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DNA Cloning and Assembly
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Table of Contents

Part I: In Silico Tools for DNA Design and Assembly

1. An Integrated Computer-Aided Design and Manufacturing Workflow for Synthetic Biology

Ernst Oberortner, Robert Evans, Xianwei Meng, Sangeeta Nath, Hector Plahar, Lisa Simirenko, Angela Tarver, Samuel Deutsch, Nathan J. Hillson, and Jan-Fang Cheng

2. Combinatorial-Hierarchical DNA Library Design Using the TeselaGen DESIGN Module with j5

Michael J Fero, James K Craft, Trang Vu, and Nathan J Hillson

3. The AssemblX Toolkit for Reliable and User-friendly Multi-gene Assemblies

Fabian Machens and Lena Hochrein

Part II: High Throughput Workflows

4. High-Throughput PCR for DNA Part Generation

David Reif

5. High-Throughput DNA Assembly Using Yeast Homologous Recombination

Kristy Ip, Ron Yadin, and Kevin W. George

6. Highly-Multiplexed, Semi-Automated Nextera Next Generation Sequencing (NGS) Library Preparation

William Christie, Ron Yadin, Kristy Ip, and Kevin W. George

Part III: DNA Assembly Standards

7. Generation of MoClo Standard Parts Using Golden Gate Cloning

Ramona Grutzner and Sylvestre Marillonnet

8. Assembly of Multigene Constructs using the Modular Cloning System MoClo

Sylvestre Marillonnet and Stefan Werner

9. Hierarchical Modular DNA Assembly using MetClo

Da Lin and Christopher A. O'Callaghan

10. PaperClip DNA Assembly: Reduce, Reuse, Recycle

Maryia Trubitsyna, Annegret Honsbein, Uma Jayachandran, Alistair Elfick, and Christopher E. French

11. Phytobricks: Manual and Automated Assembly of Constructs for Engineering Plants

Yao-Min Cai , Jose A. Carrasco Lopez, and Nicola J. Patron

12. Mobius Assembly

Andreas I. Andreou and Naomi Nakayama

13. Design and Implementation of Multi-Protein Expression Constructs and Combinatorial Libraries using Start-Stop Assembly

George M. Taylor and John T. Heap

14. BASIC - A Simple and Accurate Modular DNA Assembly Method

Marko Storch, Ari Dwijayanti, Haris Mallick, and Matthew C. Haines, and Geoff S. Baldwin

15. Joint Universal Modular Plasmids: A Flexible Platform for Golden Gate Assembly in Any Microbial Host

Marcos Valenzuela-Ortega and Christopher E. French

Part IV: Combinatorial Methods For Pathway Optimization

16. A Step-by-Step Protocol for COMPASS, a Synthetic Biology Tool for Combinatorial Gene Assembly

Gita Naseri and Bernd Mueller-Roeber

17. SCRaMbLE-in: A Fast and Efficient Method to Diversify and Improve the Yields of Heterologous Pathways in Synthetic Yeast

Reem Swidah, Jamie Auxillos, Wei Liu, Sally Jones, Ting-Fung Chan, Junbiao Dai, and Yizhi Cai

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