Difference between revisions of "Part:BBa K598001"
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<partinfo>BBa_K598001 short</partinfo>
 
<partinfo>BBa_K598001 short</partinfo>
  
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This is a GFP generator with a theophylline responsive riboswitch sequence. The mRNA with a theophylline riboswitch in it would respond to theophylline concerntration, producing different amount of GFP measured by GFP fluorescence intensity. Under the control of different promoters, it could be used to demonstrate the theophylline responsive curve, providing data for modeling. The theophylline riboswitch sequence could also be used to modulate other downstream gene expression.
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This is a GFP generator regulated by theophylline responsive riboswitch. mRNA with a theophylline riboswitch in it responds to theophylline concerntration, producing different fluorescence strength of GFP. Regulated by different promoters, it would be used to demonstrate theophylline responsive curve, providing data for [http://2011.igem.org/Team:Peking_R/Project/RNAToolkit modeling].
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In this part, the theophylline responsive riboswitch contains an engineered ribosome binding site.
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<partinfo>BBa_K598001 parameters</partinfo>
 
<partinfo>BBa_K598001 parameters</partinfo>
 
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<h2>Background</h2>
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Riboswitches are structured non-coding RNA domains performing as genetic control elements, regulating gene expression through ligand-RNA interactions without assistance of proteins. Several natural riboswitches have been reported, sensing small molecules including vitamin B1 and B12, FMN, SAM, lysine, guanine, adenine, TPP and theophylline [1]. Various mechanisms are utilized to regulate gene expression, ranging from transcription initiation to translation attenuation.
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[[Image:PekingR parts theo Growth curve.png|right|thumb|500px| '''Figure.1 Growth curves of E.coli under treatments of different theophylline concentrations.''' Adding theophylline into the medium after incubating at 37 degrees in shaker for 8 hours, consistent with induce experiment. Under 10mM theophylline concentration, there is negligible growth inhibition..]]
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Theophylline responsive riboswitches have been widely studied in recent years. Theophylline is a small molecule which is passable through bacterial cytomembrane, but not an essential nutrient of bacteria. Although theophylline has moderate toxicity leading to growth inhibition in logarithmic phase with 15mM theophylline in LB medium, this theophylline responsive riboswitch shows an approving regulation curve under 10mM theophylline concentration with negligible growth inhibition in M9 liquid medium (Fig.1).
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<h2>Experimental Data</h2>
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'''Parental 1G1'''
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We adopted the original theophylline responsive riboswitch, named Parental 1G1 (P1G1) in our project, designed by Beatrix Suess on Nucleic Acids Research, as a candidate of our [http://2011.igem.org/Team:Peking_R/Project/RNAToolkit RNA controller toolbox]. Stereo representation of the three-dimensional structure of theophylline aptamer is schematized in Fig.2.
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[[Image:PekingR parts theo1G1 3D.png|right|thumb|500px| '''Figure.2 Schematic of the theophylline aptamer structure.'''Red: theophylline; yellow: theophylline binding site.]]
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Theophylline responsive riboswitch P1G1 integrates the theophylline aptamer with a helical communication module based on a ligand–dependent one-nucleotide slipping mechanism (Fig.3) [2]. This structural element lies at a position just interfering with translation in the non ligand-binding form. Addition of ligand shifts the inhibitory secondary structure element that is originally closed to RBS to a distance that permits efficient translation. This slippage mechanism regulating gene expression makes it different from natural riboswtiches those are based on sequenstration or antitermination [3].
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[[Image:PekingR parts theo PIG1 2D.jpg|right|thumb|500px| '''Figure.3 Predicted secondary structure of P1G1 in the absence and presence of theophylline. '''Theophylline aptamer is boxed. 1nt slipping mechanism is shown in yellow. UGGA is shown in red as RBS sequence. AUG initiation codon is in black.]]
