A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts

Yizhi Cai, Brian Hartnett, Claes Gustafsson, Jean Peccoud

    Research output: Contribution to journalArticlepeer-review

    Abstract

    Motivation: The sequence of artificial genetic constructs is composed of multiple functional fragments, or genetic parts, involved in different molecular steps of gene expression mechanisms. Biologists have deciphered structural rules that the design of genetic constructs needs to follow in order to ensure a successful completion of the gene expression process, but these rules have not been formalized, making it challenging for non-specialists to benefit from the recent progress in gene synthesis.
    Results: We show that context-free grammars (CFG) can formalize these design principles. This approach provides a path to organizing libraries of genetic parts according to their biological functions, which correspond to the syntactic categories of the CFG. It also provides a framework for the systematic design of new genetic constructs consistent with the design principles expressed in the CFG. Using parsing algorithms, this syntactic model enables the verification of existing constructs. We illustrate these possibilities by describing a CFG that generates the most common architectures of genetic constructs in Escherichia coli.
    Original languageEnglish
    Pages (from-to)2760-2767
    Number of pages8
    JournalBioinformatics
    Volume23
    Issue number20
    DOIs
    Publication statusPublished - 15 Oct 2007

    Keywords

    • Chromosome Mapping
    • Computer Simulation
    • DNA
    • Genetic Code
    • Genetic Engineering
    • Genomic Islands
    • Models, Genetic

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