The Constructor: a web application optimizing cloning strategies based on modules from the registry of standard biological parts

Journal of Biological Engineering

Mark W J van Passel¹  Floor Hugenholtz²  Dorett I Odoni³  Thijs Slijkhuis³  Jasper J Koehorst³  Matthijn C Hesselman³ 

[1] Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands;Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands;iGEM Wageningen UR, Wageningen University, Wageningen, The Netherlands

关键词: Genetic circuit;    Transcription units;    BioBrick parts;    Synthetic Biology;   

Others  :  813411
DOI  :  10.1186/1754-1611-6-14

 received in 2012-06-27, accepted in 2012-09-02,  发布年份 2012

【 摘 要 】

Synthetic biology is an emerging field that combines molecular biology with engineering principles, which requires abstraction levels applied to a modular biological componentry. The Registry of Standard Biological Parts harbours such a repository of standardized parts, and thereby facilitates the combination of complex molecular modules to novel genetic circuits and devices. However, since finding the best parts for a pre-determined genetic design can be time consuming, we devised the Constructor, a web tool that recommends the smallest number of cloning steps for pre-designed circuits, and implements user-defined quality checks.

We present the Constructor ( http://www.systemsbiology.nl/the_constructor webcite) as a constructive web tool that simplifies the in silico assembly of pre-designed gene circuitries from standard parts, reducing both planning and subsequent cloning time.

【 授权许可】

   
2012 Hesselman et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

【 参考文献 】

• [1]Gardner TS, Cantor CR, Collins JJ: Construction of a genetic toggle switch in Escherichia coli. Nature 2000, 403(6767):339-342.
• [2]Elowitz MB, Leibler S: A synthetic oscillatory network of transcriptional regulators. Nature 2000, 403(6767):335-338.
• [3]Bonnet J, Subsoontorn P, Endy D: Rewritable digital data storage in live cells via engineered control of recombination directionality. Proc Natl Acad Sci USA 2012, 109(23):8884-8889.
• [4]Conrado RJ, Wu GC, Boock JT, Xu H, Chen SY, Lebar T, Turnsek J, Tomsic N, Avbelj M, Gaber R, et al.: DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency. Nucleic Acids Res 2011, 40(4):1879-1889.
• [5]Leprince A, van Passel MW, Dos Santos VA: Streamlining genomes: toward the generation of simplified and stabilized microbial systems. Curr Opin Biotechnol 2012.
• [6]Posfai G, Plunkett G, Feher T, Frisch D, Keil GM, Umenhoffer K, Kolisnychenko V, Stahl B, Sharma SS, de Arruda M, et al.: Emergent properties of reduced-genome Escherichia coli. Science 2006, 312(5776):1044-1046.
• [7]Leprince A, de Lorenzo V, Voller P, van Passel MW, Martins Dos Santos VA: Random and cyclical deletion of large DNA segments in the genome of Pseudomonas putida. Environ Microbiol 2012, 14(6):1444-1453.
• [8]Constante M, Grunberg R, Isalan M: A biobrick library for cloning custom eukaryotic plasmids. PLoS One 2011, 6(8):e23685.
• [9]Smolke CD: Building outside of the box: iGEM and the BioBricks Foundation. Nat Biotechnol 2009, 27(12):1099-1102.
• [10]Hesselman MC, Odoni DI, Ryback BM, de Groot S, van Heck RG, Keijsers J, Kolkman P, Nieuwenhuijse D, van Nuland YM, Sebus E, et al.: A multi-platform flow device for microbial (co-) cultivation and microscopic analysis. PLoS One 2012, 7(5):e36982.
• [11]Boyle PM, Burrill DR, Inniss MC, Agapakis CM, Deardon A, Dewerd JG, Gedeon MA, Quinn JY, Paull ML, Raman AM, et al.: A BioBrick compatible strategy for genetic modification of plants. J Biol Eng 2012, 6(1):8. BioMed Central Full Text
• [12]Kelly JR, Rubin AJ, Davis JH, Ajo-Franklin CM, Cumbers J, Czar MJ, de Mora K, Glieberman AL, Monie DD, Endy D: Measuring the activity of BioBrick promoters using an in vivo reference standard. J Biol Eng 2009, 3:4. BioMed Central Full Text