COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY

VOLUME XLVII--PART 1 COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY

VOLUME XLVII

STRUCTURES OF DNA

COLD SPRING HARBOR LABORATORY

1983 COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY VOLUME XLVII 1983 by The Cold Spring Harbor Laboratory International Standard Book Number 0-87969-046-1 International Standard Serial Number 0091-7451 Library of Congress Catalog Card Number 34-8174 Printed in the United States of America All rights reserved

COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY

Founded in 1933 by REGINALD G. HARRIS Director of the Biological Laboratory 1924 to 1936

Previous Symposia Volumes

I (1933) Surface Phenomena XXIH (1958) Exchange of Genetic Material: Mechanism and II (1934) Aspects of Growth Consequences IU (1935) Photochemical Reactions XXIV (1959) Genetics and Twentieth Century Darwinism IV (1936) Excitation Phenomena XXV (! 960) Biological Clocks V (1937) Internal Secretions XXVI (1961) Cellular Regulatory Mechanisms VI (1938) Protein Chemistry XXVII (1962) Basic Mechanisms in Animal Virus Biology VII (1939) Biological Oxidations XXVIU (1963) Synthesis and Structure of Macromolecules VIII (1940) Permeability and the Nature of Cell Membranes XXIX (1964) Human Genetics IX (1941) Genes and Chromosomes: Structure and Organization XXX (1965) Sensory Receptors X (1942) The Relation of Hormones to Development XXXI (1966) The Genetic Code XI (1946) Heredity and Variation in Microorganisms XXXII (1967) Antibodies XII (1947) Nucleic Acids and Nucleoproteins XXXIU (1968) Replication of DNA in Microorganisms XIII (1948) Biological Applications of Tracer Elements XXXIV (1969) The Mechanism of Protein Synthesis XIV (1949) Amino Acids and Proteins XXXV (1970) Transcription of Genetic Material XV (1950) Origin and Evolution of Man XXXVI (1971) Structure and Function of Proteins at the Three- XVI (1951) Genes and Mutations dimensional Level XVII (1952) The Neuron XXXVII (1972) The Mechanism of Muscle Contraction XVIII (1953) Viruses XXXVIII (1973) Chromosome Structure and Function XIX (1954) The Mammalian Fetus: Physiological Aspects of XXXIX (1974) Tumor Viruses Development XL (1975) The Synapse XX (1955) Population Genetics: The Nature and Causes of XLI (1976) Origins of Lymphocyte Diversity Genetic Variability in Population XLII (1977) XXI (1956) Genetic Mechanisms: Structure and Function XLIII (1978) DNA: Replication and Recombination XXH (1957) Population Studies: Animal Ecology and XLIV (1979) Viral Oncogenes Demography XLV (1980) Movable Genetic Elements XLVI (1981) Organization of the Cytoplasm

All Cold Spring Harbor Laboratory publications are available through booksellers or may be ordered directly from Cold Spring Harbor Laboratory, Box 100, Cold Spring Harbor, New York 11724. SAN 203-6185 Symposium Participants

ABRAHAM,JUDITH, Cold Spring Harbor Laboratory, New CAIRNS, JOHN, Harvard School of Public Health, Boston, York Massachusetts ALaERTS, BRUCE, Dept. of Biochemistry and Biophysics, CALABRETTA, BRUNO, Dept. of Molecular Biochemistry, University of California, San Francisco M.D. Anderson Hospital and Tumor Institute, Houston, AUDEgSON, WAYNE, F., Dept. of Biochemistry, University of Texas Alberta, Edmonton, Canada CANTOR, CHARLES, Dept. of Human Genetics, Columbia A~mtE~, NORMAN, Dept. of Biochemistry, State University University College of Physicians & Surgeons, New York, of New York, Stony Brook New York ARNOTT, STRUTHER, Dept. of Biological Sciences, Purdue CARBON, JOHN, DL~. of Biological Sciences, University of University, West Lafayette, Indiana California, Sama Barbara ARUNIIr, KaM T., Dept. of Chemistry, University of Penn- CARPOUSIS, A.J., Molecular Biology Institute, University of sylvania, Philadelphia California, Los Angeles AXEL, RICHAItO, Institute of Cancer Research, New York, C~trrnE~, MArtyrs, Dept. of Chemistry, University of Col- New York orado, Boulder BABCOCK-HARMS, MARLA, Dept. of Biology, University of CASrLEMAN, H., , New York, New York North Carolina, Chapel Hill CEDAR, HOWARD, Dept. of Molecular Biology, Hebrew BAILLm, DAVID, Dept. of Biological Sciences, Simon Fraser University, Hada.~sah Medical School, Jerusalem, Israel University, Bumaby, Canada CHAMBON, PIERRE, Dept. of Molecular Genetics, Institute of BARTON, J., Dept. of Chemistry, City University of New Biological Chemistry, Strasbourg, France York, New York CHAN, CLARENCE,Dept. of Biochemistry, Cornell University, BELL, LESt.m, Dept. of Genetics, University of Washington, Ithaca, New York Seattle CHATI'ORAJ,DHRUBA, NCI, FrederickCancer Research Facili- BENHAM, CRAIG, Dept. of Mathematics, University of Ken- ty, Frederick, Maryland tucky, Lexington CHUNG, So-YoN, Dept. of Biochemical Sciences, Princeton BERMAN, HELEN, Institute for Cancer Research, Philadelphia, University, New Jersey Pennsylvania CLARKE, LOUISE, Dept. of Biological Sciences, University BEm~ARDI, GIORGIO,University of Paris, France of California, Santa Barbara Bt~Ncm, MARCO, Dept. of Human Genetics, Yale University CLARKSON, S.G., Dept. of Microbiology, University of School of Medicine, New Haven, Connecticut Geneva Medical School, Switzerland BINA, MINOU, Dept. of Chemistry, Purdue University, West Cox, MICHAEL, Dept. of Biochemistry, Stanford Univer- Lafayette, Indiana sity School of Medicine, California BIRD, ADRIAN, Dept. of Zoology, Medical Research Council, COZZARELLI, NICHOLAS, Dept. of Biochemistry, Univer- Edinburgh, Scotland sity of Chicago, Illinois BLACKnUnN, E., Dept. of Molecular Biology, University of CROTHE~, DONALD, Dept. of Chemistry, Yale University, California, Berkeley New Haven, Connecticut BLOOM, KERRY, Dept. of Biological Sciences, University of CSOROLAS-TOTH,EVA, NIADDKD, National Institutes of California, Santa Barbara Health, Bethesda, Maryland BOYCE, FREDRICK,HI, Dept. of Medical Sciences, University DANIELS, DONNA, Dept. of Genetics, University of of Michigan Medical School, Ann Arbor Wisconsin, Madison BozzoNl, IgENE, Centro Acidi Nucle, Citta Universitaria, DAVlSON, BARRY, INSERM, Institute of Biological Chem- Rome, Italy istry, Strasbourg, France BRAHMS, J.G., Institut de Recherche Biologie Mol6culaire, DAY, LOmSN, Public Health Research Institute, New York, University of Pads, France New York BROACH, JAMES, Dept. of Microbiology, State University of DE ASUA, LOIS J., Friedrich Miescher-Institut, Basel, New York, Stony Brook Switzerland BROWN, DAVID R., Dept. of Developmental Biology, Albert DE HASETH, PIETER, Dept. of Chemistry, University of Einstein College of Medicine, Bronx, New York Colorado, Boulder BUKHARI, AHMAD, Cold Spring Harbor Laboratory, New DEAN, FRANK, Dept. of Biochemistry, University of York. Chicago, Illinois BUSBY, SHARONJ., Dept. of Developmental Biology, Fred DERVAN, PETER, Dept. of Chemistry and Chemical Engi- Hutchinson Cancer Center, Seattle, Washington neering, California Institute of Technology, Pasadena BUSHMAN, WADE, Dept. of Biology and Medicine, Brown DI CAPUA, ELISABETH,Institute for Cell Biology, Zurich, University, Providence, Rhode Island Switzerland BYERS, BRECK,Dept. of Genetics, University of Washington, DI MAURO, ERNESTO, Institute of General Physiology, Seattle University of Rome, Italy v vi SYMPOSIUM PARTICIPANTS

