Vectors (eBook)

Front Cover 1
Vectors: A Survey of Molecular Cloning Vectors and Their Uses 6
Copyright Page 7
Table of Contents 11
CONTRIBUTORS 8
PREFACE 14
PART I: Bacterial Cloning Vectors 16
General Cloning Vectors for Gram-Negative Bacteria 18
Chapter 1. The Plasmid, pBR322 20
1.1 CRITERIA FOR PLASMID VECTOR DESIGN 21
1.2 CONSTRUCTION AND STRUCTURE 21
1.3 TRANSCRIPTIONAL SIGNALS 30
1.4 DNA REPLICATION 32
1.5 RECOMBINATION 36
1.6 MOBILIZATION 37
1.7 PLASMID STABILITY 38
1.8 DNA TOPOLOGY 38
1.9 pBR322 AND ITS DISADVANTAGES 41
1.10 OTHER GENERALIZED CLONING PLASMIDS FOR GRAM-NEGATIVE BACTERIA 43
1.11 DESIGNING FUTURE MOLECULAR CLONING VECTORS 43
REFERENCES 52
Chapter 2. Bacteriophage Lambda Cloning Vectors 58
2.1 OVERVIEW OF LAMBDA BACTERIOPHAGE REPLICATION 58
2.2 LAMBDA VECTORS FOR CLONING 10- TO 20-kb DNA FRAGMENTS 64
2.3 LAMBDA VECTORS FOR CLONING 0- TO 10-KB LONG INSERTS (cDNA) 70
REFERENCES 74
Chapter 3. Filamentous Phages as Cloning Vectors 76
3.1 VIRION STRUCTURE AND INFECTION CYCLE 76
3.2 SPECIAL CONSIDERATIONS IN DESIGN AND USE OF FILAMENTOUS PHAGE VECTORS 80
3.3 SURVEY OF FILAMENTOUS PHAGE VECTORS 87
3.4 SURVEY OF THE USES OF Ff PHAGE VECTORS 91
3.5 SUMMARY 96
REFERENCES 97
Chapter 4. Chimeric Single-Stranded DNA Phage-Plasmid Cloning Vectors 100
4.1 FILAMENTOUS PHAGE BIOLOGY AND DEVELOPMENT OF PHAGEMID CLONING VECTORS 101
4.2 APPLICATIONS, ADVANTAGES, AND DISADVANTAGES OF ssDNA PHAGEMID VECTORS 102
4.3 BASIC PHAGEMID CLONING VECTORS 104
4.4 MULTIFUNCTIONAL PHAGEMID CLONING VECTORS 110
4.5 INTERGENIC REGION CASSETTE PLASMID SIMPLIFICATION OF PHAGEMID CLONING VECTOR CONSTRUCTION 112
4.6 HELPER PHAGES FOR OBTAINING ssDNA FROM PHAGEMID VECTORS 113
4.7 SUMMARY 115
REFERENCES 115
Chapter 5. Phage-Plasmid Hybrid Vectors 118
5.1 f1-ColE1 HYBRIDS 119
5.2 pEMBL PLASMIDS 119
REFERENCES 126
Chapter 6. Cosmids 128
6.1 COSMID VECTORS 129
6.2 LIBRARY CONSTRUCTION 129
6.3 COSMID RESCUE 135
6.4 SUMMARY AND PROSPECTS 140
REFERENCES 140
Specialized Cloning Vectors for Gram-Negative Bacteria 144
Chapter 7. Plasmid Positive Selection Vectors 146
7.1 POSITIVE SELECTION VECTORS ENCODING A KILLING FUNCTION OF BACTERIOPHAGE ORIGIN 149
7.2 POSITIVE SELECTION VECTORS USING PLASMIDENCODED LETHAL FUNCTION 150
7.3 POSITIVE SELECTION VECTORS ENCODING THE EcoRl RESTRICTION ENDONUCLEASE 153
7.4 INACTIVATION OF DOMINANT FUNCTIONS CONFERRING CELL SENSITIVITY TO METABOLITES 155
7.5 POSITIVE SELECTION VECTORS USING DEREPRESSION OF AN ANTIBIOTIC RESISTANCE FUNCTION 158
