Difference between revisions of "Part:BBa K2066116"

Revision as of 03:02, 29 October 2016

Synthetic Enhancer Project: 3x TetO Binding Cassette (52s) + sfGFP on UNS

This part takes the synthetic enhancer circuit with a three TetO binding cassette and puts it onto a single BioBrick backbone flanked by the UNS regions. It includes a sfGFP reporter coding sequence downstream of the sigma 54 promoter. This part allows for a four step output response due to the three TetO binding cassette in the spacer region between the enhancer and promoter.The number of filled TetO sites influences the rigidity and the thermodynamics of the looping.

This part should be transformed with the helper plasmid Bba_K2066037 to get a consititutive expression of TetR repressor and NRII2302 (which is a kinase and phosphorylates NRI to activate it and allow it to bind to the enhancer).

Source: The enhancer, tet cassette, glnAp2 synthetic promoter, and NRI coding region sequences were derived from Amit, R., Garcia, H. G., Phillips, R. & Fraser, S. E. Building enhancers from the ground up: a synthetic biology approach. Cell146, 105–118 (2011). The sfGFP flourescent reporter design is inspired by C. Lou, B. Stanton, Y.-J. Chen, B. Munsky, C. A. Voigt, Ribozyme-based insulator parts buffer synthetic circuits from genetic context. Nat. Biotechnol. 30, 1137 (2012). doi:10.1038/nbt.2401 pmid:23034349. The UNS sequences at the ends of the insert are derived from Torella, J. P., Boehm, C. R., Lienert, F., Chen, J. H., Way, J. C., & Silver, P. A. (2013). Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly. Nucleic acids research, gkt860. A huge thanks to all the researchers involved in its original creation!

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
INCOMPATIBLE WITH RFC[12]
Illegal NheI site found at 111
Illegal NheI site found at 206
21
INCOMPATIBLE WITH RFC[21]
Illegal XhoI site found at 171
23
COMPATIBLE WITH RFC[23]
25
INCOMPATIBLE WITH RFC[25]
Illegal AgeI site found at 951
1000
INCOMPATIBLE WITH RFC[1000]
Illegal SapI.rc site found at 1939

@@ Line 3: / Line 3: @@
 <partinfo>BBa_K2066116 short</partinfo>
-This part takes the synthetic genetic circuit from Amit et. al. and puts it onto a BioBrick backone flanked by the UNS regions. Used for the synthetic enhancer project, this part consists of an enhancer region, that when bound to phosphorylated NRI protein, can bind to the promoter after the DNA loops to allow for these kinetics.  Once the looping and interaction between the enhancer and promoter happens, transcription of the NRI protein for positive feedback as well as the output flourescent reporter (sfGFP) is initiated.  This part (52s) is from the synthetic enhancer genetic circuits created by Amit et. al where there is a tetR binding cassette with three TetO binding sites in the spacer region between the enhancer and the promoter.  The three binding sites allows for four discrete states of output: a repressed, two intermediate, and unrepressed states. Small chemical induction with aTc binds to and inactivates available TetR repressor.  When a small amount of aTc is present, there isn't enough aTc to find TetR proteins and there is enough repressor available to allow for a constant filling of the three available TetO binding sites. When all TetO sites are bound, the DNA becomes very rigid and makings looping of the enhancer to the promoter extremely difficult, thus not allowing for very minimal transcription of the NRI and reporter proteins.  When more aTc is added to the system, more TetR is bound and inactivated and this creates two intermediate steps where enough TetR is bound that at any point only one or two TetR are bound to the teto sites and this decreases the flexibility of the DNA and allows for looping and activation and reporter output less frequently.  Finally, when aTc conentration is high, you reach a saturation point where almost all TetR repressors are bound and inactivated and you get maximal amount of looping and thus maximal amount of NRI and reporter transcribed and translated.
+This part takes the synthetic enhancer circuit with a three TetO binding cassette and puts it onto a single BioBrick backbone flanked by the UNS regions. It includes a sfGFP reporter coding sequence downstream of the sigma 54 promoter. This part allows for a four step output response due to the three TetO binding cassette in the spacer region between the enhancer and promoter.The number of filled TetO sites influences the rigidity and the thermodynamics of the looping.
 This part should be transformed with the helper plasmid Bba_K2066037 to get a consititutive expression of TetR repressor and NRII2302 (which is a kinase and phosphorylates NRI to activate it and allow it to bind to the enhancer).