Integration of standardized cloning methodologies and sequence handling to support synthetic biology studies

The assembly and downstream transformation of genetic constructs has been a fundamental scientific technology for the last thirty years. Synthetic biology is an engineering based approach to molecular biology as emphasizing the standardized assembly of characterized DNA fragments. The standards promoted by the BioBricks™ Foundation have enabled novel constructs to be developed based upon the expected function of these constructs. However scientists need a software environment that enables them to curate large collections of parts and assemblies, combined with appropriate tools to facilitate quick creation of constructs and identification of potential design issues in silico. In this paper, we present the implementation of BioBrick™ and GENEART® Assembly tools, coupled with an enhanced database to manage and develop such parts collections. Integration of these tools and data into the VectorNTI® software suite is a step towards implementation of BioCAD™, a computer based design approach to facilitate development of complex circuit based perturbation of cellular systems.