Essential information for synthetic DNA sequences

Peccoud, Jean; Anderson, Janet S.; Chandran, Deepak; Densmore, Douglas; Galdzicki, Michal; Lux, Matthew W.; Rodriguez, Cesar; Stan, Guy-Bart; Sauro, Herbert M.

doi:10.1038/nbt.1753

Cited by 47 publications

(38 citation statements)

References 8 publications

(8 reference statements)

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“…The specification of a quality standard for synthetic DNA sequences would greatly simplify the reporting of essential information for synthetic DNA sequences (26). …”

Section: Discussionmentioning

confidence: 99%

Sequence verification of synthetic DNA by assembly of sequencing reads

Wilson

Cai

Hanlon

et al. 2012

Nucleic Acids Research

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Gene synthesis attempts to assemble user-defined DNA sequences with base-level precision. Verifying the sequences of construction intermediates and the final product of a gene synthesis project is a critical part of the workflow, yet one that has received the least attention. Sequence validation is equally important for other kinds of curated clone collections. Ensuring that the physical sequence of a clone matches its published sequence is a common quality control step performed at least once over the course of a research project. GenoREAD is a web-based application that breaks the sequence verification process into two steps: the assembly of sequencing reads and the alignment of the resulting contig with a reference sequence. GenoREAD can determine if a clone matches its reference sequence. Its sophisticated reporting features help identify and troubleshoot problems that arise during the sequence verification process. GenoREAD has been experimentally validated on thousands of gene-sized constructs from an ORFeome project, and on longer sequences including whole plasmids and synthetic chromosomes. Comparing GenoREAD results with those from manual analysis of the sequencing data demonstrates that GenoREAD tends to be conservative in its diagnostic. GenoREAD is available at www.genoread.org.

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“…The specification of a quality standard for synthetic DNA sequences would greatly simplify the reporting of essential information for synthetic DNA sequences (26). …”

Section: Discussionmentioning

confidence: 99%

Sequence verification of synthetic DNA by assembly of sequencing reads

Wilson

Cai

Hanlon

et al. 2012

Nucleic Acids Research

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“…This power arises from the Registry of Standard Biological Parts which can be further maintained and improved when a quality control of the BioBricks is included in order to maximize the benefits for its users [Peccoud et al 2008]. In addition, the reusability of biological parts will also be slightly improved by systematically disclosing annotated sequence information when reporting synthetic gene networks in research articles, as recently addressed by Peccoud et al [2011]. As a consequence, a combination of such small changes and new technologies will ultimately encourage the successful design of novel synthetic biological systems.…”

Section: Discussionmentioning

confidence: 99%

Synthetic Biology and Microdevices

Venken

Marchal

Vanderleyden

2013

J. Emerg. Technol. Comput. Syst.

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Recent developments demonstrate that the combination of microbiology with micro-and nanoelectronics is a successful approach to develop new miniaturized sensing devices and other technologies. In the last decade, there is a shift from the optimization of the abiotic components, e.g. the chip, to the improvement of the processing capabilities of cells through genetic engineering. The synthetic biology approach will not only give rise to systems with new functionalities, but will also improve the robustness and speed of their response towards applied signals. To this end, the development of new genetic circuits has to be guided by computational design methods that enable to tune and optimize the circuit response. As the successful design of genetic circuits is highly dependent on the quality and reliability of its composing elements, intense characterization of standard biological parts will be crucial for an efficient rational design process in the development of new genetic circuits. Microengineered devices can thereby offer a new analytical approach for the study of complex biological parts and systems. By summarizing the recent techniques in creating new synthetic circuits and in integrating biology with microdevices, this review aims at emphasizing the power of combining synthetic biology with microfluidics and microelectronics.

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“…The wide adoption of a design standard would allow the growing number of software tools to more directly support an integrated design workflow 8 involving synthetic biologists from both research and commercial institutions. p e r s p e c t i v e Furthermore, a 'standard exchange format' for synthetic biology designs would dramatically improve the ability to reproduce published results 9 . Currently, it is extremely difficult to extract workable designs from literature because designs are usually described using imprecise and error-prone English prose.…”

Section: P E R S P E C T I V Ementioning

confidence: 99%

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology

et al. 2014

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The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. Here we describe the Synthetic Biology Open Language (SBOL), a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a communitydriven, formalized format for exchange between software tools, research groups and commercial service providers. The SBOL Developers Group has implemented SBOL as an XML/RDF serialization and provides software libraries and specification documentation to help developers implement SBOL in their own software. We describe early successes, including a demonstration of the utility of SBOL for information exchange between several different software tools and repositories from both academic and industrial partners. As a community-driven standard, SBOL will be updated as synthetic biology evolves to provide specific capabilities for different aspects of the synthetic biology workflow.Synthetic biology treats biological organisms as a new technological medium with a unique set of characteristics, such as the ability to self-repair, evolve and replicate. These characteristics create their own engineering challenges, but offer a rich and largely untapped source of potential applications across a broad range of sectors 1,2 . Applications such as biomolecular computing 3 , metabolic engineering 4 , or reconstruction and exploration of natural cell biology 5,6 commonly require the design of new genetically encoded systems. As engineers, synthetic biologists most often base their designs on previously described 'DNA segments' (see Supplementary Table 1 for definitions of selected terms) to meet their design requirements. Reuse of the DNA sequence for these segments involves their exchange between laboratories and their hierarchical composition to form devices and systems with higher level function.Every engineering field relies on a set of 'standards' 7 that practitioners follow to enable the exchange and reuse of designs for 'systems' , 'devices' and 'components' . Similarly, the representation of synthetic biology designs using computer-readable 'data standards' has the potential to facilitate the forward engineering of novel biological systems from previously characterized devices and components. For example, such standards could enable synthetic biology companies to offer catalogs of devices and components by means of computerreadable data sheets, just as modern semiconductor companies do for electronics. Such standards could also enable a synthetic biologist to develop portions of a design using one software tool, refine the design using another tool, and finally transmit it electronically to a colleague or commercial fabrication company.In order for synthetic biology designs to scale up in complexity, researchers will need to make greater use of specialized design tools and parts repositories. Seamless inter-tool communication would, for example, allow the separation of gene...

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Essential information for synthetic DNA sequences

Cited by 47 publications

References 8 publications

Sequence verification of synthetic DNA by assembly of sequencing reads

Sequence verification of synthetic DNA by assembly of sequencing reads

Synthetic Biology and Microdevices

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology

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