A Step-by-Step Introduction to Rule-Based Design of Synthetic Genetic Constructs Using GenoCAD

Wilson, Mandy; Hertzberg, R.Y.; Adam, Laura; Peccoud, Jean

doi:10.1016/b978-0-12-385120-8.00008-5

Cited by 10 publications

(8 citation statements)

References 18 publications

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“…Field researchers are focused on designing of grammar rules in GenoCAD because GenoCAD software has broad applications, and related design in this programme can be highly diverse, as supported by recent designs for plant and synthetic genetic construct grammar [19]. Such design processes focus on the grammar itself and do not prove information on the rationale of the design.…”

Section: Resultsmentioning

confidence: 99%

Use of processed data to design an orderly logic gate to construct plasmids in GenoCAD

Shi

et al. 2017

IET syst. biol.

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Rapid developments have been made in synthetic biology within the past two decades, particularly in combination with chemistry, computer science, and other disciplines. Genetic components and internal features have been a main focus of research for synthetic biologists. Logic gates can be applied in various disciplines, but have not yet been used for plasmid design. GenoCAD is a computer-aided design software programme for synthetic biology that can be used to design complex structures. Thus, in this study, the authors analysed a large, commonly used data set containing over 70,000 feature sequences and eventually obtained comprehensive information for a complete data set without redundancy. By analysing the internal feature sequences, the authors input the most representative data in the GenoCAD platform, along with design rules and grammar for constructing high-quality practical parts. Additionally, the orderly logic gate for building biological parts designed in this study may be useful for professionals and non-professionals and may have applications in the design of a new biological computer. Finally, the authors compared the constructed plasmid with other successful examples in BLAST and PlasMapper software to demonstrate the rationality of the orderly logic gate.

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Section: Resultsmentioning

confidence: 99%

Use of processed data to design an orderly logic gate to construct plasmids in GenoCAD

Shi

et al. 2017

IET syst. biol.

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“…The ability to rapidly and automatically validate plasmids by Illumina sequencing will be especially applicable to large-scale plasmid production projects associated with synthetic biology (42). The rapidly decreasing cost of DNA synthesis and sophisticated computer-aided design tools (43,44) have facilitated disciplined factorial experiments involving large libraries of plasmids with various genetic parts (45) for applications such as improved genetic circuit design (46), multiplexed CRISPR-Cas (47) or metabolic engineering (48). These workflows, which are often automated (49,50), necessitate an automated sequence verification pipeline like the one we've described.…”

Section: Discussionmentioning

confidence: 99%

Rapid, robust plasmid verification byde novoassembly of short sequencing reads

Gallegos

Rogers²,

Cialek

et al. 2020

Preprint

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AbstractPlasmids are a foundational tool for basic and applied research across all subfields of biology. Increasingly, researchers in synthetic biology are relying on and developing massive libraries of plasmids as vectors for directed evolution, combinatorial gene circuit tests, and for CRISPR multiplexing. Verification of plasmid sequences following synthesis is a crucial quality control step that creates a bottleneck in plasmid fabrication workflows. Crucially, researchers often elect to forego the cumbersome verification step, potentially leading to reproducibility and— depending on the application—security issues. In order to facilitate plasmid verification to improve the quality and reproducibility of life science research, we developed a fast, simple, and open source pipeline for assembly and verification of plasmid sequences from Illumina reads. We demonstrate that our pipeline, which relies on de novo assembly, can also be used to detect contaminating sequences in plasmid samples. In addition to presenting our pipeline, we discuss the role for verification and quality control in the increasingly complex life science workflows ushered in by synthetic biology.

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“…Further, it was clear that user errors, custom notes, and non-standardized formats to freeform documents make conversion into a standardized form difficult and cumbersome. Despite rapid progress in the area of BioCAD tools [6,23-27], basic day-to-day usability and integration into wet-lab workflows remains one of the outstanding challenges to fully realizing the benefits of these tools.…”

Section: Discussionmentioning

confidence: 99%

2ab assembly: a methodology for automatable, high-throughput assembly of standard biological parts

et al. 2013

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There is growing demand for robust DNA assembly strategies to quickly and accurately fabricate genetic circuits for synthetic biology. One application of this technology is reconstitution of multi-gene assemblies. Here, we integrate a new software tool chain with 2ab assembly and show that it is robust enough to generate 528 distinct composite parts with an error-free success rate of 96%. Finally, we discuss our findings in the context of its implications for biosafety and biosecurity.

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A Step-by-Step Introduction to Rule-Based Design of Synthetic Genetic Constructs Using GenoCAD

Cited by 10 publications

References 18 publications

Use of processed data to design an orderly logic gate to construct plasmids in GenoCAD

Use of processed data to design an orderly logic gate to construct plasmids in GenoCAD

Rapid, robust plasmid verification byde novoassembly of short sequencing reads

2ab assembly: a methodology for automatable, high-throughput assembly of standard biological parts

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