Voigt Synthetic Biology, Part B

Computer Aided Design and DNA Assembly
1. Auflage 2011
ISBN: 978-0-12-385121-5
Verlag: Elsevier Science & Techn.
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, Band Volume 498, 550 Seiten, Web PDF

Reihe: Methods in Enzymology

Synthetic biology encompasses a variety of different approaches, methodologies and disciplines, and many different definitions exist. This Volume of Methods in Enzymology has been split into 2 Parts and covers topics such as Measuring and Engineering Central Dogma Processes, Mathematical and Computational Methods and Next-Generation DNA Assembly and Manipulation. - Encompasses a variety of different approaches, methodologies and disciplines - Split into 2 parts and covers topics such as measuring and engineering central dogma processes, mathematical and computational methods and next-generation DNA assembly and manipulation

Autoren/Hrsg.

Voigt, Chris

Inhaltsverzeichnis

1;Front Cover;1
2;Synthetic Biology, Part B : Computer Aided Designand DNA Assembly;2
3;Copyright;5
4;Contents;6
5;Contributors;12
6;Preface;18
7;Methods in Enzymology;20
8;Section One: Mathematical and Computational Methods;50
8.1;Chapter 1: DNA-Binding Specificity Prediction with FoldX;52
8.1.1;1. Introduction;53
8.1.2;2. Description of the Force Field, FoldX, and the Implementation of DNA Energy Terms and Base Mutation;54
8.1.3;3. Predicting Specificities;58
8.1.4;4. Changing Binding Capabilities;61
8.1.5;5. Designing New Specificities;62
8.1.6;6. Known Caveats;63
8.1.7;7. Conclusions and Future Outlook;65
8.1.8;Acknowledgments;65
8.1.9;Appendix Mutation Protocol;65
8.1.10;References;66
8.2;Chapter 2: The Ribosome Binding Site Calculator;68
8.2.1;1. Introduction;69
8.2.2;2. Applications of the RBS Calculator;71
8.2.3;3. RBSs and Bacterial Translation;73
8.2.4;4. A Biophysical Model and Optimization Method for RBSs;76
8.2.5;5. Precise Measurements of Fluorescent Protein Expression Levels;87
8.2.6;Acknowledgments;89
8.2.7;References;90
8.3;Chapter 3: Designing Genes for Successful Protein Expression;92
8.3.1;1. Introduction;93
8.3.2;2. Gene Design Software;94
8.3.3;3. General Sequence Parameters Affecting Protein Expression;94
8.3.4;4. Protein-Specific Factors Providing Additional Complexity;105
8.3.5;5. Conclusions;110
8.3.6;References;111
8.4;Chapter 4: Application of Metabolic Flux Analysis in Metabolic Engineering;116
8.4.1;1. Introduction;117
8.4.2;2. General Structure of Constraints-Based Flux Analysis;119
8.4.3;3. Algorithms of Metabolic Flux Analysis;122
8.4.4;4. Concluding Remarks;134
8.4.5;Acknowledgments;135
8.4.6;References;136
9;Section Two: Grammars, Languages, and Computer-Aided Design;144
9.1;Chapter 5: Developer's and User's Guide to Clotho v2.0;146
9.1.1;1. Introduction;147
9.1.2;2. Developers;156
9.1.3;3. Users;161
9.1.4;4. Concluding Remarks;184
9.1.5;Acknowledgments;184
9.1.6;References;184
9.2;Chapter 6: SynBioSS-Aided Design of Synthetic Biological Constructs;186
9.2.1;1. Introduction;186
9.2.2;2. SynBioSS Components;188
9.2.3;3. Simulations of Biologic AND Gates;191
9.2.4;4. Advantages and Disadvantages of SynBioSS;196
9.2.5;5. Concluding Remarks;199
9.2.6;Acknowledgments;199
9.2.7;References;200
9.3;Chapter 7: The Eugene Language for Synthetic Biology;202
9.3.1;1. Overview;203
9.3.2;2. Installation and Use;203
9.3.3;3. Design and Implementation;204
9.3.4;4. Examples;218
9.3.5;Acknowledgments;220
9.3.6;References;221
9.4;Chapter 8: A Step-by-Step Introduction to Rule-Based Design of Synthetic Genetic Constructs Using GenoCAD;222
9.4.1;1. Introduction;223
9.4.2;2. Overview of GenoCAD;224
9.4.3;3. Requesting an Account on GenoCAD.org;225
9.4.4;4. Browsing the Parts Catalog;225
9.4.5;5. Searching for Parts;227
9.4.6;6. Using My Cart to Create Libraries;228
9.4.7;7. My Libraries;230
9.4.8;8. My Parts;232
9.4.9;9. Designing Sequences;232
9.4.10;10. Installing GenoCAD;234
9.4.11;11. Anticipated Evolutions;235
9.4.12;Acknowledgments;236
9.4.13;References;237
9.5;Chapter 9: Methods for Open Innovation on a Genome-Design Platform Associating Scientific, Commercial, and Educational Commun;238
9.5.1;1. Introduction;239
9.5.2;2. Various Platforms for Rational Genome Design;242
9.5.3;3. Research Use of Patents;246
9.5.4;4. Copyrights on Designed Sequences in Genetically Modified Organisms;247
9.5.5;5. Auditability of Designed Sequences for Safety Guidelines;248
9.5.6;6. Infrastructure for GenoCon;249
9.5.7;7. Cultivating Young Specialists for Genome Design;250
9.5.8;8. Perspectives;251
9.5.9;References;251
10;Section Three : Next-Generation DNA Assembly and Manipulation;254
