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Synthetic biology encompasses several 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 sssembly and manipulation.

Table 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



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 factors and identifying promoters genome-wide

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