DICKERSON, R.E., Dept. of Molecular Biology, University GELLERT, MARTIN, NIADDKD, National Institutes of of California, Los Angeles Health, Bethesda, Maryland DmKMANN, S., Dept. of Biochemistry, Harvard University, GEORGIEV, GEORGI1, Institute of Molecular Biology, Cambridge, Massachusetts Academy of Sciences, Moscow, USSR D1ERKS, PETER, Dept. of Molecular Biology, University of GEZAR1, WALTER, A2D Ultrasound Co., New Haven, Zurich, Switzerland Connecticut DOERFLER, WALTER,Genetics Institute, University of Col- GLICKMAN, BARRY, Laboratory of Genetics, National In- ogne, Federal Republic of Germany stitute of Environmental Health Sciences, Research DUTY, PAUL, Dept. of Biochemistry and Molecular Biol- Triangle Park, North Carolina ogy, Harvard University, Cambridge, Massachusetts GOLDFARB, ALEXANDER, Dept. of Microbiology, Colum- DUTY, HELGA, Dept. of Biochemistry and Molecular Biol- bia University, New York, New York ogy, Harvard University, Cambridge, Massachusetts GOLDMAN, ADMAN, Dept. of Molecular Biophysics, Yale DREW, HORACE, Dept. of Molecular Biology, University University, New Haven, Connecticut of California, Los Angeles GOLDSTEIN, SAMUEL, Dept. of Medicine and Biochem- DRLICA, KARL, Dept. of Biology, University of Rochester, istry, University of Arkansas Medical Sciences, Little New York Rock DUNN, JOHN J., Dept. of Biology, Brookhaven National GONDA, DAVID, Dept. of Molecular Biophysics and BiD- Laboratory, Upton, New York chemistry, Yale University, New Haven, Connecticut EDENBERG, HOWARD, Dept. of Biochemistry, Indiana GRALLA, JAY D., Molecular Biology Institute, University University, Indianapolis of California, Los Angeles EICHHORN, GUNTHER, National Institutes of Health, GREENE, ROBERT S., Dept. of Biology, Niagara Univer- Gerontology Center, Baltimore City Hospital, sity, New York Maryland GUPTA, GOUTAM,Molecular Biology Unit, Indian Institute EISENSTADT,ERIC, Dept. of Microbiology, Harvard School of Science, Banalore, India of Public Health, Boston, Massachusetts GURSKY, G.V., Institute of Molecular Biology, Academy ELGIN, SARAH, Dept. of Biology, Washington University, of Sciences, Moscow, USSR St. Louis, Missouri HATTMAN, STANLEY, Dept. of Biology, University of ENGELS, JOACHIM,Dept. of Chemistry, University of Col- Rochester, New York orado, Boulder HEARST, JOHN E., Dept. of Chemistry, University of ENGLUND, PAUL T., Dept. of Physiological Chemistry, California, Berkeley Johns Hopkins School of Medicine, Baltimore, Mary- HOOD, LEROY, Dept. of Biology, California Institute of land Technology, Pasadena EPSTEIN, DAVID, NIADDKD, National Institutes of HOPKINS, ROBERT,Molecular Biology Institute, University Health, Bethesda, Maryland of California, Los Angeles ESSIOMANN, JOHN M., Dept. of Nutrition and Food HOPKINS, NANCY, Dept. of Cancer Research, Massachu- Science, Massachusetts Institute of Technology, setts Institute of Technology, Cambridge Cambridge HUBERMAN, JOEL A., Dept. of Cell and Tumor Biology, FASY, THOMAS, Dept. of Pathology, Mt. Sinai School of Roswell Park Memorial Institute, Buffalo, New York Medicine, New York, New York HURWITZ, J., Dept. of Developmental Biology and FEIGON, JULI, Dept. of Chemistry, University of Califor- Cancer, Albert Einstein College of Medicine, Bronx, nia, San Diego, La Julia New York FELSENFELD, GARY, NIADDKD, National Institutes of IKEMURA, T., Dept. of Biophysics, Kyoto University, Health, Bethesda, Maryland Japan FITZGERALD-HAVES, MOLLY, Dept. of Biological Sci- ITAKURA, KEIICHI, Biology Division, City of Hope ences, University of California, Santa Barbara Hospital, Duarte, California FLAVELL, PdCHARO, Plant Breeding Institute, Cambridge, IKUTA, S., Dept. of Molecular Genetics, City of Hope England Research Institute, Durate, California FLORY, JOAN, Dept. of Human Genetics, Yale University, JACK, ROBERT,Dept. of Cell Biology, Biozentrnm, Univer- New Haven, Connecticut sity of Basel, Switzerland FRIED, MICHAEL, Dept. of Chemistry, Yale University, JACKSON, IAN, Dept. of Embryology, Carnegie Institution New Haven, Connecticut of Washington, Baltimore, Maryland FULLER, CARL W., Dept. of Biological Chemistry, Har- JAEHNER, DETLEV, Heinrich-Pette-Institute, Hamburg, vard Medical School, Boston, Massachusetts Federal Republic of Germany FURANO, ANTHONY, NIADDKD, National Institutes of JELINEK, WARREN, New York University Medical Center, Health, Bethesda, Maryland New York GAIT, MICHAEL, Laboratory of Molecular Biology, Medi- JOHNSTON, BRIAN, Dept. of Biochemistry and Biophysics, cal Research Council, Cambridge, England University of California, San Francisco GAMPER, HOWARD, Dept. of Chemistry, University of JONES, JONATHAN, Biological Laboratories, Harvard California, Berkeley University, Cambridge, Massachusetts GARGIULO, GIUSEPPE, Dept. of Biology, University of JUST, JEAN-P., Friedrich Miescher Institut, Basel, Rochester, New York Switzerland SYMPOSIUM PARTICIPANTS vii