10.1;Chapter 10: Recursive Construction and Error Correction of DNA Molecules and Libraries from Synthetic and Natural DNA;256
10.1.1;1. Introduction;257
10.1.2;2. Protocols;265
10.1.3;Appendix;268
10.1.4;References;293
10.2;Chapter 11: Industrial Scale Gene Synthesis;296
10.2.1;1. Brief History of Gene Synthesis;297
10.2.2;2. Applications of Synthetic Genes;299
10.2.3;3. State-of-the-Art Gene Synthesis;302
10.2.4;4. Gene Synthesis and Synthetic Biology-From Genes to Genomes;303
10.2.5;5. Industrial Gene Synthesis-From Bench to Manufacturing;307
10.2.6;6. Design Tool-GeneOptimizer;313
10.2.7;7. Production Processing-LIMS;315
10.2.8;8. Case Study: Large-Scale Gene Production;319
10.2.9;9. Conclusion;321
10.2.10;References;321
10.3;Chapter 12 : Gene Synthesis: Methods and Applications;326
10.3.1;Introduction;327
10.3.2;Oligonucleotide Synthesis;327
10.3.2.1;Solid phase phosphoramidite synthesis;327
10.3.2.2;Microchip-based oligonucleotide synthesis;329
10.3.3;Gene Assembly Methodologies;331
10.3.3.1;Ligation-mediated assembly;331
10.3.3.2;PCR-mediated assembly;333
10.3.4;Gene Design Software;340
10.3.5;Synthesis Fidelity/Error Correction Methods and Considerations;342
10.3.5.1;Oligonucleotide purification;343
10.3.5.2;Reading frame selection;343
10.3.5.3;Mismatch binding and cleavage;344
10.3.5.4;Correcting errors in synthetic genes by site-directed mutagenesis;346
10.3.6;Applications of Gene Synthesis;346
10.3.6.1;Codon optimization;346
10.3.6.2;Synthetic biology;348
10.3.7;Example of High-Throughput Gene Synthesis Using Protein Fabrication Automation;349
10.3.8;Conclusions;352
10.3.9;References;352
10.4;Chapter 13: Assembly of BioBrick Standard Biological Parts Using Three Antibiotic Assembly;359
10.4.1;1. Introduction;360
10.4.2;2. Construction of New BioBrick Standard Biological Parts;364
10.4.3;3. 3A Assembly of BioBrick Standard Biological Parts;366
10.4.4;4. Verification of Correct Assembly of BioBrick Standard Biological Parts;368
10.4.5;5. Preparation of Linearized Destination Vector by PCR to Improve 3A Assembly;369
10.4.6;6. Available BioBrick Destination Vectors;371
10.4.7;7. Preparation of Chemically Competent Cells;371
10.4.8;8. Conclusions;373
10.4.9;Acknowledgments;373
10.4.10;References;373
10.5;Chapter 14: Genetic Assembly Tools for Synthetic Biology;375
10.5.1;1. Overview;376
10.5.2;2. Yeast-Based Homologous Recombination;377
10.5.3;3. In Vitro Recombineering-DNA Assembly;385
10.5.4;4. In Vitro Recombineering-Site-Directed Mutagenesis;389
10.5.5;5. Concluding Remarks;393
10.5.6;6. Disclosure;393
10.5.7;References;394
10.6;Chapter 15: Enzymatic Assembly of Overlapping DNA Fragments;397
10.6.1;1. Introduction;398
10.6.2;2. Design and Preparation of the dsDNA for In Vitro Recombination;400
10.6.3;3. Two-Step Thermocycled Assembly of Overlapping dsDNA;401
10.6.4;4. One-Step Thermocycled Assembly of Overlapping dsDNA;403
10.6.5;5. One-Step ISO Assembly of Overlapping dsDNA;405
10.6.6;6. One-Step ISO DNA Assembly of Overlapping ssDNA;406
10.6.7;Acknowledgments;408
10.6.8;References;408
10.7;Chapter 16: Automated Assembly of Standard Biological Parts;411
10.7.1;1. Introduction;412
10.7.2;2. Materials and Methods;421
10.7.3;3. Troubleshooting;441
10.7.4;4 Concluding Remarks;444
10.7.5;Acknowledgments;445
10.7.6;References;445
10.8;Chapter 17: MEGAWHOP Cloning;447
10.8.1;1. Introduction;448
10.8.2;2. Methods;449
10.8.3;3. Applications of MEGAWHOP;451
10.8.4;References;453
11;Section Four: Genome-scale Engineering;455
11.1;Chapter 18: Multiplexed Genome Engineering and Genotyping Methods;457
11.1.1;1. Introduction;458
11.1.2;2. Design Protocol;464
11.1.3;3. Experimental Protocol;467
11.1.4;4. Concluding Remarks;472
11.1.5;Acknowledgments;472
11.1.6;References;472
11.2;Chapter 19: Construction and Manipulation of Giant DNA by a Genome Vector;475
11.2.1;1. Introduction;476
11.2.2;2. Basics for B. subtilis as a Novel Host;478
11.2.3;3. Large DNA Reconstruction via Small DNA Fragments Assembly in the BGM Vector;481
11.2.4;4. Assembly of Multiple DNA Fragments with Designed Order Connecting by a Few Bases;486
11.2.5;5. Future Perspectives;491
11.2.6;Acknowledgments;493
11.2.7;References;493
11.3;Chapter 20: Mapping E. coli RNA Polymerase and Associated Transcription Factors and Identifying Promoters Genome-Wide;497
11.3.1;1. Introduction;498
11.3.2;2. Protocol: ChIP-chip;502
11.3.3;3. Chemical Genomics;515
11.3.4;4. Future Directions;517
11.3.5;Acknowledgments;518
11.3.6;References;518
11.4;Author Index;521
11.5;Subject Index;539
11.6;Color Plate ;549