Synthetic biology: B Computer aided design and DNA assembly
Gespeichert in:
| Weitere Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Amsterdam [u.a.]
Elsevier, Acad. Press
2011
|
| Ausgabe: | 1. ed. |
| Schriftenreihe: | Methods in enzymology
498 |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XLVIII, 500 S., [4] Bl. Ill., graph. Darst. |
| ISBN: | 9780123851208 |
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Datensatz im Suchindex
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|---|---|
| adam_text | Titel: Bd. B. Synthetic biology. Computer aided design and DNA assembly
Autor:
Jahr: 2011
Contributors xi
Preface xvii
Volumes in Series xix
Section I. Mathematical and Computational Methods 1
1. DNA-Binding Specificity Prediction with FoldX 3
Alejandro D. Nadra, Luis Serrano, and Andreu Atibes
1. Introduction 4
2. Description of the Force Field, FoldX, and the Implementation
of DNA Energy Terms and Base Mutation 5
3. Predicting Specificities 9
4. Changing Binding Capabilities 12
5. Designing New Specificities 13
6. Known Caveats 14
7. Conclusions and Future Outlook 16
Acknowledgments 16
References 17
2. The Ribosome Binding Site Calculator 19
Howard M. Salis
1. Introduction 20
2. Applications of the RBS Calculator 22
3. RBSs and Bacterial Translation 24
4. A Biophysical Model and Optimization Method for RBSs 27
5. Precise Measurements of Fluorescent Protein Expression Levels 38
Acknowledgments 40
References 41
3. Designing Genes for Successful Protein Expression 43
Mark Welch, Alan Villalobos, Claes Gustafsson, and Jeremy Minshull
1. Introduction 44
2. Gene Design Software 45
3. General Sequence Parameters Affecting Protein Expression 45
vi Contents
4. Protein-Specific Factors Providing Additional Complexity 56
5. Conclusions 61
References 62
4. Application of Metabolic Flux Analysis in Metabolic Engineering 67
Sang Yup Lee, Jong Myoung Park, and Tae Yong Kim
1. Introduction 68
2. General Structure of Constraints-Based Flux Analysis 70
3. Algorithms of Metabolic Flux Analysis 73
4. Concluding Remarks 85
Acknowledgments 86
References 87
Section II. Grammars, Languages, and
Computer-Aided Design 95
5. Developer s and User s Guide to Clotho v2.0: A Software
Platform for the Creation of Synthetic Biological Systems 97
BingXia, Swapnil Bhatia, Ben Bubenheim, Maisam Dadgar,
Douglas Densmore, and J. Christopher Anderson
1. Introduction 98
2. Developers 107
3. Users 112
4. Concluding Remarks 135
Acknowledgments 135
References 135
6. SynBioSS-Aided Design of Synthetic Biological Constructs 137
Yiannis N. Kaznessis
1. Introduction 137
2. SynBioSS Components 139
3. Simulations of Biologic AND Gates 142
4. Advantages and Disadvantages of SynBioSS 147
5. Concluding Remarks 150
Acknowledgments 150
References 151
7. The Eugene Language for Synthetic Biology 153
Lesia Bilitchenko, Adam Liu, and Douglas Densmore
1. Overview 154
2. Installation and Use 154
3. Design and Implementation 155
Contents vii
4. Examples 169
Acknowledgments 171
Reference 172
8. A Step-by-Step Introduction to Rule-Based Design of Synthetic
Genetic Constructs Using GenoCAD 173
Mandy L. Wilson, Russell Hertzberg, Laura Adam, and lean Peccoud
1. Introduction 174
2. Overview of GenoCAD 175
3. Requesting an Account on GenoCAD.org 176
4. Browsing the Parts Catalog 176
5. Searching for Parts 178
6. Using My Cart to Create Libraries 179
7. My Libraries 181
8. My Parts 183
9. Designing Sequences 183
10. Installing GenoCAD 185
11. Anticipated Evolutions 186
Acknowledgments 187
References 188
9. Methods for Open Innovation on a Genome-Design