JOVIN, THOMAS, Dept. of Biophysiological Chemistry, MARGOLIN, PAUL, Public Health Research Institute of the Max-Planck-Institute, Goettingen, Federal Republic of City of New York, New York Germany MARINI, JOAN C., Dept. of Physiological Chemistry, KAHMANN, REGINA, Dept. of Biochemistry, Max-Planck- Johns Hopkins School of Medicine, Baltimore, Institute, Munich, Federal Republic of Germany Maryland KANS, JONATHAN, Cummings Life Science Center, Uni- MATSUBARA, KENICHI, Dept. of Molecular Genetics, versity of Chicago, Illinois Osaka University Medical School, Japan KEARNS, DAVID, Dept. of Chemistry, University of Cal- MATTHEWS, BRIAN, Institute of Molecular Biology, Uni- ifornia, San Diego, La Jolla versity of Oregon, Eugene KELLY, JEFFREY, Dept. of Biochemistry, Stanford Univer- McCLURE, WILLIAM, Dept. of Biological Science, Car- sity, California negie-Mellon University, Pittsburgh, Pennsylvania K1M, BYUNG D., Dept. of Biological Sciences, Florida MCINTOSH, L., Dept. of Medical Biochemistry, University State University, Tallahassee of Calgary, Canada KIM, S.-H., Dept. of Chemistry, University of California, McKNIGHT, STEVEN, Dept. of Developmental Biology, Berkeley Fred Hutchinson Cancer Center, Seattle, Washington KLEVAN, LEONARD, Bethesda Research Laboratories, Gai- MIGEON, BARBARA, Dept. of Pediatrics, Johns Hopkins thersburg, Maryland University Hospital, Baltimore, Maryland KLUO, AARON, Dept. of Molecular Biology, Medical MILLER, JEFFREY, Dept. of Molecular Biology, University Research Council, Cambridge, England of Geneva, Switzerland KOLLER,T., Institute for Cell Biology, Zurich, Switzerland MIRZABEKOV, ANDREI, Institute of Molecular Biology, KOWALSKI, DAVID, Dept. of Cell and Tumor Biology, Academy of Sciences, Moscow, USSR Roswell Park Memorial Institute, Buffalo, New York Moss, BERNARD, NIAID, National Institutes of Health, KOZLOWSKI, SHARON, Bell Laboratories, Murray Hill, Bethesda, Maryland New Jersey MOSSING, MlCHAEL, Dept. of Chemistry, University of KREUZER, KENNETH, Dept. of Biochemistry and Bio- Wisconsin, Madison physics, University of California, San Francisco MUGHARBIL, USAMA, Berbir Medical Center, Beirut, Leb- KUHN, HANS, Dept. of Biophysical Chemistry, Max- anon Planck-Institute for Biophysical Medicine, Goettingen, MUNSON, BENJAMIN, Roswell Park Memorial Institute, Federal Republic of Germany Buffalo, New York KURTZ, DAVID T., Cold Spring Harbor Laboratory, New NOBLE, S.A., Dept. of Chemistry, University of Colorado, York Boulder LAFER, EILEEN, Dept. of Biology, Massachusetts Institute NORDHEIM, ALFRED, Dept. of Biology, Massachusetts In- of Technology, Cambridge stitute of Technology, Cambridge LAMISCHA,IHOR, Dept. of Biology, Massachusetts Institute OLLIS, DAVID, Dept. of Molecular Biology and Biophysics, of Technology, Cambridge Yale University, New Haven, Connecticut LEROWITZ, JACOB, Dept. of Microbiology, University of OLSON, WILMA K., Dept. of Chemistry, Rutgers Univer- Alabama, Birmingham sity, Piscataway, New Jersey LENq3, MARC, Dept. of Molecular Biophysics, Centre Na- OTTO, ANGELA, Friedrich-Miescher Institut, Basel, Swit- tional de Recherche Scientifique, Orleans, France zerland LEVENE, STEPHEr~,Dept. of Chemistry, Yale University, PASO, CARL O., Dept. of Biochemistry, Harvard Univer- New Haven, Connecticut sity, Cambridge, Massachusetts LEVITT, MICHAEL, Dept. of Chemical Physics, Weizmann PAN, JULIAN, Dept. of Human Genetics, Yale University Institute of Science, Rehovot, Israel School of Medicine, New Haven, Connecticut LEWIS, MITCHELL, Dept. of Molecular Biology, Harvard PARDUE, MARY L., Dept. of Biology, Massachusetts In- University, Cambridge, Massachusetts stitute of Technology, Cambridge LICHV, JACK H., Dept. of Developmental Biology, Albert PARNES, JANE, NICHHD, National Institutes of Health, Einstein College of Medicine, Bronx, New York Bethesda, Maryland LILLEY, DAVID, Dept. of Molecular Genetics, University PATEL, DINSHAW, Bell Laboratories, Murray Hill, New of Dundee, Scotland Jersey LIPPARD, STEPHEN,Dept. of Chemistry, Columbia Univer- POHL, F., University of Konstanz, Federal Republic of sity, New York, New York Germany LIVNEH, ZVI, Dept. of Biochemistry, Stanford University, PRIMKE, MARION, Dept. of Biology, University of Col- California orado, Boulder LONBERG, NILS, The Biological Laboratories, Harvard PROFOUS-JUCHELKA,HELEN, Dept. of Biochemical Genet- University, Cambridge, Massachusetts ics, Merck, Sharp & Dohme Research Laboratories, LOWENHAUPT,KY, Dept. of Biology, Washington Univer- Rahway, New Jersey sity, St. Louis, Missouri RADDING, CHARLES, Dept. of Human Genetics, Yale MAINE, GREGORY,Dept. of Biochemistry, Cornell Univer- University School of Medicine, New Haven, Conn- sity, Ithaca, New York ecticut MALCOLM, ALAN, Dept. of Chemistry, Yale University, RECORD, THOMAS, Dept. of Chemistry, University of New Haven, Connecticut Wisconsin, Madison viii SYMPOSIUM PARTICIPANTS

