Synthetic Biology, Part B book cover

Synthetic Biology, Part B

Computer Aided Design and DNA Assembly

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.

Audience

Researchers and students in cell, molecular and developmental biology

Included in series
Methods in Enzymology

Hardbound, 550 Pages

Published: June 2011

Imprint: Academic Press

ISBN: 978-0-12-385120-8

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
    2. Alejandro D. Nadra, Luis Serrano, Andreu Alibés

    3. The Ribosome Binding Site Calculator
    4. Howard M. Salis

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

    7. Application of Metabolic Flux Analysis in Metabolic Engineering
    8. Sang Yup Lee, Jong Myoung Park and Tae Yong Kim

      Section II. Grammars, Languages, and Computer-Aided Design

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

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

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

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

    17. Methods for open innovation on a genome-design platform associating scientific, commercial, and educational communities in synthetic biology
    18. Tetsuro Toyoda

      Section III. Next-Generation DNA Assembly and Manipulation

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

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

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

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

    27. Genetic Assembly Tools for Synthetic Biology
    28. 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

    29. Enzymatic assembly of overlapping DNA fragments
    30. Daniel G. Gibson

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

    33. MEGAWHOP Cloning: A method of creating random mutagenesis libraries via megaprimer PCR of whole plasmids
    34. Kentaro Miyazaki

      Section III. Genome-scale Engineering

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

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

    39. 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

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