Platform Associating Scientific, Commercial, and Educational
Communities in Synthetic Biology 189
Tetsuro Toyoda
1. Introduction 190
2. Various Platforms for Rational Genome Design 193
3. Research Use of Patents 197
4. Copyrights on Designed Sequences in Genetically
Modified Organisms 198
5. Auditability of Designed Sequences for Safety Guidelines 199
6. Infrastructure for GenoCon 200
7. Cultivating Young Specialists for Genome Design 201
8. Perspectives 202
References 202
Section III. Next-Generation DNA Assembly
and Manipulation 205
10. Recursive Construction and Error Correction of DNA Molecules
and Libraries from Synthetic and Natural DNA 207
Tuval Ben Yehezkel, Gregory Linshiz, Shai Kaplan, Dan Gronau, Sivan Ravid,
Rivka Adar, and Ehud Shapiro
1. Introduction 208
2. Protocols 216
References 244
viii Contents
11. Industrial Scale Gene Synthesis 247
Frank Notka, Michael Liss, and Ralf Wagner
1. Brief History of Gene Synthesis 248
2. Applications of Synthetic Genes 250
3. State-of-the-Art Gene Synthesis 253
4. Gene Synthesis and Synthetic Biology-From Genes to Genomes 254
5. Industrial Gene Synthesis-From Bench to Manufacturing 258
6. Design Tool-GeneOptimizer 264
7. Production Processing-LIMS 266
8. Case Study: Large-Scale Gene Production 270
9. Conclusion 272
References 272
12. Gene Synthesis: Methods and Applications 277
Randall A. Hughes, Aleksandr E. Miklos, and Andrew D. Ellington
1. Introduction 278
2. Oligonucleotide Synthesis 278
3. Gene Assembly Methodologies 282
4. Gene Design Software 291
5. Synthesis Fidelity/Error Correction Methods and Considerations 293
6. Applications of Gene Synthesis 297
7. Example of High-Throughput Gene Synthesis Using Protein
Fabrication Automation 300
8. Conclusions 303
References 303
13. Assembly of BioBrick Standard Biological Parts Using Three
Antibiotic Assembly 311
Reshma Shetty, Meagan Lizarazo, Randy Rettberg, and
Thomas F. Knight
1. Introduction 312
2. Construction of New BioBrick Standard Biological Parts 316
3. 3A Assembly of BioBrick Standard Biological Parts 318
4. Verification of Correct Assembly of BioBrick Standard
Biological Parts 320
5. Preparation of Linearized Destination Vector by PCR to Improve
3A Assembly 321
6. Available BioBrick Destination Vectors 323
7. Preparation of Chemically Competent Cells 323
8. Conclusions 325
Acknowledgments 325
References 325
Contents ix
14. Genetic Assembly Tools for Synthetic Biology 327
Billyana Tsvetanova, Lansha Peng, Xiquan Liang, Ke Li,
Jian-Ping Yang, Tony Ho, Josh Shirley, Liewei Xu, Jason Potter,
Wieslaw Kudlicki, Todd Peterson, and Federico Katzen
1. Overview 328
2. Yeast-Based Homologous Recombination 329
3. In Vitro Recombineering-DNA Assembly 337
4. In Vitro Recombineering-Site-Directed Mutagenesis 341
5. Concluding Remarks 345
6. Disclosure 345
References 346
15. Enzymatic Assembly of Overlapping DNA Fragments 349
Daniel G. Gibson
1. Introduction 350
2. Design and Preparation of the dsDNA for In Vitro Recombination 352
3. Two-Step Thermocycled Assembly of Overlapping dsDNA 353
4. One-Step Thermocycled Assembly of Overlapping dsDNA 355
5. One-Step ISO Assembly of Overlapping dsDNA 357
6. One-Step ISO DNA Assembly of Overlapping ssDNA 358
Acknowledgments 360
References 360
16. Automated Assembly of Standard Biological Parts 363
Mariana Leguia, Jennifer Brophy, Douglas Densmore, and
J. Christopher Anderson
1. Introduction 364
2. Materials and Methods 373
3. Troubleshooting 393
4. Concluding Remarks 396
Acknowledgments 397
References 397
17. MEGAWHOP Cloning: A Method of Creating Random
Mutagenesis Libraries via Megaprimer PCR of Whole
