Contents


Symposium Participants    vii

Foreword    xix



Introduction

The DNA Enzymology of Protein Machines B.M. Alberts    1



Chromosomal Mechanics

Origins of Gene Conversion and Reciprocal Exchange in Ascobolus J.-L. Rossignol, A. Nicholas, H. Hamza, and T. Langin    13

Meiotic Roles of Crossing-over and of Gene Conversion A. T. C. Carpenter    23

Interallelic and Intergenic Conversion in Three Serine tRNA Genes of Schizosac- charomyces pombe J. Kohli, P. Munz, R. Aebi, H. Amstutz, C. Gysler, W. -D. Heyer, L. Lehmann, P. Schuchert, P. Szankasi, P. Thuriaux, U. Leupold, J. Bell, V. Gamulin, H. Hottinger, D. Pearson, and D. Söll    31

Recombination in Saceharomyces cerevisiae: REC-gene Mutants and DNA-binding Proteins M. S. Esposito, J. Hosoda, J. Golin, H. Moise, K. Bjornstad, and D. Maleas    41

Measurement of Restoration and Conversion: Its Meaning for the Mismatch Repair Hypothesis of Conversion P. J. Hastings    49



Yeast Systems

Meiotic Gene Conversion Mediates Gene Amplification in Yeast S. Fogel, J. W. Welch, and E.J. Louis    55

Physical Monitoring of Meiotic Recombination in Saccharomyces cerevisiae R.H. Borts, M. Lichten, M. Hearn, L.S. Davidow, and J.E. Haber    67

Involvement of Double-strand Chromosomal Breaks for Mating-type Switching in Saccharomyces cerevisiae A.J.S. Klar, J.N. Strathern, and J.A. Abraham    77

The Product of the HO Gene Is a Nuclease: Purification and Characterization of the Enzyme R. Kostriken and F. Heifron    89

Directionality and Regulation of Cassette Substitution in Yeast R.E. Jensen and I. Herskowitz    97

The Role of DNA Replication in the Repression of the Yeast Mating-type Silent Loci A.M. Miller, R. Sternglanz, and K.A. Nasmyth    105

Kinetics and Intermediates of Yeast Mitochondrial DNA Recombination A.R. Zinn and R.A. Butow    115



Mammalian Homologous Recombination

Analysis of Homologous Recombination in Cultured Mammalian Cells K. Folger, K. Thomas, and M.R. Capecchi    123

Homologous Recombination in Mouse L Cells F.-L. Lin, K. Sperle, and N. Stern- berg    139

The Recombination and Integration of DNAs Introduced into Mouse L Cells D.A. Brenner, S. Kato, R.A. Anderson, A.C. Smigocki, and R.D. Camerini-Otero    151

Homologous Recombination with DNA Introduced into Mammalian Cells O. Smi- thies, M.A. Koralewski, K.-Y. Song, and R.S. Kucherlapati    161

Homologous Recombination between Defective neo Genes in Mouse 3T6 Cells A.J.H. Smith and P. Berg    171

Homologous Recombination between Repeated Chromosomal Sequences in Mouse Cells R.M. Liskay, J.L. Stachelek, and A. Letsou    183

Homologous Recombination in Monkey Cells and Human Cell-free Extracts R. S. Kucherlapati, D. Ayares, A. Hanneken, K. Noonan, S. Rauth, J.M. Spencer, L. Wallace, and P.D. Moore    191



Transposons

Origin of Cryptic l Prophages in Escherichia coli K-12 R.J. Redfield and A.M. Campbell    199

Functional Difference of the Two Ends of Insertion Sequence IS1 in Transposition and Cointegration K. Ishizaki and E. Ohtsubo    207

Transposon Tn5: Specific Sequence Recognition and Conservative Transposition D.E. Berg, J. Lodge, C. Sasakawa, D.K. Nag, S.H. Phadn is, K. Weston-Hafer, and G.F. Cane    215

Site-specific Recombination in Transposition and Plasmid Stability D. Sherratt, P. Dyson, M. Boocock, L. Brown, D. Summers, G. Stewart, and P. Chan    227

Mechanism and Regulation of Tnl0 Transposition N. Kieckner, D. Morisato, D. Roberts, and J. Bender    235

Resolvase-mediated Recombination Intermediates Contain a Serine Residue Co- valently Linked to DNA R.R. Reed and C.D. Moser    245

