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Team:Virginia Commonwealth/Internal/Experimentation
From 2009.igem.org
Experimental (wetlab) planning
The figure above depicts the work flow involved with biological engineering projects. The design and synthesis phases are dependent on product specifications, components to build with and tools to put them together - these phases are synthetic biology-driven. The systems biology-driven steps are the analysis and model steps, which take advantage of high-throughput omics measurement technologies, bioinformatic approaches to organizing the generated data and computational biology methods to simulate biological systems. The design and model stages are largely carried out computationally whereas the synthesis and analysis steps require the use of the laboratory (i.e., wetlab).
Synthesis
The substrate we're working with is DNA, which we can isolate and clone from a natural source, find within a repository such as the Registry of Standard Biological Parts, or have fabricated (i.e., chemically synthesized) by a DNA synthesis company such as DNA2.0 or GENEART.
Once you have your DNA, you're ready to get started with the realization of your design. Usually, the first step is the bacterial amplification of your starting material, DNA, which is usually housed on a plasmid. Therefore, first transform E. coli with the appropriate DNA and allow the bacteria to propagate, thereby amplifying the amount of your DNA. The properly transformed bacteria can be selected for by including the appropriate antibiotic in the growth medium.
Specifically, you should spread out the (hopefully) transformed cells on an LB-agar dish and culture overnight. After selecting 5 colonies from the dish the next day, you should grow up 5 overnight liquid cultures (5mL volume is good).
