Synthetic Biology, Part BComputer Aided Design and DNA Assembly

Content: 
Series Editors
Page ii

Copyright
Page iv

Contributors
Pages xi-xvi

Preface
Page xvii

Volume in series
Pages xix-xlviii

Chapter one - DNA-Binding Specificity Prediction with FoldX
Pages 3-18
Alejandro D. Nadra, Luis Serrano, Andreu AlibГ©s

Chapter two - The Ribosome Binding Site Calculator
Pages 19-42
Howard M. Salis

Chapter three - Designing Genes for Successful Protein Expression
Pages 43-66
Mark Welch, Alan Villalobos, Claes Gustafsson, Jeremy Minshull

Chapter four - Application of Metabolic Flux Analysis in Metabolic Engineering
Pages 67-93
Sang Yup Lee, Jong Myoung Park, Tae Yong Kim

Chapter five - Developer\'s and User\'s Guide to Clotho v2.0: A Software Platform for the Creation of Synthetic Biological Systems
Pages 97-135
Bing Xia, Swapnil Bhatia, Ben Bubenheim, Maisam Dadgar, Douglas Densmore, J. Christopher Anderson

Chapter six - SynBioSS-Aided Design of Synthetic Biological Constructs
Pages 137-152
Yiannis N. Kaznessis

Chapter seven - The Eugene Language for Synthetic Biology
Pages 153-172
Lesia Bilitchenko, Adam Liu, Douglas Densmore

Chapter eight - A Step-by-Step Introduction to Rule-Based Design of Synthetic Genetic Constructs Using GenoCAD
Pages 173-188
Mandy L. Wilson, Russell Hertzberg, Laura Adam, Jean Peccoud

Chapter nine - Methods for Open Innovation on a Genome-Design Platform Associating Scientific, Commercial, and Educational Communities in Synthetic Biology
Pages 189-203
Tetsuro Toyoda

Chapter ten - Recursive Construction and Error Correction of DNA Molecules and Libraries from Synthetic and Natural DNA
Pages 207-245
Tuval Ben Yehezkel, Gregory Linshiz, Shai Kaplan, Ilan Gronau, Sivan Ravid, Rivka Adar, Ehud Shapiro

Chapter eleven - Industrial Scale Gene Synthesis
Pages 247-275
Frank Notka, Michael Liss, Ralf Wagner

Chapter twelve - Gene Synthesis: Methods and Applications
Pages 277-309
Randall A. Hughes, Aleksandr E. Miklos, Andrew D. Ellington

Chapter thirteen - Assembly of BioBrick Standard Biological Parts Using Three Antibiotic Assembly
Pages 311-326
Reshma Shetty, Meagan Lizarazo, Randy Rettberg, Thomas F. Knight

Chapter fourteen - Genetic Assembly Tools for Synthetic Biology
Pages 327-348
Billyana Tsvetanova, Lansha Peng, Xiquan Liang, Ke Li, Jian-Ping Yang, Tony Ho, Josh Shirley, Liewei Xu, Jason Potter, Wieslaw Kudlicki, Todd Peterson, Federico Katzen

Chapter fifteen - Enzymatic Assembly of Overlapping DNA Fragments
Pages 349-361
Daniel G. Gibson

Chapter sixteen - Automated Assembly of Standard Biological Parts
Pages 363-397
Mariana Leguia, Jennifer Brophy, Douglas Densmore, J. Christopher Anderson

Chapter seventeen - MEGAWHOP Cloning: A Method of Creating Random Mutagenesis Libraries via Megaprimer PCR of Whole Plasmids
Pages 399-406
Kentaro Miyazaki

Chapter eighteen - Multiplexed Genome Engineering and Genotyping Methods: Applications for Synthetic Biology and Metabolic Engineering
Pages 409-426
Harris H. Wang, George M. Church

Chapter nineteen - Construction and Manipulation of Giant DNA by a Genome Vector
Pages 427-447
Mitsuhiro Itaya, Kenji Tsuge

Chapter twenty - Mapping E. coli RNA Polymerase and Associated Transcription Factors and Identifying Promoters Genome-Wide
Pages 449-471
Sarah E. Davis, Rachel A. Mooney, Elenita I. Kanin, Jeff Grass, Robert Landick, Aseem Z. Ansari

Author Index
Pages 473-490

Subject Index
Pages 491-500