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GFP fluorescence intensity is measured to demonstrate the ability of P1G1 riboswitches to modulate downstream gene expression. GFP fluorescence intensity is measured with increasing concentrations of theophylline(Fig.4). P1G1 displays a 6-fold activation ratio of the absence to presence of 10mM theophylline (Fig.5). Inspection of the highest translation rate reveals that although high concentration of ligand fully motivates translation, the GFP fluorescence intensity is still low, indicating relatively low translation strength. However, we expect wider translation strength available for theophylline riboswitch, thus the performance of P1G1 needs to be genetically optimized.
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[[Image:PekingR parts exp data.jpg|left|thumb|450px|'''Figure.4 Dose responses of P1G1 riboswitch and 1G1 riboswitch.'''(A) Photo shows GFP fluorescence intensity induced by gradients of theophylline concentration. The left most well denotes induction in the absence of theophylline. GFP fluorescence intensity increases with the concentration of theophylline. (B) Dose responsive curves of 1G1 and P1G1 with a theophylline concentration gradient in the presence of arabinose. RBS sequences and corresponding dG are also presented in the graph. Arrow indicates the global increase of translation strength variation range.
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[[Image:PekingR parts Fold-1G1&P1G1.jpg|right|thumb|430px|'''Figure.5''' The ability of P1G1 and 1G1 to activate translation strength under induction by a theophylline concentration gradient.
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'''Engineered Theophylline riboswitch—Theo 1G1'''
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On account of the circumscribed property of RNA controllers, insertion of RNA controller probably makes even the highest expression level lower than sole RBS sequence upstream AUG start codon. Insertion of RNA controller could expediently down-regulate downstream gene translation, but it is impossible to up-regulate downstream gene translation rate exceeding that of sole RBS. A strong RBS is thought to proportionally shift the modulating range/activation ratio of RNA controllers without changing the width to a higher level, as they are turned gradually from completely OFF state to fully ON state in the presence of ligand. [[Image:PekingR parts theo 1G1 2D.jpg|right|thumb|400px|'''Figure.6 Predicted secondary structure of 1G1 in the absence and presence of theophylline.''' Theophylline aptamer is boxed. 1nt slipping mechanism is shown in yellow. UGGA is shown in red as RBS sequence. AUG start codon is in black.
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Therefore, we optimized original RBS sequence of P1G1 to AGGAGGU, the consensus RBS sequence predicted to initiate high rate of translation according to the [http://2011.igem.org/Team:Peking_R/Project/RBSAutomatedDesign RBS calculator]. Simultaneously, as we positioned RNA controller 1G1 upstream of GFP coding sequence by standard assembly, the spacing between RBS and AUG strat codon is ACUAG (scar generated during standard assembly). The modification of RBS sequence and spacing between RBS and AUG start codon had inappreciable influence on the core secondary stem-loop structure of functional original riboswitch P1G1 and almost preserves the quondam base-pairing region. Stem-loop structure of 1G1 is schematized in Fig.6. 1G1 shares the same slipping mechanism with P1G1.
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Dose response curve is shown in Fig.5. 1G1 displays a 10-fold activation ratio of the absence to presence of 10mM theophylline (Fig.5). However, under a concentration of 5mM theophylline, 1G1 shares similar activation ratio with P1G1, consistent with the prediction that alteration of RBS provides more flexible absolute translation strength with a fixed regulative range. Inspection of these two version of theophylline riboswitch reveals that 1G1 with the highest level of expression in the presence of theophylline not only possesses a longer RBS sequence (AGGAGGU) than P1G1, but also a more optimal spacing (5nt upstream to AUG start codon). Comparison of basal level of P1G1 and 1G1 suggests that 1G1 holds a more significant leakage in the absence of theophylline than P1G1, coincident with the holistic high expression of 1G1. According to our experiment data, engineered riboswitch possesses a more optimal absolute translation rate range, consistent with the prediction that a stronger RBS provides the RNA controller with a stronger regulation capability.