Replicative and Conservative Transpositional Recombination of the Insertion Sequences T.A. Weinert, K. Derbyshire, F.M. Hughson, and N.D.F. Grindley    251



Mu

Mapping and Properties of the gam and sot Genes of Phage Mu: Their Possible Roles in Recombination J. Akroyd, B. Barton, P. Lund, S. Maynard Smith, K. Sul tana, and N. Symonds    261

Analysis of the Regulation of the Transposition Functions of Bacteriophage Mu by Using Gene Fusions T.A. Patterson, K.A. Martin, and A.I. Bukhari    267

Nonreplicative DNA Transposition: Integration of Infecting Bacteriophage Mu R.M. Harshey    273

Transposition of Bacteriophage Mu DNA: Expression of the A and B Proteins from lPL and Analysis of Infecting Mu DNA G. Chaconas, G. Gloor, J.L. Miller, D.L. Kennedy, E.B. Giddens, and C.R. Nagainis    279

Substrate and Enzyme Requirements for In Vitro Site-specific Recombination in Bac- teriophage Mu R. Kahmann, F. Rudt, and G. Mertens    285

Inversion of DNA In Vivo and In Vitro by Gin and Pin Proteins R.H.A. Plasterk and P. van de Putte    295

Comparative Analysis of Invertible DNA in Phage Genomes D. Kamp, E. Kardas, W. Ritthaler, R. Sandulache, R. Schumucker, and B. Stern    301

Programming of DNA Rearrangements Involving Mu Phrophages J.A. Shapiro and P.M. Brinkley    313



Plant Transposons/T4 Recombination

Endogenous Transposable Elements Associated with Virus Infection in Maize S.L. Dellaporta, P.S. Chomet, J.P. Mottinger, J.A. Wood, S.-M. Yu, and J.B. Hicks    321

Transposable Elements Ac and Ds at the Shrunken, Waxy, and Alcohol Dehydroge- nase 1 Loci in Zea mays L U. Courage, H.-P. Döring, W.-B. Frommer, R. Kunze, Laird, A. Merckelbach, M. Muller-Neumann, J. Riegel, P. Starlinger, E. Till- mann, E. Weck, W. Werr, and J. Yoder    329

Isolation of Spin Controlling Elements from Maize N. Fedoroff, M. Shure, S. Kelly, M. Johns, D. Furtek, J. Schiefelbein, and O. Nelson    339

Insertion and Excision of Ds Controlling Elements in Maize W. J. Peacock, E. S. Dennis, W.L. Gerlach, M.M. Sachs, and D. Schwartz    347

Transposable Elements in Antirrhinum majus and Zea mays H. Saedler, U. Bonas, A. Gierl, B.J. Harrison, R.B. Klösgen, E. Krebbers, P. Nevers, P.A. Peterson, Z. Schwarz-Sommer, H. Sommer, K. Upadhyaya, and U. Wienand    355

The Use of Affinity Chromatography to Study Proteins Involved in Bacteriophage T4 Genetic Recombination T. Formosa and B.M. Alberts    363

On the Role of DNA Replication, Endonuclease VII, and rII Proteins in Processing of Recombinational Intermediates in Phage T4 G. Mosig, M. Shaw, and G.M. Garcia    371



Topoisomerase, Resolvase, and Gyrase

A Topological Treatment of Recombination and Topoisomerases N.R. Cozzarelli, M.A. Krasnow, S.P. Gerrard, and J.H. White    383

Nonhomologous Recombination Mediated by Escherichia coli DNA Gyrase: Possible Involvement of DNA Replication H. Ikeda and M. Shiozaki    401

The Cleavage of DNA by Type-I DNA Topoisomerases K. Kirkegaard, G. Pflug- felder, and J. C. Wang    411

Site-specific Recombination in the oriV1 Region of the F Factor M.B. O'Connor and M.H. Malamy    421

DNA Structural Features That Lead to Strand Breakage by Eukaryotic Type-I Topoisomerase J.J. Champoux, W.K. McCoubrey, Jr., and M.D. Been    435



Escherichia coli General Recombination

Host Functions in Amplification/Deamplification of Tn9 in Escherichia coli K-12: A New Model for Amplification S.K. Mahajan, N.N. Pandit, and J.F. Sarkari    443

