1982: Structures of DNA, Vol. XLVII
Organizer: James Watson
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
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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
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