REDFIELD, A.G., Dept. of Biochemistry, Brandeis Univer- SRINIVASAN, A.R., Dept. of Chemistry, Rutgers Univer- sity, Waltham, Massachusetts sity, New Brunswick, New Jersey REEDER, RONALD, Fred Hutchinson Cancer Research STAHL, FRANKLIN,Dept. of Molecular Biology, University Center, Seattle, Washington of Oregon, Eugene REIS, ROBERT, Dept. of Medicine and Biochemistry, STASIAK, ANDRZEY, Institute of Cell Biology, Zurich, University of Arkansas Medical Sciences, Little Rock Switzerland RICH, ALEX, Dept. of Biology, Massachusetts Institute of STAYTON, MARK M., Dept. of Biochemistry, Stanford Technology, Cambridge University School of Medicine, California RICHMOND, T.J., Laboratory of Molecular Biology, STEIN, ARNOLD, Dept. of Biological Sciences, Purdue Medical Research Council, Cambridge, England University, West Lafayette, Indiana RIPLEY, LYNN S., Dept. of Genetics, National Institute of STEITZ, JOAN A., Dept. of Biophysics and Biochemistry, Environmental Health Services, Research Triangle Yale University, New Haven, Connecticut Park, North Carolina STEITZ, THOMAS, Dept. of Biophysics and Biochemistry, ROBERTS, JEFFREY, Dept. of Biochemistry, Cornell Uni- Yale University, New Haven, Connecticut versity, Ithaca, New York STERNGLANZ,ROLF, Dept. of Biochemistry, State Univer- ROBERTS, RICHARDJ., Cold Spring Harbor Laboratory, sity of New York, Stony Brook New York STILLMAN, BRUCE, Cold Spring Harbor Laboratory, New RosE, ANN, Dept. of Biological Science, Simon Fraser York University, Burnaby, Canada STRAUS, DONALD, The Biological Laboratories, Harvard ROUVIER-YANIV, J., Institut Pasteur, Paris, France University, Cambridge, Massachusetts RUIZ-CARmLLO, ADOLFO, Dept. of Molecular Biology, In- STRUHL, KEVIN, Dept. of Biological Chemistry, Harvard stitut Pasteur, Paris, France University School of Medicine, Boston, Massachusetts SANFORD, JANET P., Dept. of Cell and Tumor Biology, SUGGS, WILLIAM, Dept. of Chemistry, Brown University, Roswell Park Memorial Institute, Buffalo, New York Providence, Rhode Island SANTELLA, R.M., Cancer Center, Columbia University SWERDLOW, PAUL S., Massachusetts Institute of Tech- College of Physicians & Surgeons, New York, New nology, Cambridge York SZOSTAK, JACK W., Sidney Farber Cancer Institute, SASlSEKHAREN,V., Dept. of Molecular Biophysics, Indian Boston, Massachusetts Institute of Science, Bangalore, India TAKEDA, Y., Dept. of Chemistry, University of Maryland SAUER, ROBERT, Dept. of Biology, Massachusetts Institute Baltimore County, Catonsville of Technology, Cambridge THOMA, FRITZ, Cell Biology Institute, ETH-Honggerberg, SAVlNO, MAMA, Dept. of Gli Acidi Nucleici, Citta Univer- Zurich, Switzerland sitaria, Rome, Italy TLSTY, THEA D., Dept. of Biological Science, Stanford SCHAFFNER, WALTER, Dept. of Molecular Biology, Uni- University, California versity of Zurich, Switzerland TOCCHINI-VALENTINI,G.P., Cell Biology Laboratory, Na- SCHMID, CARL W., Dept. of Chemistry, University of tional Research Center, Rome, Italy California, Davis TRIFONOV, E.N., Polymer Dept., Weizmann Institute of SCHOPF, THOMAS,Dept. of Biology, California Institute of Science, Rehovot, Israel Technology, Pasadena TSUmMOTO, TOSHIKI, Dept. of Molecular Genetics, Osaka SCHWARTZ, DAVID C., Dept. of Chemistry, Columbia University School of Medicine, Japan University, New York, New York Tu, HELEN, Chicago, Illinois SENEAR, ALLEN, Dept. of Biochemistry, University of VAN BOOM, JACQUES, Gorleaus Laboratories, Leiden, The Washington, Seattle Netherlands SGARANELLA, VITTOmO, Institute of Genetics, National VAN DE SANDE, J.H., Dept. of Medical Biochemistry, Research Center, Pavia, Italy University of Calgary, Canada SHAPIRO, L.J., Dept. of Medical Genetics, University of VARDIMON, LILY, Institute of Genetics, University of Col- California, Los Angeles Medical Center, Torrence ogne, Federal Republic of Germany SHEPHERD, JOHN, Biozentrum, University of Basel, VARSHAVSKY, A., Dept. of Biology, Massachusetts In- Switzerland stitute of Technology, Cambridge SKINNER, DOROTHY,Dept. of Biology, Oakridge National VENKARESAN, S., NIAID, National Institutes of Health, Laboratory, Tennessee Bethesda, Maryland SMITH, CHARLES, Dept. of Biological Sciences, Stanford VISWAMITRA, M.A., Dept of Physics, Indian Institute of University, California Science, Bangalore, India SOBELL, HENRY M., Dept. of Radiation Biology and Bio- WANG, ANDREW, Dept. of Biology, Massachusetts Insti- physics, University of Rochester School of Medicine, tute of Technology, Cambridge New York WANG, JAMES C., Fairchild Laboratory, Harvard Univer- SOLTIS, DANIEL, Dept. of Biochemistry, Stanford Univer- sity, Cambridge, Massachusetts sity, California WARD, DAVID C., Dept. of Human Genetics, Yale Univer- SPENGLER, SYLVIA; Dept. of Biochemistry, University of sity, New Haven, Connecticut Chicago, Illinois WEBER, PATRICIA, Dept. of Molecular Biophysics and SYMPOSIUM PARTICIPANTS ix