Genes of the RecE and RecF Pathways of Conjugational Recombination in Esche- richia coli A.J. Clark, S.J. Sandler, K.D. Willis, C.C. Chu, M.A. Blanar, and S. T. Lovett    453

Purification and Characterization of Exonuclease V from Escherichia coli K- 12 C. C. Dykstra, K.M. Palas, and S.R. Kushner    463

Genetic Analysis and Regulation of Inducible Recombination in Escherichia coli K- 12 S.M. Picksley, R.G. Lloyd, and C. Buckman    469

RecF and RecBC Function during Recombination of Nonreplicating, UV-irradiated Phage l DNA and during Other Recombination Processes J.B. Hays, T.A. G. Smith, S.A. Friedman, F. Lee, and G.L. Coffman    475

Roles of RecBC Enzyme and Chi Sites in Homologous Recombination G.R. Smith, S.K. Amundsen, A.M. Chaudhury, K.C. Cheng, A.S. Ponticelli, C.M. Roberts, D. W. Schultz, and A.F. Taylor    485

The Mechanism of the Chi-cos Interaction in RecA-RecBC-mediated Recombination in Phage l I. Kobayashi, M.M. Stahl, and F. W. Stahl    497



RecA

A Model for the Core Structure of the Escherichia coli RecA Protein M.A. Blanar, D. Kneller, A.J. Clark, A.E. Karu, F.E. Cohen, R. Lan gridge, and I.D. Kuntz    507

Intermediates in Homologous Pairing Promoted by RecA Protein and Correlations of Recombination In Vitro and In Vivo S.S. Flory, J. Tsang, K. Muniyappa, M. Bianchi, D. Gonda, R. Kahn, F. Azhderian, C. Egner, S. Shaner, and C.M Radding    513

Unidirectional Branch Migration Promoted by Nucleoprotein Filaments of RecA Pro- tein and DNA M.M. Cox, S. W. Morrical, and S.K. Neuendorf    525

Studies of the Mechanism of DNA Pairing by the RecA Protein of Escherichia coli F.R. Bryant, P. W. Riddles, and I.R. Lehman    535

Roles of Processive Unwinding in Recombination Reactions Promoted by RecA Pro- tein of Escherichia coli: A Study Using a Monoclonal Antibody T. Shibata, O. Makino, S. Ikawa, T. Ohtani, M. Iwabuchi, Y. Shibata, H. Maeda, and T. Ando    541

Visualization of SSB-ssDNA Complexes Active in the Assembly of Stable RecA-DNA Filaments J.D. Griffith, L.D. Harris, and J. Register III    553

Visualization of RecA-DNA Complexes Involved in Consecutive Stages of an In Vitro Strand Exchange Reaction A. Stasiak, A. Z. Stasiak, and T. Koller    561

Molecular Mechanisms of General Genetic Recombination: The DNA-binding Sites of the RecA Protein P. Howard-Flanders, S.C. West, J.R. Rusche, and E.H. Egel- man    571



Repair

Studies of HeLa DNA Polymerases during Excision-repair In Vitro with DNA and Chromatin Substrates D. W. Mosbaugh, D.H. Evans, and S. Linn    581

Repair of DNA Base-pair Mismatches in Extracts of Escherichia coli A -L. Lu, K. Welsh, S. Clark, S.-S. Su, and P. Modrich    589

The mutH, mutL, mutS, and uvrD Genes of Salmonella typhimurium LT2 P.P. Pang, S. -D. Tsen, A .S. Lundberg, and G. C. Walker    597

An Escherichia coli Cell-free System That Catalyzes the Repair of Symmetrically Methylated Heteroduplex DNA R.A. Fishel and R. Kolodner     Involvement of Escherichia coil Mismatch Repair in DNA Replication and Recombination R. Wagner, C. Dohet, M. Jones, M. -P. Doutriaux, F. Hutch- inson, and M. Radman    611

Formation of Inverted Dimer Plasmids after Transformation of Yeast with Linearized Plasmid DNA S. Kunes, D. Botstein, and M. S. Fox    617

Double-strand-break Repair, Gene Conversion, and Postdivision Segregation R. Roth- stein    629



Eukaryotic Enzymes

Changes in the Chromosomal DNA of Yeast during Meiosis in Repair Mutants and the Possible Role of a Deoxyribonuclease M.A. Resnick, T. Chow, J. Nitiss, and J. Game    639

