosendahl, and Y. Stabinsky    411

DNA-Protein Interactions

Catabolite Gene Activator Protein: Structure, Homology with Other Proteins, and Cyclic AMP and DNA Binding T. A. Steitz, I. T. Weber, and J. B. Matthew    419

Cro Repressor Protein and Its Interaction with DNA B. W. Matthews, D. H. Ohlendorf, W. F. Anderson, R. G. Fisher, and Y. Takeda    427

Structure of the Operator-binding Domain of Bacteriophage l Repressor: Implications for DNA Recognition and Gene Regulation M. Lewis, A. Jeffrey, J. Wang, R. Ladner, M. Ptashne, and C. O. Pabo    435

Mutations Defining the Operator-binding Sites of Bacteriophage l Repressor H. C. M. Nel- son, M. H. Hecht, and R. T. Sauer    441

Direct Measurement of DNA Unwinding Angle in Specific Interaction between lac Operator and Repressor R. Kim and S.-H. Kim    451

Size of the Unwound Region of DNA in Escherichia coli RNA Polymerase and Calf Thymus RNA Polymerase II Ternary Complexes H. B. Gamper and J. E. Hearst    455

Ion Effects on the Aggregation and DNA-binding Reactions of Escherichia coli RNA Poly- merase S. L Shaner, P. Melan~on, K. S. Lee, R. R. Burgess, and M. T. Record, Jr    463

In Vivo Expression of lac Promoter Variants with Altered -10, -35, and Spacer Sequences J. W. Ackerson and J. D. Gralla    473

DNA Determinants of Promoter Selectivity in Escherichia coli W. R. McClure, D. K. Hawley, P. Youderian, and M. M. Susskind    477

Protein Blotting as a Means of Detecting Sequence-specific DNA-binding Proteins R. S. Jack, M. T. Brown, and W. I. Gehring    483

DNA within Nucleosomes

Studies of Nucbeosome Structure T. J. Richmond, J. T. Finch, and A. Klug    493

Structure of Nucleosomes, Chromatin, and RNA Polymerase-Promoter Complex as Re- vealed by DNA-Protein Cross-linking A. D. Mirzabekov, S. G. Bavykin, V. L Karpov, O. V. Preobrazhenskaya, K. K. Ebralidze, V. M. Tuneev, A. F. Melnikova, F. G. Goguadze, A. A. Chenchick, and R. S. Beabealashvili    503

Cellular and SV40 Chromatin: Replication, Segregation, Ubiquitination, Nuclease-hyper- sensitive Sites, HMG-containing Nucleosomes, and Heterochromatin-specific Protein A. Varshavsky, L. Levinger, O. Sundin, J. Barsoum, E. Özkaynak, P. Swerdlow, and D. Finley    511

Cleavage Reagents as Probes of DNA Sequence Organization and Chromatin Structure: Drosophila melanogaster Locus 67B1 S. C. R. Elgin, I. L Cartwright, G. Fleischmann, K Lowenhaupt, and M. A. Keene    529

Expression of the Mouse Metallothionein-I Gene Alters the Nuclease Hypersensitivity of Its 5' Regulatory Region A. W. Senear and R. D. Palmiter    539

Properties of the Chromatin Assembled on DNA Injected into Xenopus Oocytes and Eggs G. Gargiulo, W Wasserman, and A. Worcel    549

Model for the Structure of the Active Nucloolar Chromatin P. Labbort, P. Ness, E. Banz, R. Parish, and T. Koller    557

SV40 Morphogenesis M. Bina, V. Blasquez, S.-C. Ng, and S. Beecher    565

Nucleosome-core Assembly on B and Z Forms of Polytd(G-m5C)] F. D. Miller, J. B. Rattner, and J. H. van de Sande    571

Part 2

DNA Methylation

Methylation and Chromatin Structure G. Felsenfeld, J. Nickol, M. Behe, J. McGhee, and D. Jackson    577

Coupled Demethylation of Sites in a Conserved Sequence of Xenopus Ribosomal DNAA. La Volpe, M. Taggart, D. Macleod, and A Bird    585

DNA Methylation and Gene Activity: The Adenovirus System as a Model W. DoerflerI. Kruczek, D. Eick, L. Vardimon, and B. Kron    593

Effect of DNA Methylationon Gene Expression H. Cedar, R. Stein, Y. Gruenbaum, T. Naveh-Many, N. Sciaky-Gallili, and A. Razin    605

Retroviruses and Embryogenesis: De Novo Methylation Activity Invovled in Gene Epression D. Jähner, C. L. Stewart, H. Stuhlmann, K. Harbers, R. Jaenisch    611

Implications for X-Chromosome Regulation from Studies of Human X Chromosome S. F. Wolfe and B. R. Midgeon    621

DNA Methylation and Control of Gene Expression on the Human X Chromosome L.J. Sharpiro and T. Mohandas    631

Methylation Regulates the Expression of a DNA-modification Function Encoded by Bacteriopage Mu R. Kahnmann    639

Regulation of the DNA-modification Function of Bacteriopage Mu S. Hattman, M. Goradia, and c. Monoghan, and A. I. Bukhari    647

DNA Replication

Studies on DNA Replication in the Bacteriopage T4 In Vitro System B. M. Alberts,J. Barry, P. Bedinger, T. Formosa, C. V. Jongeneel, and K.N. Kreuzer    655

Mechanisms for the Initiation of Bacteriopage T7 DNA Replication C.W. Fuller, B. B. Beauchamp, M. J. Engler, R. L. Lechner, S. W. Matson, S. Tabor, J. H. White, and C.C. Richardson    669

Replication of Bacterioopage l DNA T. Tsurimoto and K. Matsubara    681

Enzymatic Recognition of DNA Replication Origins M. M. Stayton, L. Betsch, S. Biswas, P. Burgers, N. Dixon, J. E. Flynn, Jr., R. Fuller, J. Kaguni, J. Kobori, M. KOdaira, R. Low, and A. Kornberg    693

DNA Structures Required for f X174 A Protien-directed Initiation and Termination of DNA Replication D. R. Brown, D. Reinberg, T. Schmidt-Glenewinkel, M. Roth, S. L. Zipursky, and J. Hurwotz    701

Signals for the Initation and Termination of Synthesis of the Viral Strand of Bacteriopage f1 G. P. Dotto, K. Horiuchi, K. S. Jakes, and N. D. Zinder    717

Structure and Replication of Vaccina Virus Telomers B. M. Baroudy, S. Venkateson, andB. Moss    723

Isolation of Proteins Involved in the Replication of Adenoviral DNA IN Vitro J.H. Lichy,K. Nagata, B. R. Friefeld, T. Enomoto, J. Field, R. A. Guggenheimer, J.-E. Ikeda,M.S. Horowitz, and J. Hurwitz    731

Adenovirus DNA Replication: DNA Sequences and Enzymes Required for Initiation In Vitro B. W. Stillman and F. Tamanoi    741

Structure and Replication of Minute Virus of Mice DNA C. R. Astell, M. Thomson, M. B. Chow, and D. C. Ward    751

Gyrases and Topoisomerases

Regulation of DNA Supercoiling in Escherichia coli M. Gellert, R. Menzel, K. Mizuuchi, M.H. O'Dea, and D.I. Friedman    763

Escherichia coli Type 1- Topoisomerases: Identification, Mechanism, and Role in Recombina- tion F. Dean, M. A. Krasnov, R. Otter, M. M. Matzuk, S. J. Spengler, and N.R. Co