Biochemistry, Yale University, New Haven, Conn- WORMINGTON,MICHAEL, Dept. of Embryology, Carnegie ecticut Institution of Washington, Baltimore, Maryland WEINER, ALAN M., Dept. of Molecular Biophysics, Yale YAGER, LAWRENCE,Dept. of Biology, University of Penn- University School of Medicine, New Haven, Con- sylvania, Philadelphia necticut YAMAMOTO, KEITH R., Dept. of Biochemistry and Bio- WE1NTRAUB, HAL, Fred Hutchinson Cancer Center, Seat- physics, University of California, San Francisco tle, Washington YANAGIDA, M., Dept. of Biophysics, Kyoto University, WEiss, MICHAEL, Dept. of Biochemistry, Harvard Univer- Japan sity, Cambridge, Massachusetts YANIV, MOSHE, Dept. of Molecular Biology, Institut Pas- WEISSMAN, SHERMAN, Dept. of Human Genetics, Yale teur, Paris, France University School of Medicine, New Haven, Con- ZACHAmAS, WOLFGANG,Dept. of Biochemistry, Univer- necticut sity of Wisconsin, Madison WELLS, ROBERT, Dept. of Biochemistry, University of ZA1N, S.C., Dept. of Radiation Biology, University of Alabama, Birmingham Rochester School of Medicine, New York WlTNEY, FRANK, National Institutes of Health, Bethesda, ZARLING, DAVID, Dept. of Biophysical Chemistry, Max- Maryland Planck-Institute, Goettingen, Federal Republic of WOLF, STANLEY,Dept. of Pediatrics, Johns Hopkins Univer- Germany sity Hospital, Baltimore, Maryland ZIMMEm~IAN, STEyEN, NIADDKD, National Institutes of WOLCEMOTH, DEBRA J., Dept. of Human Genetics, Col- Health, Bethesda, Maryland umbia University, New York, New York ZOLAN, MIRIAM, Dept. of Biological Sciences, Stanford WORCEL, ABRAHAM,University of Rochester, New York University, California First row: A. Mirzabekov, M.L. Pardue; G, Felsenfeld, A. Klug, M. Gellert Second row: N. Cozzarelli, F. Tamanoi, C. Fuller; D. Ward, M. Yaniv Third row: C. Cantor, A. Rich; K. Matsubara, R. Sternglanz Fourth row: T. Koller; D. Crothers; H. Doty; S.-H. Kim First row: J. Parries, R. Axel, L. Hood; J. Van Boom, G.V. Gursky Second row: E.N. Trifonov, G. Georgiev; S. Weissman, B. Alberts, B. McClintock, K. Kreuzer Third row: A. Senear, G. Bernardi, M. Weiss, J.G. Brahms; S.G. Clarkson, S.I. Busby, R. Flavell Fourth row: N. Hopkins, D. Chattoraj; H. Sobell, D. Lilley First row: J. Feigon, I. Jackson; Ms. Stasiak, A. Stasiak; J. Abraham Second row: J. Wang; K. Yamamoto; J. Shepherd; T. Schopf; S. Hattman Third row: W. McClare, J. Lebowitz, C. Benham; R. Reeder, J. Hurwitz Fourth row: A. Nordheim, R. Kahmann; D. Daniels, L. Bell; S. Spengler, K. Bloom First row: K. Lowenhaupt; V. Sgaranella; J. Huberman; M. Wormington; R.E. Dickerson Second row: W. Schaffner; H. Berman; J. Dunn; M. Leng Third row: S. Ikuta, M.A. Viswamitra; R. Sauer, W. Jelinek; E.N. Trifonov, B. Stillman; G.P. Tocchini Valentini Fourth row: L. Ripley, B. Alberts, B. Glickman; D. Skinner, A. Klug First row: C. Cantor; M. Caruthers; A.G. Redfield; J. Cairns Second row: J. Miller, G. Bernardi; W. Zacharias, E. Lafer, H. Drew Third row: R. Axel, J. Steitz; C. Schmid, S. Weissman Fourth row: A. Rich, G. Georgiev; T. Steitz, T.J. Richmond First row: Y. Takeda, W. Anderson; P. Chambon, H. Weintraub Second row: J. Van Boom, K. Matsubara, J.D. Watson; S. Hattman, A. Bukhari Third row: F. Pohl, T. Koller; K. Bloom, M. Fitzgerald-Hayes, S. Elgin Fourth row: D. Lilley; D. Kearns, M. Leng Foreword

The double helix is deceptively simple. When first found in 1953, it appeared so beautifully clear that for a brief period it seemed that by mere visual inspection we must learn all its mysteries. Now almost 30 years later, DNA structure is no longer a child's game, and those who play with it must be both experienced and of the courage to seek elegance among the almost overwhelming perturba- tions of its basic double-helical configuration. Not only can DNA be overcoiled or undercoiled, all under strict enzymatic control, it can turn to the left as well as to the right. Since these complexities are not laboratory artifacts but, in fact, provide the molecular underpinnings for the successful functioning of our genetic material, further progress in more firmly establishing the various forms of DNA is likely to be essential for the future of much biological research. The moment thus was propitious for a high-level meeting in which all aspects of DNA could be presented and analyzed. So, for the topic of our 47th annual Symposium, we chose "The Structures of DNA." From the start we realized that the number of speakers was likely to be very large, and so we sought the advice of many experts as to whom to invite. In particular, I wish to acknowledge the invaluable counsel given by Charles Cantor, Pierre Chambon, Don Crothers, Richard Dicker- son, Gary Felsenfeld, , Alex Rich, and Jim Wang. The formal program contained 114 speakers with many additional, last-minute informal presentations made during the course of the various sessions. Given the inherent complexity of the topics, this was indeed a very demanding Symposium. But because of the consistently high quality of the presentations, this Symposium was also felt by virtually all of the 244 participants to rank among the most stimulating of scientific meetings that they had ever attended. Again we were aided by the cheerfully courteous competence of our Meetings Office, and we are indeed fortunate that it is so well staffed by Gladys Kist, Maureen Berejka, and Barbara Ward. Herb Parsons again saw to it that our audio-visual arrangements performed perfectly, unaccom- panied by the frequent upside-down slide projections that often accompany large meetings. The most necessary financial help that let us assemble such a massive program was again pro- vided by the National Institutes of Health, the National Science Foundation, and the Department of Energy. Serving as the coeditors of these transcriptions have been Douglas Owen and Dorothy Brown, assisted in particular by Joan Ebert, Mary Cozza, and Karen Sundin, as well as by our active Publications Department, most ably presided over by Nancy Ford.