Integrative Recombination-A Role for the Retroviral Reverse Transcriptase A.M. Skalka, G. Duyk, M. Longiaru, P. DeHaseth, R. Terry, and J. Leis    651

Endonuclease J: A site-specific Endonuclease Cleaving Immunoglobulin Genes S. Kondo, T. Kataoka, M. Nishi, M. Kodaira, S. Takeda, and T. Honjo    661

Biochemical Characterization of recI Mutants and the Genetics Control of Recombi- nation in Ustilago maydis R. Holliday, S. Y. Taylor, E.B. Kmiec, and W.K. Hol- loman    669

Homologous Pairing Promoted by Ustilago Red Protein F. Kmiec, P. Kroeger, R. Holliday, and W. Holloman    675

Poly(ADP-ribosylation) of DNA Topoisomerase I: A Nuclear Response to DNA-strand Interruptions A .M. Ferro, M. C. McElwain, and B.M. Olivera    683



Integration and Excision of Bacteriophage

Primary Structure and the himA Gene of Escherichia coli: Homology with DNA-bind- ing Protein HU and Association with the Phenylalanyl-tRNA Synthetase Operon H.I. Miller    691

DNA Interactions during Bacteriophage l Site-Specific Recombination C.E. Bauer, S.D. Hesse, J.F. Gardner, and R.I. Gumport    699

Site-specific Recombination Systems of Phages f 80 and P22: Binding Sites of Integra- tion Host Factor and Recombination-induced Mutations J. Leong, S. Nunes- Duby, A. Oser, C. Lesser, P. Youderian, M.M. Susskind, and A. Landy    707

Enzymes and Sites of Genetic Recombination: Studies with Gene-3 Endonuclease of Phage T7 and with Site-affinity Mutants of Phage l B. de Massy, F. W. Studier, L. Dorgai, E. Appelbaum, and R.A. Weisberg    715

The Role of Specialized Nucleoprotein Structures in Site-specific Recombination and Initiation of DNA Replication H. Echo Is, M. Dodson, M. Better, J.D. Roberts, and R. McMacken    727

l Integrative Recombination: Supercoiling, Synapsis, and Strand Exchange P. Kitts, E. Richet, and H.A. Nash    735

Quantitative Analysis of the Contributions of Enzyme and DNA to the Structure of l Integrative Recombinants S.J. Spengler, A. Stasiak, A.Z. Stasiak, and N.R. Cozzarelli    745



Site-specific Recombination

In Vitro Analysis of Hin-mediated Site-specific Recombination R. C. Johnson, M.B. Bruist, M.B. Glaccum, and M.L Simon    751

The Nature of the Interaction of the P1 Recombinase Cre with the Recombining Site loxP R. Hoess, K. Abremski, and N. Sternberg    761

The Bacteriophage P1 Site-specific Recombinase Cm: Recombination Events and DNA Recognition Sequences S. Jida, H. Huber, R. Hiestand-Nauer, J. Meyer, T.A. Bickle, and W. Arber    769

Components of the Site-specific Recombination System Encoded by the Yeast Plasmid 2-micron Circle M. McLeod, F. Volkert, and J. Broach    779

In Vitro Systems for Genetic Recombination of the DNAs of Bacteriophage T7 and Yeast 2-micron Circle P.D. Sadowski, D.D. Lee, B.J. Andrews, D. Babineau, L. Beatty, M.J. Morse, G. Proteau, and D. Vetter    789

Site-Specific Genetic Recombination Promoted by the FLP Protein of the Yeast 2- micron Plasmid In Vitro L. Meyer-Leon, J.F. Senecoff, R. C. Bruckner, and M.M. Cox    797



Recombination in Vitro

Genetic Recombination Catalyzed by Cell-free Extracts of Saccharomyces cerevisiae L.S. Symington, P. T. Morrison, and R. Kolodner    805

Resolution of Holliday Structures by Endonuclease VII As Observed in Interactions with Cruciform DNA B. Kemper, F. Jensch, M. v. Depka-Prondzynski, H.-J. Fritz, U. Borgmeyer, and K. Mizuuchi    815

On the Mu Repressor and Early DNA Intermediates of Transposition H.M. Krause and N.P. Higgins    827

The Mechanism of Transposition of Bacteriophage Mu K. Mizuuchi, M. Mizuuchi, and R.. Craigie    835



Summary

Types of Recombination: Common Problems and Common Strategies A. Campbell    839