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IGEM:Caltech/2007/Project/Riboregulator: Difference between revisions
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IGEM:Caltech/2007/Project/Riboregulator (view source)
Revision as of 19:10, 26 October 2007
, 26 October 2007→Riboregulator Design
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To initiate translation, five trans-activating elements (ta1-ta5) were designed. Each sequence binds to the cis-repressive elements and opens up the RBS. For ta1-ta4, part of the sequence was complementary to the hairpin loop of the cr element and extending in the 5’ direction. Element ta5 was designed to bind to the 5’ end of the cis regulator and open up the hairpin in the 3’ direction. ta1 and ta2 were complimentary to cr1-4; ta3-5 were complimentary to cr5-8. The activation with these ta elements is currently being determined. | To initiate translation, five trans-activating elements (ta1-ta5) were designed. Each sequence binds to the cis-repressive elements and opens up the RBS. For ta1-ta4, part of the sequence was complementary to the hairpin loop of the cr element and extending in the 5’ direction. Element ta5 was designed to bind to the 5’ end of the cis regulator and open up the hairpin in the 3’ direction. ta1 and ta2 were complimentary to cr1-4; ta3-5 were complimentary to cr5-8. The activation with these ta elements is currently being determined. | ||
[[Image:Cis1 4 and trans1 2.JPG|left|thumb|800px|The cis1-cis4 repressive riboregulators are shown with their corresponding activators, trans1 and trans2. All structures differ in the number of base-pairs in end-loops, number of bulges, and number of base pairs on the 5' toe-hold. They were designed this way to find the optimal dynamic range in repression/activation of protein expression.]] | [[Image:Cis1 4 and trans1 2.JPG|left|thumb|800px|The cis1-cis4 repressive riboregulators are shown with their corresponding activators, trans1 and trans2. All structures differ in the number of base-pairs in end-loops, number of bulges, and number of base pairs on the 5' toe-hold. They were designed this way to find the optimal dynamic range in repression/activation of protein expression.]] | ||
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[[Image:Cis7 trans4.JPG|left|thumb|600px|The cis7 repressor was the only structure that gave an unfavorable activating structure with trans3 from the cis5-8 set; thus, a separate trans structure was designed to specifically target cis7.]] | [[Image:Cis7 trans4.JPG|left|thumb|600px|The cis7 repressor was the only structure that gave an unfavorable activating structure with trans3 from the cis5-8 set; thus, a separate trans structure was designed to specifically target cis7.]] | ||
[[Image: Cis5678 trans5.JPG|left|thumb|800px|The trans5 riboregulator was designed differently from trans1-4 in that it should bind to the 5’ end of the cis regulator and open up the hairpin in the 3’ direction. Bimolecular structures with cis5-8 all showed favorable activation in terms of free energies.]] | |||
[[Image:Cis trans compliments.JPG|right|thumb|500px|A schematic diagram showing the parts of cis1 repressor and trans1 activator that are complimentary to each other. Note that the RBS is now open.]] | [[Image:Cis trans compliments.JPG|right|thumb|500px|A schematic diagram showing the parts of cis1 repressor and trans1 activator that are complimentary to each other. Note that the RBS is now open.]] | ||