October 27, 1982 J.D. Watson

xiii Contents

Part 1

Symposium Participants V Foreword xiii

Introduction Right-handed and Left-handed DNA: Conformational Information in Genetic Material A. Rich

The Handedness of DNA Helix 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 13 Structural Diversity in DNA: From Monomer Structures to Oligonucleotides M. A. Fiswamitra 25 Right-handed and Left-handed Double-helical DNA: Structural Studies A.H.-J. Wang, S. Fujii, J.H. van Boom, and A. Rich 33 Left-handed DNA Duplexes V. Sasisekharan 45 DNA Secondary Structures: Helices, Wrinkles, and Junctions S. Arnott, R. Chandra- sekaran, L H. Hall, L. C. Puigjaner, J. K. Walker, and M. Wang 53 DNA Structures and Transitions: X-Ray Diffraction Studies of Solvated Fibers S.B. Zim- merman and B. H. Pheiffer 67 Left-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 77 DNA Supercoiling and Its Effects on DNA Structure and Function J.C. Wang, L. J. Peck, and K. Becherer 85 Supercoiling and Left-handed Z-DNA A. Nordheim, L. J. Peck, E. M. Lafer, B. D. Stollar, J. C. Wang, and A. Rich 93 Dynamic, Sequence-dependent DNA Structures as Exemplified by Cruciform Extrusion from Inverted Repeats in Negatively Supercoiled DNA D.M.J. Lilley 101 Salt-induced Transition between Two Double-helical Forms of Oligo(dC-dG) F.M. Pohl 113 DNA Formed by Reassociation of Complementary Single-stranded Circles from Natural DNA Is Shown to Contain Left- and Right-handed Double Helices S. Brahms, J. Fergne, J. G. Brahms, E. DiCapua, P. Bucher, and T. Koller 119 Transitions Induced by Metal Complexes among Several Forms of DNA G.L. Eichhorn, Y. A. Shin, and J. J. Butzow 125 Alternative Description of the Transition between B-DNA and Z-DNA R.C. Hopkins 129 Electron Microscopy of "Z-DNA" H. Castleman and B. F. Erlanger 133 Generation 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, 1-1. H. Fdldner, C. Greider, L Grieger, E. Hamori, B. Kalisch, L.P. Mclntosh, and M. Robert-Nicoud 143 Antibody Recognition of Z-DNA E. M. Lafer, A. MbTler, R. P. C. Valle, A. Nordheim, A. Rich, and B. D. Stollar 155 Interactions between Nucleic Acids and Antibodies to Z-DNA M. Leng, B. Hartmann, B. Malfoy, J. Pilet, J. Ramstein, and E. Sage 163 Z-DNA and the Polytene Chromosome M. L. Pardue, A. Nordheim, E. M. Lafer, B. D. Stollar, and A. Rich 171

XV xvi CONTENTS

Conformational Analysis Dynamic Behaviors of DNA Molecules in Solution Studied by Fluorescence Microscopy M. Yanagida, Y. Hiraoka, and L Katsura 177 New Techniques for Purifying Large and Studying Their Properties and Packaging D. C. Schwartz, W. Saffran, J. Welsh, R. Haas, M. Goldenberg, and C. R. Cantor 189 NMR Studies of DNA Conformation and Dynamics in Solution D.J. Patel, S.A. Kozlowski, S. Ikuta, K. Itakura, R. Bhau, and D. R. Hare 197 Application of Multiple-pulse ~H-NMR Techniques to the Study of Two Synthetic DNA Decamers J. Feigon, J. M. Wright, W. A. Denny, W. Leupin, and D. R. Kearns 207 Statistical Mechanical Analysis of Competing Conformational Transitions in Superhelical DNA C. J. Benham 219 Theoretical Probes of DNA Conformation Examining the B--Z Conformational Transition W. K. Olson, A. R. Srinivasan, N. L. Marky, and V. N. Balafi 229 Cooperative Transitions in DNA with No Separation of Strands V.I. lvanov, L.E. Minchenkova, E. E. Minyat, and A. K. Schyolkina 243 Computer Simulation of DNA Double-helix Dynamics M. Levitt 251 Transmission of Long-range Effects in DNA D.M. Crothers and M. Fried 263 Sequence-dependent Variations of B-DNA Structure and Protein-DNA Recognition E. N. Trifonov 271 A Bent Helix in Kinetoplast DNA J.C. Marini, S. D. Levene, D. M. Crothers, and P. T. Englund 279 Helical Periodicity of DNA On and Off the Nucleosome as Probed by Nucleases A. Klug, L. C. Lutter, and D. Rhodes 285

Chemically Modified DNA /3-Kinked DNA--a Structure That Gives Rise to Drug Intercalation and DNA Breathing--and Its Wider Significance in Determining the Premelting and Melting Behavior of DNA H. M. Sobell, T. D. Sakore, S. C. Jain, A. Banerjee, K. K. Bhandary, B. S. Reddy, and E. D. Lozansky 293 Some New Aspects of Actinomycin D-Nucleic Acid Binding F. Takusagawa and H. M. Berman 315 Netropsin Increases the Linking Number of DNA A.D.B. Malcolm and G. Snounou 323 Interactions of Aflatoxin B, and AIkylating Agents with DNA: Structural and Functional Studies J. M. Essigmann, C. L. Green, R. G. Croy, K. W. Fowler, G. H. Biichi, and G. N. Wogan 327 Carcinogens Can Induce Alternate Conformations in Nucleic Acid Structure R.M. Santella, D. Grunberger, and I. B. Weinstein 339 Footprinting with MPE.Fe(II). Complementary-strand Analyses of Distamycin- and Actinomycin-binding Sites on Heterogeneous DNA M. W. Van Dyke and P. B. Dervan 347 Ethidium Bromide Alters the Binding Mode of cis-Diamminedichloroplatinum(II) to pBR322 DNA C. M. Merkel and S. J. Lippard 355 Sharp 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 361 Synthetic 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 367 Altered Structure of Ultraviolet-irradiated DNA" Evidence for Unwinding H.J. Edenberg 379

