Synthetic Biology - Methods for Building and Programming Life

Klappentext Synthetic biology is a new area of biological research that combines science and engineering. Synthetic biology encompasses many different approaches, methodologies and disciplines, and many different definitions exist. What they all have in common, however, is that they see synthetic biology as the design and construction of new biological functions and systems not found in nature. 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. Zusammenfassung Synthetic biology encompasses a variety of different approaches! methodologies and disciplines! and many different definitions exist. This Volume 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. Inhaltsverzeichnis Voigt / MIE Vol Table of Contents Synthetic biology, Part B Subtitle: Computer Aided Design and DNA Assembly Section I. Mathematical and Computational Methods DNA-binding specificity prediction with FoldX Alejandro D. Nadra, Luis Serrano, Andreu Alibés The Ribosome Binding Site Calculator Howard M. Salis Designing Genes for Successful Protein Expression Mark Welch, Alan Villalobos, Claes Gustafsson and Jeremy Minshull Application of Metabolic Flux Analysis in Metabolic Engineering Sang Yup Lee, Jong Myoung Park and Tae Yong Kim Section II. Grammars, Languages, and Computer-Aided Design Clotho: A Software Platform for the Creation of Synthetic Biological Systems Swapnil Bhatia, Bing Xia, Ben Bubenheim, Maisam Dadgar, Douglas Densmore and J. Christopher Anderson SynBioSS-Aided Design of Synthetic Biological Constructs Yiannis N. Kaznessis The Eugene Language for Synthetic Biology Lesia Bilitchenko, Adam Liu, Douglas Densmore A step by step introduction to rule-based design of synthetic genetic constructs using GenoCAD Mandy L. Wilson, Russell Hertzberg, Laura Adam, Jean Peccoud Methods for open innovation on a genome-design platform associating scientific, commercial, and educational communities in synthetic biology Tetsuro Toyoda Section III. Next-Generation DNA Assembly and Manipulation Recursive construction and error correction of DNA molecules and libraries from synthetic and natural DNA Tuval Ben Yehezkel and Ehud Shapiro Industrial scale gene synthesis Frank Notka, Michael Liss & Ralf Wagner Chemical DNA Synthesis: Methods and Applications Randall A. Hughes, Aleksandr E. Miklos, and Andrew D. Ellington Assembly of BioBrick standard biological parts using three antibiotic assembly Reshma Shetty, Meagan Lizarazo, Randy Rettberg, and Thomas F. Knight, Jr Genetic Assembly Tools for Synthetic Biology 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 Enzymatic assembly of overlapping DNA fragments Daniel G. Gibson Automated assembly of standard biological parts Mariana Leguia, Jennifer Brophy, Douglas Densmore and J. Christopher Anderson MEGAWHOP Cloning: A method of creating random mutagenesis libraries via megaprimer PCR of whole plasmids Kentaro Miyazaki Section III. Genome-scale Engineering Rapid and Multiplexed Genome Engineering and Genotyping Methods: Applications for Synthetic Biology and Protein and Pathway Engineering Harris H. Wang and George M. Church Construction and manipulation of giant DNA by a genome vector Mitsuhiro ITAYA and Kenji TSUGE Mapping E. coli RNA Polymerase and associated transcription f...

List of contents

Voigt / MIE Vol
Table of Contents
Synthetic biology, Part B
Subtitle: Computer Aided Design and DNA Assembly
Section I. Mathematical and Computational Methods

1. DNA-binding specificity prediction with FoldX
Alejandro D. Nadra, Luis Serrano, Andreu Alibés


2. The Ribosome Binding Site Calculator
Howard M. Salis


3. Designing Genes for Successful Protein Expression
Mark Welch, Alan Villalobos, Claes Gustafsson and Jeremy Minshull


4. Application of Metabolic Flux Analysis in Metabolic Engineering
Sang Yup Lee, Jong Myoung Park and Tae Yong Kim
Section II. Grammars, Languages, and Computer-Aided Design


5. Clotho: A Software Platform for the Creation of Synthetic Biological Systems
Swapnil Bhatia, Bing Xia, Ben Bubenheim, Maisam Dadgar, Douglas Densmore and J. Christopher Anderson


6. SynBioSS-Aided Design of Synthetic Biological Constructs
Yiannis N. Kaznessis


7. The Eugene Language for Synthetic Biology
Lesia Bilitchenko, Adam Liu, Douglas Densmore


8. A step by step introduction to rule-based design of synthetic genetic constructs using GenoCAD
Mandy L. Wilson, Russell Hertzberg, Laura Adam, Jean Peccoud


9. Methods for open innovation on a genome-design platform associating scientific, commercial, and educational communities in synthetic biology
Tetsuro Toyoda
Section III. Next-Generation DNA Assembly and Manipulation


10. Recursive construction and error correction of DNA molecules and libraries from synthetic and natural DNA
Tuval Ben Yehezkel and Ehud Shapiro


11. Industrial scale gene synthesis
Frank Notka, Michael Liss & Ralf Wagner


12. Chemical DNA Synthesis: Methods and Applications
Randall A. Hughes, Aleksandr E. Miklos, and Andrew D. Ellington


13. Assembly of BioBrick standard biological parts using three antibiotic assembly
Reshma Shetty, Meagan Lizarazo, Randy Rettberg, and Thomas F. Knight, Jr


14. Genetic Assembly Tools for Synthetic Biology
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


15. Enzymatic assembly of overlapping DNA fragments
Daniel G. Gibson


16. Automated assembly of standard biological parts
Mariana Leguia, Jennifer Brophy, Douglas Densmore and J. Christopher Anderson


17. MEGAWHOP Cloning: A method of creating random mutagenesis libraries via megaprimer PCR of whole plasmids
Kentaro Miyazaki
Section III. Genome-scale Engineering


18. Rapid and Multiplexed Genome Engineering and Genotyping Methods: Applications for Synthetic Biology and Protein and Pathway Engineering
Harris H. Wang and George M. Church


19. Construction and manipulation of giant DNA by a genome vector
Mitsuhiro ITAYA and Kenji TSUGE


20. Mapping E. coli RNA Polymerase and associated transcription factors and identifying promoters genome-wide

Sarah E. Davis, Rachel A. Mooney, Elenita I. Kanin, Jeff Grass, Robert Landick and Aseem Z. Ansari

Product details

• Authors: Chris Voigt, Chris (EDT) Voigt
• Assisted by: Chris Voigt (Editor), Voigt Chris (Editor)
• Publisher: Academic Press London
• Languages: English
• Product format: Hardback
• Released: 31.07.2011
• EAN: 9780123851208
• ISBN: 978-0-12-385120-8
• No. of pages: 496
• Series: Academic Press; Methods in Enzymology; Methods in Enzymology
• Subjects: Natural sciences, medicine, IT, technology > Biology > Genetics, genetic engineering; SCIENCE / Biotechnology, biotechnology