Abstract
BackgroundThe design and construction of novel biological systems by combining basic building blocks represents a dominant paradigm in synthetic biology. Creating and maintaining a database of these building blocks is a way to streamline the fabrication of complex constructs. The Registry of Standard Biological Parts (Registry) is the most advanced implementation of this idea.Methods/Principal FindingsBy analyzing inclusion relationships between the sequences of the Registry entries, we build a network that can be related to the Registry abstraction hierarchy. The distribution of entry reuse and complexity was extracted from this network. The collection of clones associated with the database entries was also analyzed. The plasmid inserts were amplified and sequenced. The sequences of 162 inserts could be confirmed experimentally but unexpected discrepancies have also been identified.Conclusions/SignificanceOrganizational guidelines are proposed to help design and manage this new type of scientific resources. In particular, it appears necessary to compare the cost of ensuring the integrity of database entries and associated biological samples with their value to the users. The initial strategy that permits including any combination of parts irrespective of its potential value leads to an exponential and economically unsustainable growth that may be detrimental to the quality and long-term value of the resource to its users.
Highlights
De novo gene synthesis [1,2,3] is catalyzing a transition from the ad-hoc methods of traditional genetic engineering to the development of industrial-scale fabrication processes enabling users to quickly obtain from commercial vendors genetic constructs that would have been assembled through a custom cloning strategy just a few years ago
Designing a construct for gene synthesis often consists in combining a number of previously defined DNA sequences [4]
Catalogues of biological parts that are sufficiently well characterized to be used in the design of new genetic constructs can be described in review articles [5], embedded into software applications to design new DNA sequences [4], or made available through a web site [6,7]
Summary
De novo gene synthesis [1,2,3] is catalyzing a transition from the ad-hoc methods of traditional genetic engineering to the development of industrial-scale fabrication processes enabling users to quickly obtain from commercial vendors genetic constructs that would have been assembled through a custom cloning strategy just a few years ago. The design of an expression cassette in Escherichia coli typically includes a promoter, a Ribosome Binding Site (RBS), a coding sequence, and a transcription terminator These functional blocks are commonly referred to as biological parts or genetic parts. The process is generic because the restriction enzymes and ligation steps it includes are independent of the sequences of the two parts being combined This standardized assembly of new genetic constructs derived from standardized parts is complementary to de novo gene synthesis since both approaches can be used to fabricate designer DNA sequences. Another benefit from standardizing parts is the physical composition of BioBrick parts. The Registry of Standard Biological Parts (Registry) is the most advanced implementation of this idea
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