7.6 POSITIVE SELECTION BY LOSS OF SENSITIVITY TO STREPTOMYCIN 161
7.7 LETHALITY OF PALINDROMIC DNA SEQUENCES AND THEIR USE IN POSITIVE SELECTION VECTORS 161
7.8 SELECTION FOR LOSS OF ANTIBIOTIC RESISTANCE 162
7.9 CONCLUSION 164
REFERENCES 165
Chapter 8. Vectors for Cloning Promoters and Terminators 168
8.1 PROMOTER-CLONING DERIVATIVES OF pACYC177 AND pACYC184 EMPLOYING ACTIVATION OF ANTIBIOTIC RESISTANCE 170
8.2 PROMOTER- AND TERMINATOR-CLONING PLASMID VECTORS EMPLOYING THE ESCHERICHIA COLI ß-GALACTOSIDASE STRUCTURAL GENE 172
8.3 PROMOTER-CLONING DERIVATIVES OF pBR316 and pBR322 EMPLOYING ACTIVATION OF ANTIBIOTIC RESISTANCE 176
8.4 PROMOTER- AND TERMINATOR-CLONING VECTORS EMPLOYING THE E. COLI/ GALACTOKINASE STRUCTURAL GENE 181
8.5 PROMOTER- AND TERMINATOR-CLONING PLASMIDS EMPLOYING OTHER STRUCTURAL GENES 184
8.6 PLASMIDS FOR ANALYZING DIVERGENTLY ARRANGED PROMOTERS 188
8.7 BROAD GRAM-NEGATIVE HOST RANGE PROMOTERAND TERMINATOR-CLONING PLASMID VECTORS 188
8.8 CONCLUSION 190
REFERENCES 190
Chapter 9. A Survey of Vectors for Regulating Expression of Cloned 194
9.1 THE trp PROMOTER 195
9.2 THE lac PROMOTER 197
9.3 THE tac PROMOTER 202
9.4 THE LAMBDA PROMOTERS 202
9.5 OTHER REGULATABLE PROMOTERS 207
9.6 SECRETION VECTORS 210
9.7 PROTEIN FUSION VECTORS 212
REFERENCES 214
Chapter 10. Expression Vectors Employing Lambda-, trp-, lac-, and lpp-Derived Promoters 220
10.1 GENERAL CONSIDERATIONS 220
10.2 EXPRESSION VECTOR PROMOTERS 227
10.3 CONCLUSION 236
REFERENCES 237
Chapter 11. Vectors with Adjustable Copy Numbers 242
11.1 RATE-LIMITING STEPS OF PROTEIN PRODUCTION 242
11.2 PROMOTERS AND RIBOSOME BINDING SITES 243
11.3 COPY NUMBER AND PROTEIN PRODUCTION 243
11.4 ADJUSTABLE COPY NUMBER VECTORS 245
11.5 FUTURE EXPRESSION VECTORS 249
REFERENCES 250
Chapter 12. Specialized Plasmid Vectors for Cloning cDNA 252
12.1 OLIGONUCLEOTIDE PRIMING OF cDNA SYNTHESIS 252
12.2 VECTOR PRIMING OF cDNA SYNTHESIS 254
REFERENCES 265
Chapter 13. Vectors for the Synthesis of Specific RNAs in Vitro 268
13.1 BACTERIOPHAGE-ENCODED RNA POLYMERASES 269
13.2 VECTORS CONTAINING T7 OR SP6 PROMOTERS 270
13.3 ALTERNATIVES TO PHAGE-SPECIFIED RNA POLYMERASES 273
13.4 SYNTHESIS OF SINGLE-STRANDED RNA PROBES 274
13.5 SYNTHESIS OF RNA SUBSTRATES 276
13.6 SYNTHESIS OF mRNA TEMPLATES IN VITRO 277
13.7 DNA SEQUENCING WITH PROMOTER VECTORS 278
13.8 CONSTRUCTION AND SCREENING OF cDNA LIBRARIES 279
