Writing DNA with GenoCAD™

Chemical synthesis of custom DNA made to order calls for software streamlining the design of synthetic DNA sequences. GenoCAD™ (www.genocad.org) is a free web-based application to design protein expression vectors, artificial gene networks and other genetic constructs composed of multiple functional blocks called genetic parts. By capturing design strategies in grammatical models of DNA sequences, GenoCAD guides the user through the design process. By successively clicking on icons representing structural features or actual genetic parts, complex constructs composed of dozens of functional blocks can be designed in a matter of minutes. GenoCAD automatically derives the construct sequence from its comprehensive libraries of genetic parts. Upon completion of the design process, users can download the sequence for synthesis or further analysis. Users who elect to create a personal account on the system can customize their workspace by creating their own parts libraries, adding new parts to the libraries, or reusing designs to quickly generate sets of related constructs.

[1]  Alfonso Jaramillo,et al.  Asmparts: assembly of biological model parts , 2007, Systems and Synthetic Biology.

[2]  J. R. Coleman,et al.  Virus Attenuation by Genome-Scale Changes in Codon Pair Bias , 2008, Science.

[3]  E. O’Shea,et al.  Global analysis of protein expression in yeast , 2003, Nature.

[4]  D. Endy,et al.  Refactoring bacteriophage T7 , 2005, Molecular systems biology.

[5]  Vassilios Sotiropoulos,et al.  SynBioSS: the synthetic biology modeling suite , 2008, Bioinform..

[6]  Mudita Singhal,et al.  COPASI - a COmplex PAthway SImulator , 2006, Bioinform..

[7]  R. Reid,et al.  GeMS: an advanced software package for designing synthetic genes , 2005, Nucleic acids research.

[8]  M. Bennett,et al.  A fast, robust, and tunable synthetic gene oscillator , 2008, Nature.

[9]  D. Searls,et al.  Robots in invertebrate neuroscience , 2002, Nature.

[10]  Timothy B. Stockwell,et al.  Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome , 2008, Science.

[11]  Ron Weiss,et al.  Engineering life: building a fab for biology. , 2006, Scientific American.

[12]  David E. Swayne,et al.  Characterization of the Reconstructed 1918 Spanish Influenza Pandemic Virus , 2005, Science.

[13]  Jean Peccoud,et al.  A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts , 2007, Bioinform..

[14]  William Bains The parts list of life , 2001, Nature Biotechnology.

[15]  M. Elowitz,et al.  Frequency-modulated nuclear localization bursts coordinate gene regulation , 2008, Nature.

[16]  Nicholas J. Guido,et al.  A bottom-up approach to gene regulation , 2006, Nature.

[17]  김삼묘,et al.  “Bioinformatics” 특집을 내면서 , 2000 .

[18]  Brian W Bramlett,et al.  Genetic design: rising above the sequence. , 2008, Trends in biotechnology.

[19]  E. O’Shea,et al.  Global analysis of protein localization in budding yeast , 2003, Nature.

[20]  Jörg Stelling,et al.  Computational design of synthetic gene circuits with composable parts , 2008, Bioinform..

[21]  M. Elowitz,et al.  A synthetic oscillatory network of transcriptional regulators , 2000, Nature.

[22]  Jef D Boeke,et al.  Teaching Synthetic Biology, Bioinformatics and Engineering to Undergraduates: The Interdisciplinary Build-a-Genome Course , 2009, Genetics.

[23]  D. Endy Foundations for engineering biology , 2005, Nature.

[24]  Jay D Keasling,et al.  Metabolic engineering delivers next-generation biofuels , 2008, Nature Biotechnology.

[25]  Ehud Shapiro,et al.  Bringing DNA computers to life , 2006 .

[26]  J. Collins,et al.  Construction of a genetic toggle switch in Escherichia coli , 2000, Nature.

[27]  J. Boeke,et al.  GeneDesign: rapid, automated design of multikilobase synthetic genes. , 2006, Genome research.

[28]  Alan Villalobos,et al.  Gene Designer: a synthetic biology tool for constructing artificial DNA segments , 2006, BMC Bioinformatics.

[29]  A. Paul,et al.  Chemical Synthesis of Poliovirus cDNA: Generation of Infectious Virus in the Absence of Natural Template , 2002, Science.

[30]  Philip Ball,et al.  Synthetic biology: Designs for life , 2007, Nature.

[31]  J. Peccoud,et al.  Targeted Development of Registries of Biological Parts , 2008, PloS one.

[32]  Hiroaki Kitano,et al.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..

[33]  A. Ninfa,et al.  Development of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli , 2003, Cell.

[34]  D. Hoover,et al.  DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis. , 2002, Nucleic acids research.

[35]  Jean Peccoud,et al.  Gene synthesis demystified. , 2009, Trends in biotechnology.

[36]  J. Keasling Synthetic biology for synthetic chemistry. , 2008, ACS chemical biology.

[37]  Jeffrey C Way,et al.  Designing biological systems. , 2007, Genes & development.

[38]  J. Collins,et al.  Combinatorial promoter design for engineering noisy gene expression , 2007, Proceedings of the National Academy of Sciences.

[39]  Farren J. Isaacs,et al.  Engineered riboregulators enable post-transcriptional control of gene expression , 2004, Nature Biotechnology.

[40]  M. Elowitz,et al.  Programming gene expression with combinatorial promoters , 2007, Molecular systems biology.