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Cloning

Gene Composer(TM) software suite for computer-aided construct engineering and expression-optimized synthetic gene design is available for download at http://www.genecomposer.net.

Gene Composer(TM) software suite for computer-aided construct engineering and expression-optimized synthetic gene design is available for download from www.genecomposer.net. Gene Composer(TM) is a complete synthetic gene design suite for Microsoft Windows that runs on top of a single user Access database with an Alignment Viewer, Construct Design Module, and Gene Design Module. In addition, the Virtual Cloning Module features the ability to permute gene constructs into defined expression vectors by way of user-defined adaptor assemblies that recapitulate most wet lab cloning procedures. The Gene Composer(TM) Protein-to-DNA algorithm allows users to design codon optimized DNA sequences based on the original cDNA or amino acid sequence data, while introducing or eliminating other defined DNA sequence elements. For example, all ACA sequences can be silently removed from open reading frames so that they may be used in conjunction with the MazF system for single protein production.

An example of the use of synthetic gene design by Gene Composer is reported in Singh, et al. (2008). This paper demonstrates the importance of determining protein structures in translational medicine by describing the identification of human DcpS (mRNA decapping scavenger enzyme) as a therapeutic target for spinal muscular atrophy (SMA). A series of C5-substituted quinazoline molecules that inhibit DcpS were shown to enhance expression of the SMN2 gene, which may help patients with SMA. To facilitate this discovery, ATCG3D researchers synthetically engineered a novel DcpS gene for protein expression and crystallization with the aid of Gene Composer. ATCG3D researchers went on to solve the high resolution X-ray crystal structures of DcpS bound to several of the most active C5-substituted quinazolines. In a recent article, Lorimer and co-workers describe the use of Gene Composer in the structural genomics effort of the Seattle Structural Genomics Center for Infectious Diseases (SSGCID).

Virtual cloning in Gene Composer. Once constructs have been created, they can be virtually cloned. The vector is chosen from a pull-down menu and the appropriate adapters added to facilitate the cloning strategy. In this example, a stop codon has been inserted at the end of all the constructs and BamHI and HindIII adapters have been added (Figure 6 from Lorimer, et al., 2011).

Singh J, Salcius M, Liu SW, Staker BL, Mishra R, Thurmond J, Michaud G, Mattoon DR, Printen J, Christensen J, Bjornsson JM, Pollok BA, Kiledjian M, Stewart L, Jarecki J, Gurney ME. "DcpS as a therapeutic target for spinal muscular atrophy." ACS Chem. Biol. 3, 711-22 (2008). PubMed ID: 18839960 | Search SBKB Publications portal | PMC Link

Lorimer D, Raymond A, Mixon M, Burgin A, Staker B, Stewart L. "Gene Composer in a structural genomics environment." Acta Crystallogr. Sect. F: Struct. Biol. Cryst. Commun. 67:985-91 (2011). PubMed ID:21904038 | PMC Link

Lance Stewart, Email: lstewart@embios.com

Accelerated Technologies Center for Gene to 3D Structure

Emerald Bio is responsible for commercialization of Gene Composer, http://www.embios.com.

http://www.genecomposer.net