Chemical Synthesis of DNA Solid-phase Synthesis of Polynucleotides. VIII. A Simplified Synthesis of Oligodeoxy- ribonucleotides Z.-K. Tan, S. Ikuta, T. Haung, A. Dugaiczyk, and K. ltakura 383 Continuous-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 393 Synthesis 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 403 CONTENTS xvii

Chemical Synthesis and Biological Studies on Mutated Gene-control Regions M. H. Caruthers, S. L 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, L 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 k 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 k 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. Melanfon, 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. J. Gehring 483

DNA within Nucleosomes Studies of Nucleosome 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, E. 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. Ozkaynak, 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 Nucleolar Chromatin P. Labhart, 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 Poly[d(G-msC)] F.D. Miller, J. B. Rattner, and J. H. van de Sande 571 xviii CONTENTS 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 DNA A. La Volpe, M. Taggart, D. Macleod, and A. Bird 585 DNA Methylation and Gene Activity: The Adenovirus System as a Model W. Doerfler, L Kruczek, D. Eick, L. Vardimon, and B. Kron 593 Effect of DNA Methylation on 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 Involved in Gene Expression D. Jiihner, C. L. Stewart, H. Stuhlmann, K. Harbers, and R. Jaenisch 611 Implications for X-Chromosome Regulation from Studies of Human X-Chromosome DNA S. F. Wolf and B. R. Migeon 621 DNA Methylation and Control of Gene Expression on the Human X Chromosome L. J. Shapiro and T. Mohandas 631 Methylation Regulates the Expression of a DNA-modification Function Encoded by Bacteriophage Mu R. Kahmann 639 Regulation of the DNA-modification Function of Bacteriophage Mu S. Hattman, M. Goradia, C. Monaghan, and A. I. Bukhari 647

DNA Replication Studies on DNA Replication in the Bacteriophage 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 Bacteriophage T7 DNA Replication C. W. Fuller, B. B. Beauchamp, M. J. Engler, R. L. Lechner, S. IV. Matson, S. Tabor, J. H. White, and C. C. Richardson 669 Replication of Bacteriophage )~ DNA T. Tsurimoto and K. Matsubara 681 Enzymatic Recognition of DNA Replication Origins M. M. Stayton, L. Bertsch, 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 ~bX174 A Protein-directed Initiation and Termination of DNA Replication D. R. Brown, D. Reinberg, T. Schmidt-Glenewinkel, M. Roth, S. L. Zipursky, and J. Hurwitz 701 Signals for the Initiation and Termination of Synthesis of the Viral Strand of Bacteriophage fl G. P. Dotto, K. Horiuchi, K. S. Jakes, and N. D. Zinder 717 Structure and Replication of Vaccinia Virus Telomeres B. M. Baroudy, S. Venkatesan, and B. 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-I Topoisomerases: Identification, Mechanism, and Role in Recombina- tion F. Dean, M. A. Krasnow, R. Otter, M. M. Matzuk, S. J. Spengler, and N. R. Cozzarelli 769 Escherichia coli DNA Topoisomerase I Mutants Have Compensatory Mutations at or near DNA Gyrase Genes S. DiNardo, K. A. Voelkel, R. Sternglanz, A. E. Reynolds, and A. Wright 779 CONTENTS xix

Loss of DNA Topoisomerase I Activity Alters Many Cellular Functions in Salmonella typhimurium K. M. Overbye, S. K. Basu, and P. Margolin 785 DNA Supercoiling: Changes during Cellular Differentiation and Activation of Chromatin Transcription A. N. Luchnik, V. V. Bakayev, and V. M. Glaser 793

Recombining and Mutating DNA DNA Strand Exchange Promoted by recA Protein and Single-stranded DNA-binding Protein of Escherichia coli M. M. Cox, D. A. Soltis, Z. Livneh, and L R. Lehman 803 Unwinding of Duplex DNA in Complexes with recA Protein A. Stasiak, E. DiCapua, and T. Koller 811 Three Phases in Homologous Pairing: Polymerization of recA Protein on Single-stranded DNA, Synapsis, and Polar Strand Exchange C. M. Radding, J. Flory, A. Wu, R. Kahn, C. DasGupta, D. Gonda, M. Bianchi, and S.S. Tsang 821 Homologous Association of Chromosomal DNA during Yeast Meiosis L.R. Bell and B. Byers 829 Analysis of Spontaneous Deletions and Gene Amplification in the lac Region of Escherichia coli A. M. Albertini, M. Hofer, M. P. Calos, T. D. Tlsty, and J. H. Miller 841 Unique Self-complementarity of Palindromic Sequences Provides DNA Structural Inter- mediates for Mutation L. S. Ripley and B. W. Glickman 851 A Directed-mutagenesis Method for the Analysis of Ultraviolet-induced Mutagenesis Z. Livneh 863

Transcription of DNA and Its Regulation Evidence for Two Functional Regions in the Xenopus laevis RNA polymerase I Promoter R. H. Reeder, J. Wilkinson, A. Bakken, G. Morgan, S. J. Busby, J. Roan, and B. Sollner-Webb 867 DNA Conformation and Transcription Initiation of Eukaryotic tRNA Genes R.A. Hipskind, A. Mazabraud, J. Corlet, and S. G. Clarkson 873 Developmental Regulation of Xenopus 5S RNA Genes W.M. Wormington, M. Schlissel, and D. D. Brown 879 Role of tRNA Gene Structure in Transcription and Processing G.P. Tocchini-Valentini, E. Mattoccia, M. I. Baldi, R. Ogden, and G. Pande 885 Small Ribonucleoproteins from Eukaryotes: Structures and Roles in RNA Biogenesis J. A. Steitz, S. L. Wolin, J. Rinke, L Pettersson, S. M. Mount, E. A. Lerner, M. Hinterberger, and E. Gottlieb 893 Promoter Elements, Regulatory Elements, and Chromatin Structure of the Yeast his3 Gene K. Struhl 901 Analysis of the Transcriptional Enhancer Effect J. de Villiers, L. Olson, J. Banerji, and W. Schaffner 911 Potentiator Effect of the SV40 72-bp Repeat on Initiation of Transcription from Heterologous Promoter Elements B. Wasylyk and P. Chambon 921 Structure and Function of the Promoter-Enhancer Region of Polyoma and SV40 S. Cereghini, P. Herbomel, J. Jouanneau, S. Saragosti, M. Katinka, B. Bourachot, B. de Crombrugghe, and M. Yaniv 935 Constitutive Transcriptional Control Signals of the Herpes Simplex Virus tk Gene S.L. McKnight 945 Appendix: Transcription of Circular and Linear DNA in Amphibian Oocytes R. M. Harland, H. Weintraub, and S. L. McKnight 958 Interaction of Eukaryotic Class-B Transcription Factors and Chick Progesterone-Receptor Complex with Conalbumin Promoter Sequences B. L. Davison, E. R. Mulvihill, J. M. Egly, and P. Chambon 965 Biological Activity of Cloned Mammary Tumor Virus DNA Fragments That Bind Purified Glucocorticoid Receptor Protein In Vitro K. R. Yamamoto, F. Payvar, G. L. Firestone, B. A. Maler, (). Wrange, J. Carlstedt-Duke, J.,4. Gustafsson, and V. L. Chandler 977 DNA Sequences Required for Hormonal Induction of Rat a2~-globulin Genes D.T. Kurtz, L. McCullough, D. K. Bishop, and M. M. Manos 985 xx CONTENTS

