Difference between revisions of "Part:BBa K2206000"

 
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This part can be used to regulate the expression of any protein in response to the levels of hsa-miR-15b-5p present in a system.  
 
This part can be used to regulate the expression of any protein in response to the levels of hsa-miR-15b-5p present in a system.  
  
The transcripts produced by this part are toxic to E. coli. We recommend the use of an inducible non-leaky promoter to allow for amplification in E. coli. For reference, we found BBa_K808000 suitable for expressing this part.
+
The transcripts 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 suitable for expressing this part.
 +
 
 +
See part BBa_K2206006 to see how this part works when regulating GFPmut3b.  
  
 
This part contains a strong RBS sequence.
 
This part contains a strong RBS sequence.
  
 
{{Template:CLSB-UK 17 Images 15p5p 1}}
 
{{Template:CLSB-UK 17 Images 15p5p 1}}
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 +
===Information contributed by City of London UK (2021)===
 +
[[File:ToeholdTools.png|x200px|center]]
 +
 +
This toehold switch was characterized <i>in silico</i> using the ToeholdTools project that our team developed.
 +
See https://github.com/lkn849/thtools for more information.
 +
 +
Metadata:
 +
*'''Group:''' City of London UK 2021
 +
*'''Author:''' Lucas Ng
 +
*'''Summary:''' Used our software ToeholdTools to investigate the target miRNA specificity and activation of this part.
 +
 +
Raw data:
 +
*[[Media:BBa_K2206000_thtest.txt]]
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*[[Media:BBa_K2206000_crt.txt]]
 +
 +
This contribution was autogenerated by the script '''contrib.py''', available at https://github.com/lkn849/thtools/tree/master/registry.
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 +
----
 +
 +
This switch was designed to detect the miRNA hsa-miR-15b-5p at a temperature of 37°C.
 +
We tested it against every mature <i>Homo sapiens</i> miRNA in miRBase and our analysis shows that at this temperature it is best used to detect hsa-miR-15b-5p.
 +
 +
With hsa-miR-15b-5p at 37°C, the switch has a specificity of 81 ± 30 % and an activation of 16 ± 7 %.
 +
These values represent 95% confidence limits (z=1.96).
 +
 +
The temperature&ndash;activation&ndash;specificity relationship is shown here.
 +
CRT is an acronym for CelsiusRangeTest, the class in our Python library responsible for the following graph:
 +
 +
[[File:BBa_K2206000_graph.png|500px|center]]
 +
 +
Error bars represent the standard deviation.
 +
The line of best fit was calculated using a univariate cubic spline weighted inverse to each point's standard error.
 +
  
 
<!-- Add more about the biology of this part here
 
<!-- Add more about the biology of this part here

Latest revision as of 10:29, 8 October 2021

Toehold switch for hsa-miR-15b-5p

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-15b-5p (the trigger RNA). In the presence of hsa-miR-15b-5p, translation of the downstream protein coding region occurs.

This part can be used to regulate the expression of any protein in response to the levels of hsa-miR-15b-5p present in a system.

The transcripts 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 suitable for expressing this part.

See part BBa_K2206006 to see how this part works when regulating GFPmut3b.

This part contains a strong RBS sequence.

NUPACK Structure Analysis

RBSStart codonTriggerBindingSiteTriggerBindingSitemiRNAStart codonRBS

Information contributed by City of London UK (2021)

ToeholdTools.png

This toehold switch was characterized in silico using the ToeholdTools project that our team developed. See https://github.com/lkn849/thtools for more information.

Metadata:

  • Group: City of London UK 2021
  • Author: Lucas Ng
  • Summary: Used our software ToeholdTools to investigate the target miRNA specificity and activation of this part.

Raw data:

This contribution was autogenerated by the script contrib.py, available at https://github.com/lkn849/thtools/tree/master/registry.


This switch was designed to detect the miRNA hsa-miR-15b-5p at a temperature of 37°C. We tested it against every mature Homo sapiens miRNA in miRBase and our analysis shows that at this temperature it is best used to detect hsa-miR-15b-5p.

With hsa-miR-15b-5p at 37°C, the switch has a specificity of 81 ± 30 % and an activation of 16 ± 7 %. These values represent 95% confidence limits (z=1.96).

The temperature–activation–specificity relationship is shown here. CRT is an acronym for CelsiusRangeTest, the class in our Python library responsible for the following graph:

BBa K2206000 graph.png

Error bars represent the standard deviation. The line of best fit was calculated using a univariate cubic spline weighted inverse to each point's standard error.


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]