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<h2>Further Application</h2>
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Screening for well performing devices usually requires laborious, time-consuming refinement cycles, especially in the case of information processing devices. Utilizing the platform introduced this year ([http://2011.igem.org/Team:Peking_R/Project Peking_R, iGEM2011]), we aim at making tuning devices fast, affordable and more predictable. To demonstrate the versatility and validity of the platform, it was firstly applied to modulating a genetic AND gate.
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The AND gate we utilized was designed by Anderson and his colleagues and consequently standardly redesigned by PKU_Beijing 09 team ([https://parts.igem.org/Part:BBa_K228258 BBa_K228258], Fig. 7A).
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[[Image:PekingR parts AG plasmid&mechanism.jpg|center|thumb|600px| '''Figure 7: The construction and mechanism of AND gate.''' A). The standardly redesigned AND gate of PKU_Beijing 09 team. B). The topology and mechanism of AND gate. Parts showing in box constitute the core processing module.
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Here are some of the results, for detailed description, please have a look at [http://2011.igem.org/Team:Peking_R/Project our soft-coding platform].
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[[Image:PekingR parts Theo P1G1 AG pic.jpg|left|thumb|300px|'''AND gate regulated by P1G1'''
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[[Image:PekingR parts P1G1 AG.jpg|right|thumb|300px|'''AND gate regulated by 1G1'''
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Minor differences in RBS strength may largely influence the performance of genetic program, consistent with the fact that tuning genetic circuits requires laborious and refinement cycles, especially in the case of complex systems. When applying our platform into optimizing genetic circuts, the soft-coding of genetic program, with riboswitches' assistance, makes synthetic biology fast, affordable and more predictable.
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In summary, our semi-rational method to modify RNA controller (in our case, theophylline riboswitch) offers a promising clue for optimizing the performance of RBS-related riboswitches. The application of riboswitch provides solid evidence that it contains various functional potential which would be further exploited.
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<h2>References</h2>
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[1]Nahvi,A., Sudarsan,N., Ebert,M.S., Zou,X., Brown,K.L. and Breaker ,R.R. (2002) Genetic control by a metabolite binding mRNA. ''Chem. Biol''., '''9''', 1043-1049.
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[2]Beatrix Suess, Barbara Fink, Christian Berens, Régis Stentz and Wolfgang Hillen. (2004) A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo. ''Nucleic Acids Research'', '''32''', 1610-1614.
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[3]Sean A. Lynch, Shawn K. Desai, Hari Krishna Sajja, and Justin P. Gallivan. (2006) A High-Throughput Screen for Synthetic Riboswitches Reveals Mechanistic Insights into Their Function. ''Chem. Biol''., '''14''', 173-184.
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<h2>Related Parts</h2>
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[https://parts.igem.org/wiki/index.php?title=Part:BBa_K228258 BBa_K228258]  AND gate of iGEM 09 PKU_Beijing
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[https://parts.igem.org/wiki/index.php?title=Part:BBa_K598005 BBa_K598005]  Theophylline Responsive Riboswitch P1G1 with Native RBS
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[https://parts.igem.org/wiki/index.php?title=Part:BBa_K598006 BBa_K598006]  Theophylline Responsive Riboswitch 1G1 with Engineered RBS
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[https://parts.igem.org/wiki/index.php?title=Part:BBa_K598007 BBa_K598007]  Theophylline Responsive Riboswitch P1G1 with Native RBS+E0040+B0015
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[https://parts.igem.org/wiki/index.php?title=Part:BBa_K598009 BBa_K598009]  pBAD+Theophylline Responsive Riboswitch P1G1 with Native RBS+E0040+B0015
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[https://parts.igem.org/wiki/index.php?title=Part:BBa_K598010 BBa_K598010]  pBAD+Theophylline Responsive Riboswitch 1G1 with Engineered RBS+E0040+B0015
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[https://parts.igem.org/wiki/index.php?title=Part:BBa_K598027 BBa_K598027]  AND gate (BBa_K228258) regulated by theophylline riboswitch P1G1 (BBa_K598005)