Plasmids 399
Kentaro Miyazaki
1. Introduction 400
2. Methods 401
3. Applications of MEGAWHOP 403
References 405
Contents
Section IV. Genome-Scale Engineering 407
18. Multiplexed Genome Engineering and Genotyping Methods:
Applications for Synthetic Biology and Metabolic Engineering 409
Harris H. Wang and George M. Church
1. Introduction 410
2. Design Protocol 416
3. Experimental Protocol 419
4. Concluding Remarks 424
Acknowledgments 424
References 424
19. Construction and Manipulation of Giant DNA by a
Genome Vector 427
Mitsuhiro Itaya and Kenji Tsuge
1. Introduction 428
2. Basics for ß. subtilis as a Novel Host 430
3. Large DNA Reconstruction via Small DNA Fragments Assembly
in the BGM Vector 433
4. Assembly of Multiple DNA Fragments with Designed Order
Connecting by a Few Bases 438
5. Future Perspectives 443
Acknowledgments 445
References 445
20. Mapping E. coli RNA Polymerase and Associated
Transcription Factors and Identifying Promoters Genome-Wide 449
Sarah E. Davis, Rachel A. Mooney, Elenita I. Kanin, Jeff Grass,
Robert Landick, and Aseem Z. Ansari
1. Introduction 450
2. Protocol: ChlP-chip 454
3. Chemical Genomics 467
4. Future Directions 469
Acknowledgments 470
References 470
Author Index 473
Subject Index 491
|
| any_adam_object | 1 |
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| author_facet | Voigt, Christopher |
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| ctrlnum | (OCoLC)750723752 (DE-599)BVBBV039501275 |
| discipline | Chemie / Pharmazie Biologie |
| edition | 1. ed. |
| format | Book |
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| spelling | Synthetic biology B Computer aided design and DNA assembly ed. by Christopher Voigt 1. ed. Amsterdam [u.a.] Elsevier, Acad. Press 2011 XLVIII, 500 S., [4] Bl. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Methods in enzymology 498 Methods in enzymology ... Assembly (DE-588)4378786-1 gnd rswk-swf DNS (DE-588)4070512-2 gnd rswk-swf Methode (DE-588)4038971-6 gnd rswk-swf Computerunterstütztes Verfahren (DE-588)4139030-1 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content DNS (DE-588)4070512-2 s Assembly (DE-588)4378786-1 s Computerunterstütztes Verfahren (DE-588)4139030-1 s Methode (DE-588)4038971-6 s b DE-604 Voigt, Christopher edt (DE-604)BV039160172 2 Methods in enzymology 498 (DE-604)BV000000938 498 HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=024334208&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Synthetic biology Methods in enzymology Assembly (DE-588)4378786-1 gnd DNS (DE-588)4070512-2 gnd Methode (DE-588)4038971-6 gnd Computerunterstütztes Verfahren (DE-588)4139030-1 gnd |
| subject_GND | (DE-588)4378786-1 (DE-588)4070512-2 (DE-588)4038971-6 (DE-588)4139030-1 (DE-588)4143413-4 |
| title | Synthetic biology |
| title_auth | Synthetic biology |
| title_exact_search | Synthetic biology |
| title_full | Synthetic biology B Computer aided design and DNA assembly ed. by Christopher Voigt |
| title_fullStr | Synthetic biology B Computer aided design and DNA assembly ed. by Christopher Voigt |
| title_full_unstemmed | Synthetic biology B Computer aided design and DNA assembly ed. by Christopher Voigt |
| title_short | Synthetic biology |
| title_sort | synthetic biology computer aided design and dna assembly |
| topic | Assembly (DE-588)4378786-1 gnd DNS (DE-588)4070512-2 gnd Methode (DE-588)4038971-6 gnd Computerunterstütztes Verfahren (DE-588)4139030-1 gnd |
| topic_facet | Assembly DNS Methode Computerunterstütztes Verfahren Aufsatzsammlung |
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