Standardizing Automated DNA Assembly: Best Practices, Metrics, and Protocols Using Robots

Casini, 2014, One-Pot DNA Construction for Synthetic Biology: The Modular Overlap-Directed Assembly with Linkers (MODAL) Strategy, Nucleic Acids Res., 42, e7, 10.1093/nar/gkt915 Ellis, 2011, DNA Assembly for Synthetic Biology: From Parts to Pathways and Beyond, Integr. Biol., 3, 109, 10.1039/c0ib00070a Chao, 2015, Recent Advances in DNA Assembly Technologies, FEMS Yeast Res., 15, 1 De Paoli, 2016, An Innovative Platform for Quick and Flexible Joining of Assorted DNA Fragments, Sci. Rep., 6, 19278, 10.1038/srep19278 Torella, 2014, Unique Nucleotide Sequence–Guided Assembly of Repetitive DNA Parts for Synthetic Biology Applications, Nat. Protoc., 9, 2075, 10.1038/nprot.2014.145 Iverson, 2016, CIDAR MoClo: Improved MoClo Assembly Standard and New E. coli Part Library Enable Rapid Combinatorial Design for Synthetic and Traditional Biology, ACS Synth. Biol., 5, 99, 10.1021/acssynbio.5b00124 McAdams, 2000, Gene Regulation: Towards a Circuit Engineering Discipline, Curr. Biol., 10, R318, 10.1016/S0960-9822(00)00440-1 Tschirhart, 2017, Electronic Control of Gene Expression and Cell Behaviour in Escherichia coli through Redox Signalling, Nat. Commun., 8, 14030, 10.1038/ncomms14030 Nielsen, 2016, Genetic Circuit Design Automation, Science, 352, aac7341, 10.1126/science.aac7341 Khalil, 2010, Synthetic Biology: Applications Come of Age, Nat. Rev. Genet., 11, 367, 10.1038/nrg2775 Sekine, 2013, Design and Control of Synthetic Biological Systems, 104 Hayden, 2014, The Automated Lab, Nat. News, 516, 131, 10.1038/516131a Appleton, 2017, Design Automation in Synthetic Biology, Cold Spring Harb. Perspect. Biol., 9, a023978, 10.1101/cshperspect.a023978 Hillson, 2012, j5 DNA Assembly Design Automation Software, ACS Synth. Biol., 1, 14, 10.1021/sb2000116 Linshiz, 2014, PR-PR: Cross-Platform Laboratory Automation System, ACS Synth. Biol., 3, 515, 10.1021/sb4001728 Ortiz, 2017, Automated Robotic Liquid Handling Assembly of Modular DNA Devices, J. Vis. Exp., No. 130, e54703 Appleton, 2017, Needs and Opportunities in Bio-Design Automation: Four Areas for Focus, Curr. Opin. Chem. Biol., 40, 111, 10.1016/j.cbpa.2017.08.005 New England BioLabs. Synthetic Biology/DNA Assembly Selection Chart. https://www.neb.com/tools-and-resources/selection-charts/synthetic-biology-dna-assembly-selection-chart (accessed Jan 7, 2019). Krane, 1988 Zuvela, 2014, Determining the Best Approach to Commercial Fusion Power, PAM Rev. Energy Sci. Technol., 1, 3, 10.5130/pamr.v1i0.1383 Cidar Lab. LCP SynBioHub Repository. https://synbiohub.programmingbiology.org/public/LCP/bubdc_ice_folder_11/1 (accessed Jan 7, 2019). Weber, 2012 Liang, 2017, Twin-Primer Non-Enzymatic DNA Assembly: An Efficient and Accurate Multi-Part DNA Assembly Method, Nucleic Acids Res., 45, e94, 10.1093/nar/gkx132 Storch, 2015, BASIC: A New Biopart Assembly Standard for Idempotent Cloning Provides Accurate, Single-Tier DNA Assembly for Synthetic Biology, ACS Synth. Biol., 4, 781, 10.1021/sb500356d Hanahan, 1983, Studies on Transformation of Escherichia coli with Plasmids, J. Mol. Biol., 166, 557, 10.1016/S0022-2836(83)80284-8 Casini, 2015 Vladimir, P., Ong, J. L., Kucera, R. B., et al. Optimization of Golden Gate Assembly through Application of Ligation Sequence-Dependent Fidelity and Bias Profiling. bioRxiv 2018, 322297. Patrick, 2015, DNA Assembly in 3D Printed Fluidics, PloS One, 10, e0143636, 10.1371/journal.pone.0143636 Tee, 2013, Polishing the Craft of Genetic Diversity Creation in Directed Evolution, Biotechnol. Adv., 31, 1707, 10.1016/j.biotechadv.2013.08.021 McLaughlin, 2018, SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology, ACS Synth. Biol., 7, 682, 10.1021/acssynbio.7b00403