13.9 SYNTHESIS OF ANTI-mRNA 279
REFERENCES 280
Chapter 14. Improved Suppressor tRNA Cloning Vectors and Plasmid- Phage Recombination 284
14.1 IMPROVED SUPPRESSOR PLASMIDS AND HOSTS 285
14.2 DEVELOPMENTS IN THE LIBRARY RECOMBINATION SYSTEM 292
REFERENCES 297
Cloning Vectors with Broad-Host-Range Capability 300
Chapter 15. Broad-Host-Range Plasmid Cloning Vectors for Gram-Negative Bacteria 302
15.1 BASIC PROPERTIES OF BROAD-HOST-RANGE PLASMID ELEMENTS 303
15.2 VECTOR DEVELOPMENT 309
15.3 COSMID VECTORS 325
15.4 GENE FUSION VECTORS 334
15.5 GENE CLONING WITH BROAD-HOST-RANGE VECTORS 337
15.6 SUMMARY AND OUTLOOK 340
REFERENCES 341
Chapter 16. Specialized Vectors for Members of Rhizobiaceae and Other Gram-Negative Bacteria 348
16.1 STABLE RHIZOBIACEAE-SPECIFIC COSMID VECTORS 350
16.2 STABLE HIGH-COPY-NUMBER VECTORS FOR USE IN RHIZOBIACEAE 352
16.3 POSITIVE SELECTION OF CLONED FRAGMENTS USING THE LEVANSUCRASE GENE 354
REFERENCES 356
Cloning Vectors for Gram-Positive Bacteria 358
Chapter 17. Generalized Cloning Vectors for Bacillus subtilis 360
17.1 PLASMID VECTORS 360
17.2 BACTERIOPHAGE VECTORS 366
17.3 OTHER APPROACHES TO CLONING B. SUBTILIS GENES 372
REFERENCES 374
Chapter 18. Promoter Probe Plasmids for Gram-Positive Bacteria 378
18.1 IDEAL PROMOTER CLONING PLASMID FOR B. SUBTILIS 380
18.2 PROMOTER CLONING PLASMIDS 382
18.3 GENE FUSIONS MEDIATED BY TN917 394
REFERENCES 397
PART II: FUNGAL CLONING VECTORS 400
Chapter 19. Molecular Cloning Vectors of Saccharomyces: Generalized Cloning Vectors 402
19.1 VECTOR REQUIREMENTS 403
19.2 NOMENCLATURE AND ORIGIN 407
19.3 VECTOR CHOICE 413
19.4 CLONING VECTORS FOR YEAST OTHER THAN S. CEREVISIAE 417
REFERENCES 418
Chapter 20. Plasmid Vectors for the Analysis of Regulatory Sequences in Yeast 420
20.1 VECTOR COMPONENTS 421
20.2 MARKER GENES 424
20.3 VECTORS 426
20.4 CONCLUSIONS 429
REFERENCES 430
Chapter 21. Molecular Cloning Vectors for Aspergillus and Neurospora 434
21.1 TRANSFORMATION SYSTEMS AND SELECTABLE MARKERS 435
21.2 TRANSFORMATION MECHANISMS 438
21.3 AUTONOMOUSLY REPLICATING VECTORS 439
21.4 CLONING STRATEGIES 440
21.5 EXPRESSION VECTORS FOR ASPERGILLUS 442
21.6 CONCLUSIONS 446
REFERENCES 446
PART III: INSECT AND ANIMAL CELL CLONING VECTORS 450
Chapter 22. Vectors for P-Mediated Transformation in Drosophila 452
22.1 PROPERTIES OF P VECTORS 453
22.2 CARNEGIE VECTORS 454
22.3 CARNEGIE 20 454
22.4 CaSpeR VECTOR 456
22.5 Adh VECTOR pPA-1 457
22.6 pUChsneo 457
22.7 CosPneo 460