Latest revision as of 16:18, 10 May 2013

Theophylline Responsive Riboswitch 1G1 with Engineered RBS+GFP generator

This is a GFP generator regulated by theophylline responsive riboswitch. mRNA with a theophylline riboswitch in it responds to theophylline concerntration, producing different fluorescence strength of GFP. Regulated by different promoters, it would be used to demonstrate theophylline responsive curve, providing data for [http://2011.igem.org/Team:Peking_R/Project/RNAToolkit modeling].


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal XhoI site found at 71
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 730


Background


Riboswitches are structured non-coding RNA domains performing as genetic control elements, regulating gene expression through ligand-RNA interactions without assistance of proteins. Several natural riboswitches have been reported, sensing small molecules including vitamin B1 and B12, FMN, SAM, lysine, guanine, adenine, TPP and theophylline [1]. Various mechanisms are utilized to regulate gene expression, ranging from transcription initiation to translation attenuation.


Figure.1 Growth curves of E.coli under treatments of different theophylline concentrations. Adding theophylline into the medium after incubating at 37 degrees in shaker for 8 hours, consistent with induce experiment. Under 10mM theophylline concentration, there is negligible growth inhibition..


Theophylline responsive riboswitches have been widely studied in recent years. Theophylline is a small molecule which is passable through bacterial cytomembrane, but not an essential nutrient of bacteria. Although theophylline has moderate toxicity leading to growth inhibition in logarithmic phase with 15mM theophylline in LB medium, this theophylline responsive riboswitch shows an approving regulation curve under 10mM theophylline concentration with negligible growth inhibition in M9 liquid medium (Fig.1).


Experimental Data


Parental 1G1


We adopted the original theophylline responsive riboswitch, named Parental 1G1 (P1G1) in our project, designed by Beatrix Suess on Nucleic Acids Research, as a candidate of our [http://2011.igem.org/Team:Peking_R/Project/RNAToolkit RNA controller toolbox]. Stereo representation of the three-dimensional structure of theophylline aptamer is schematized in Fig.2.


Figure.2 Schematic of the theophylline aptamer structure.Red: theophylline; yellow: theophylline binding site.




Theophylline responsive riboswitch P1G1 integrates the theophylline aptamer with a helical communication module based on a ligand–dependent one-nucleotide slipping mechanism (Fig.3) [2]. This structural element lies at a position just interfering with translation in the non ligand-binding form. Addition of ligand shifts the inhibitory secondary structure element that is originally closed to RBS to a distance that permits efficient translation. This slippage mechanism regulating gene expression makes it different from natural riboswtiches those are based on sequenstration or antitermination [3].

Figure.3 Predicted secondary structure of P1G1 in the absence and presence of theophylline. Theophylline aptamer is boxed. 1nt slipping mechanism is shown in yellow. UGGA is shown in red as RBS sequence. AUG initiation codon is in black.







GFP fluorescence intensity is measured to demonstrate the ability of P1G1 riboswitches to modulate downstream gene expression. GFP fluorescence intensity is measured with increasing concentrations of theophylline(Fig.4). P1G1 displays a 6-fold activation ratio of the absence to presence of 10mM theophylline (Fig.5). Inspection of the highest translation rate reveals that although high concentration of ligand fully motivates translation, the GFP fluorescence intensity is still low, indicating relatively low translation strength. However, we expect wider translation strength available for theophylline riboswitch, thus the performance of P1G1 needs to be genetically optimized.

Figure.4 Dose responses of P1G1 riboswitch and 1G1 riboswitch.(A) Photo shows GFP fluorescence intensity induced by gradients of theophylline concentration. The left most well denotes induction in the absence of theophylline. GFP fluorescence intensity increases with the concentration of theophylline. (B) Dose responsive curves of 1G1 and P1G1 with a theophylline concentration gradient in the presence of arabinose. RBS sequences and corresponding dG are also presented in the graph. Arrow indicates the global increase of translation strength variation range. .








Figure.5 The ability of P1G1 and 1G1 to activate translation strength under induction by a theophylline concentration gradient. .











Engineered Theophylline riboswitch—Theo 1G1





On account of the circumscribed property of RNA controllers, insertion of RNA controller probably makes even the highest expression level lower than sole RBS sequence upstream AUG start codon. Insertion of RNA controller could expediently down-regulate downstream gene translation, but it is impossible to up-regulate downstream gene translation rate exceeding that of sole RBS. A strong RBS is thought to proportionally shift the modulating range/activation ratio of RNA controllers without changing the width to a higher level, as they are turned gradually from completely OFF state to fully ON state in the presence of ligand.
Figure.6 Predicted secondary structure of 1G1 in the absence and presence of theophylline. Theophylline aptamer is boxed. 1nt slipping mechanism is shown in yellow. UGGA is shown in red as RBS sequence. AUG start codon is in black. .

Therefore, we optimized original RBS sequence of P1G1 to AGGAGGU, the consensus RBS sequence predicted to initiate high rate of translation according to the [http://2011.igem.org/Team:Peking_R/Project/RBSAutomatedDesign RBS calculator]. Simultaneously, as we positioned RNA controller 1G1 upstream of GFP coding sequence by standard assembly, the spacing between RBS and AUG strat codon is ACUAG (scar generated during standard assembly). The modification of RBS sequence and spacing between RBS and AUG start codon had inappreciable influence on the core secondary stem-loop structure of functional original riboswitch P1G1 and almost preserves the quondam base-pairing region. Stem-loop structure of 1G1 is schematized in Fig.6. 1G1 shares the same slipping mechanism with P1G1.


