Difference between revisions of "Part:BBa K2206003"
 
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<partinfo>BBa_K2206003 short</partinfo>
 
<partinfo>BBa_K2206003 short</partinfo>
  
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{{Template:CLSB-UK 17 TS|microRNA=hsa-miR-27b-3p|reporter=GFPmut3b}}
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Toehold switches are synthetic riboregulators that regulate gene expression post-transcriptionally. Gene expression can be activated in the presence of a cognate single stranded RNA molecule that contains an arbitrary sequence (the trigger RNA). The trigger RNA binds to the switch through base pairing, causing a conformational change that results in translation of the downstream protein coding region.
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This part codes for a toehold switch that contains a region that is complementary to the microRNA hsa-miR-27b-3p (the trigger RNA). The toehold switch is activated by hsa-miR-27b-3p and regulates production of GFPmut3b. The fluorescence intensity from GFPmut3b is proportional to the number of toehold switches activated (as the more switches activated, the greater the amount of GFPmut3b is produced), thus indicating the levels of hsa-miR-27b-3p present (as the more microRNA there is, the greater the number of switches activated). This part can therefore be used to quantify the levels of hsa-miR-27b-3p.
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The transcripts levels produced by this part are toxic to E. coli. Therefore, we recommend the use of an inducible non-leaky promoter to allow for amplification in E. coli. For reference, we found Bba_K808000 was not a suitable replacement for BBa_J23111 as it is too leaky.
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This part contains a strong RBS sequence.
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{{Template:CLSB-UK 17 Images 27b3p 1}}
  
 
<!-- Add more about the biology of this part here
 
<!-- Add more about the biology of this part here

Latest revision as of 23:05, 30 October 2017

Toehold switch for hsa-miR-27b-3p with GFPmut3b

Toehold switches are synthetic riboregulators that regulate gene expression post-transcriptionally. Gene expression can be activated in the presence of a cognate single stranded RNA molecule that contains an arbitrary sequence (the trigger RNA). The trigger RNA binds to the switch through base pairing, causing a conformational change that results in translation of the downstream protein coding region.

This part codes for a toehold switch that contains a region that is complementary to the microRNA hsa-miR-27b-3p (the trigger RNA). The toehold switch is activated by hsa-miR-27b-3p and regulates production of GFPmut3b. The fluorescence intensity from GFPmut3b is proportional to the number of toehold switches activated (as the more switches activated, the greater the amount of GFPmut3b is produced), thus indicating the levels of hsa-miR-27b-3p present (as the more microRNA there is, the greater the number of switches activated). This part can therefore be used to quantify the levels of hsa-miR-27b-3p.

The transcripts levels produced by this part are toxic to E. coli. Therefore, we recommend the use of an inducible non-leaky promoter to allow for amplification in E. coli. For reference, we found Bba_K808000 was not a suitable replacement for BBa_J23111 as it is too leaky.

This part contains a strong RBS sequence.

NUPACK Structure Analysis

Start codonRBSTrigger Binding SiteFree energy of secondary structure: -18.80 kcal/molACGUMFE structure at 37.0°CTrigger Binding SitemiRNAStartcodonRBSFree energy of secondary structure: -46.98 kcal/molACGUMFE structure at 37.0°C

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 7
    Illegal NheI site found at 30
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 758