22.8 COMPARISON OF VECTORS 461
22.9 PROMOTER-PROBE VECTORS 463
22.10 HELPER PLASMIDS 463
22.11 INJECTION PROCEDURE 464
22.11 EFFICIENCY OF TRANSFORMATION 465
22.12 INSERTION SPECIFICITY AND EXPRESSION 466
22.13 OTHER APPLICATIONS OF P VECTORS 467
22.14 P-MEDIATED TRANSFORMATION OF OTHER SPECIES 469
22.15 POSSIBILITIES FOR IMPROVED VECTORS 469
REFERENCES 470
Chapter 23. Baculoviruses for Foreign Gene Expression in Insect Cells 472
23.1 SIZE AND NATURE OF FOREIGN GENE INSERTS 473
23.2 AVAILABLE BACULOVIRUS EXPRESSION VECTORS 474
23.3 POSTTRANSLATIONAL MODIFICATION IN INSECT CELLS 477
23.4 SIMULTANEOUS EXPRESSION OF TWO OR MORE GENES 478
23.5 SAFETY CONSIDERATIONS 479
23.6 SUMMARY 479
REFERENCES 480
Chapter 24. Mammalian Expression Vectors 482
24.1 SOME REQUIREMENTS OF MAMMALIAN EXPRESSION VECTORS 483
24.2 INTRODUCTION OF VECTOR INTO HOST CELLS 485
24.3 PAPOVA VIRUS VECTORS 487
24.4 NONRESTRICTIVE VECTORS 488
24.5 REGULATABLE VECTORS 489
24.6 VECTORS FOR THE ANALYSIS OF SEQUENCE ELEMENTS THAT CONTROL EXPRESSION 490
24.7 VECTORS THAT PERMIT CLONING AND EXPRESSION OF cDNA INSERTS 490
24.8 VECTORS THAT REPLICATE EPISOMALLY 492
24.9 ADENOVIRUS VECTORS 494
24.10 PARVOVIRUS VECTORS 497
24.11 VACCINIA VIRUS VECTORS 498
24.12 WHAT THE FUTURE MAY HOLD 501
REFERENCES 502
Chapter 25. Retroviral Vectors 508
25.1 LIFE CYCLE 509
25.2 CONSTRUCTION OF RECOMBINANT RETROVIRUS 514
25.3 DIFFERENT TYPES OF RECOMBINANT RETROVIRUSES 521
25.4 USES OF RETROVIRAL VECTORS 523
25.5 CONCLUSIONS 525
REFERENCES 526
PART IV: PLANT CLONING VECTORS 530
Chapter 26. Agrobacterium tumefaciens Ti Plasmid-Derived Plant Vectors for Dicotyledonous and Monocotyledonous Plants 532
26.1 HOST RANGE FOR T-DNA TRANSFER BY AGROBACTERIUM 535
26.2 STRUCTURE OF T-DNA 538
26.3 ROLE OF BORDER REPEATS 538
26.4 DISARMING T-DNA 540
26.5 SELECTION OF TRANSFORMANTS 541
26.6 USE OF THE Ti PLASMID AS A PLANT VECTOR 542
26.8 CONCLUSION 548
REFERENCES 549
Chapter 27. Current Vectors for Plant Transformation 554
27.1 MOLECULAR BIOLOGY OF THE AGROBACTERIUM TUMEFACIENS TI PLASMID 555
27.2 GETTING GENES INTO THE TI PLASMID 556
27.3 pMON200 557
27.4 "DISARMING" THE T-DNA 558
27.5 USE OF pMON200 559
27.6 BINARY VECTORS 562
27.7 "DISARMED" TI PLASMIDS FOR BINARY VECTORS 564
27.8 GETTING GENES INTO PLANTS 565
27.9 BORDER SEQUENCES AND BINARY VECTOR T-DNA STRUCTURE 565
27.10 FUTURE USES FOR BINARY VECTORS 567
27.11 IMPROVEMENTS AND FUTURE NEEDS 567
REFERENCES 570
Index 574