Dose response curve is shown in Fig.5. 1G1 displays a 10-fold activation ratio of the absence to presence of 10mM theophylline (Fig.5). However, under a concentration of 5mM theophylline, 1G1 shares similar activation ratio with P1G1, consistent with the prediction that alteration of RBS provides more flexible absolute translation strength with a fixed regulative range. Inspection of these two version of theophylline riboswitch reveals that 1G1 with the highest level of expression in the presence of theophylline not only possesses a longer RBS sequence (AGGAGGU) than P1G1, but also a more optimal spacing (5nt upstream to AUG start codon). Comparison of basal level of P1G1 and 1G1 suggests that 1G1 holds a more significant leakage in the absence of theophylline than P1G1, coincident with the holistic high expression of 1G1. According to our experiment data, engineered riboswitch possesses a more optimal absolute translation rate range, consistent with the prediction that a stronger RBS provides the RNA controller with a stronger regulation capability.


Further Application


Screening for well performing devices usually requires laborious, time-consuming refinement cycles, especially in the case of information processing devices. Utilizing the platform introduced this year ([http://2011.igem.org/Team:Peking_R/Project Peking_R, iGEM2011]), we aim at making tuning devices fast, affordable and more predictable. To demonstrate the versatility and validity of the platform, it was firstly applied to modulating a genetic AND gate.


The AND gate we utilized was designed by Anderson and his colleagues and consequently standardly redesigned by PKU_Beijing 09 team (BBa_K228258, Fig. 7A).

Figure 7: The construction and mechanism of AND gate. A). The standardly redesigned AND gate of PKU_Beijing 09 team. B). The topology and mechanism of AND gate. Parts showing in box constitute the core processing module. .


Here are some of the results, for detailed description, please have a look at [http://2011.igem.org/Team:Peking_R/Project our soft-coding platform].


AND gate regulated by P1G1 .
AND gate regulated by 1G1 .

Minor differences in RBS strength may largely influence the performance of genetic program, consistent with the fact that tuning genetic circuits requires laborious and refinement cycles, especially in the case of complex systems. When applying our platform into optimizing genetic circuts, the soft-coding of genetic program, with riboswitches' assistance, makes synthetic biology fast, affordable and more predictable.






In summary, our semi-rational method to modify RNA controller (in our case, theophylline riboswitch) offers a promising clue for optimizing the performance of RBS-related riboswitches. The application of riboswitch provides solid evidence that it contains various functional potential which would be further exploited.



References

[1]Nahvi,A., Sudarsan,N., Ebert,M.S., Zou,X., Brown,K.L. and Breaker ,R.R. (2002) Genetic control by a metabolite binding mRNA. Chem. Biol., 9, 1043-1049.

[2]Beatrix Suess, Barbara Fink, Christian Berens, Régis Stentz and Wolfgang Hillen. (2004) A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo. Nucleic Acids Research, 32, 1610-1614.

[3]Sean A. Lynch, Shawn K. Desai, Hari Krishna Sajja, and Justin P. Gallivan. (2006) A High-Throughput Screen for Synthetic Riboswitches Reveals Mechanistic Insights into Their Function. Chem. Biol., 14, 173-184.


Related Parts

BBa_K228258 AND gate of iGEM 09 PKU_Beijing

BBa_K598005 Theophylline Responsive Riboswitch P1G1 with Native RBS

BBa_K598006 Theophylline Responsive Riboswitch 1G1 with Engineered RBS

BBa_K598007 Theophylline Responsive Riboswitch P1G1 with Native RBS+E0040+B0015

BBa_K598009 pBAD+Theophylline Responsive Riboswitch P1G1 with Native RBS+E0040+B0015

BBa_K598010 pBAD+Theophylline Responsive Riboswitch 1G1 with Engineered RBS+E0040+B0015

BBa_K598027 AND gate (BBa_K228258) regulated by theophylline riboswitch P1G1 (BBa_K598005)