Sites Required for Position-Effect Regulation of Mating-type Information in Yeast J. Abraham, J. Feldman, K. A. Nasmyth, J. N. Strathern, A. J. S. Klar, J. R. Broach, and J. B. Hicks 989

The Organization of Genes along DNA Organization and Expression of Bacteriophage T7 DNA F. IV. Studier and J. J. Dunn 999 Features of Bacteriophage k: Analysis of the Complete Nucleotide Sequence D.L. Daniels, F. Sanger, and A. R. Coulson 1009 Information Content of the Adenovirus-2 R.J. Roberts, D. Sciaky, R. E. Gelinas, B.-D. Jiang, C. E. Yen, M. M. Kelly, P. A. Bullock, B. L. Parsons, K. E. O'Neill, and T. R. Gingeras 1025 Procollagen Genes: Further Sequence Studies and Interspecies Comparisons V. Tate, M. Finer, H. Boedtker, and P. Doty 1039 Genes of the Major Histocompatibility Complex L. Hood, M. Steinmetz, R. Goodenow, K. Eakle, D. Fisher, J. Kobori, B. Malissen, M. Malissen, M. McMillan, J. McNicholas, A. Orn, M. Pecht, B. T. Sher, L. Smith, I. Stroynowski, H. Sun, A. Winoto, and M. Zuniga 1051 Structure and Expression of the Human Globin Genes and Murine Histocompatability Antigen Genes R. A. Flavell, F. Grosveld, M. Busslinger, E. de Boer, D. Kioussis, A. L. Mellor, L. Golden, E. Weiss, J. Hurst, H. Bud, H. Bullman, E. Simpson, R. James, A. R. M. Townsend, P. M. Taylor, W. Schmidt, J. Ferluga, L. Leben, M. Santamaria, G. Atfield, and H. Festenstein 1067 Sequences of Human Repetitive DNA, Non-ct-globin Genes, and Major Histocompatibility Locus Genes I. Repeated-sequence DNA Y. Fukumaki, F. Collins, R. Kole, C. J. Stoeckert, Jr., P. Jagadeeswaran, C. H. Duncan, and S. M. Weissman 1079 II. Sequences of Non-~-globin Genes in Man P. Jagadeeswaran, J. Pan, B.G. Forget, and S. M. Weissman 1081 III. The Major Histocompatibility Complex P. A. Biro, J. Pan, A. K. Sood, R. Kole, V. B. Reddy, and S. M. Weissman 1082 Codon Usage and Transfer RNA Contents: Organism-specific Codon-choice Patterns in Reference to the Isoacceptor Contents T. lkemura and H. Ozeki 1087 From Primeval Message to Present-day Gene J.C.W. Shepherd 1099

Repetitive DNA and Pseudogenes Dispersed Repetitive Sequences in Eukaryotic and Their Possible Biological Significance G. P. Georgiev, D. A. Kramerov, A. P. Ryskov, K. G. Skryabin, and E. M. Lukanidin 1109 The Mammalian Alu Family of Dispersed Repeats W. R. Jelinek and S. R. Haynes 1123 Alu Family Members in the Human s-like Globin-gene Cluster G.M. Fox, J. F. Hess, C.-K. J. Shen, and C. W. Schmid 1131 Genome Alteration during In Vitro and In Vivo Aging: Amplification of Extrachromosomal Circular DNA Molecules Containing a Chromosomal Sequence of Variable Repeat Fre- quency R. J. Shmookler Reis, C. K. Lumpkin, Jr., J. R. McGill, K. T. Riabowol, and S. Goldstein 1135 Either Gene Amplification or Gene Conversion May Maintain the Homogeneity of the Multigene Family Encoding Human UI Small Nuclear RNA A.M. Weiner and R. A. Denison 1141 Sites of Divergence in the Sequence of a Complex Satellite DNA and Several Cloned Variants D. M. Skinner, V. Bonnewell, and R. F. Fowler 1151 DNA Structures: The Fourth Approach to Comparative Biology T.J.M. Schopf 1159

Origins of Replication, Centromeres, and Telomeres Localization and Sequence Analysis of Yeast Origins of DNA Replication J.R. Broach, Y.-Y. Li, J. Feldman, M. Jayaram, J. Abraham, K. A. Nasmyth, and J. B. Hicks 1165 CONTENTS xxi

Structural Analysis and Sequence Organization of Yeast Centromeres K.S. Bloom, M. Fitzgerald-Hayes, and J. Carbon 1175 Replication and Resolution in Telomeres in Yeast J.W. Szostak 1187 DNA Termini in Ciliate Macronuclei E. H. Blackburn, M. L. Budarf, P. B. Challoner, J. M. Cherry, E. A. Howard, A. L. Katzen, W.-C. Pan, and T. Ryan 1195 Chromosomal Structure and Arrangement of Repeated DNA Sequences in the Telomeric Heterochromatin of Secale cereale and Its Relatives J. D. G. Jones and R.B. FlaveU 1209

Summary Structures of DNA A. Klug 1215

Author Index 1225 Su~ect Index 1229 COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY

VOLUME XLVII--PART 2