Difference between revisions of "Part:BBa K3247003"

 
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<partinfo>BBa_K3247003 short</partinfo>
  
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RNA thermometers are a form of translational regulation. Our RNA thermometers were designed to have a high fold change between 25°C and 30°C, which is a significantly lower temperature range than existing thermometers that are generally optimized for expression at 37°C or higher.
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===Design Notes===
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The stem-loop structure of the thermometer was created by taking the complement of the ribosome binding site (RBS) and adding nucleotides to either side. The additional bases were mutated; the resulting altered sequence is known as the variable region. Mutating the variable region keeps the RBS intact while modifying the RNA thermometer secondary structure to change the melting temperature. There is no internal BsaI cut site, since it would render the thermometer incompatible with our assembly method. The part is TypeIIS compatible. Figure 1a-c showing the RNA thermometer structures were designed using NUPACK software.
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<img src="https://2019.igem.org/wiki/images/d/df/T--Rice--0425.png" width = 60%>
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<p><b>Figure 1a.</b> Predicted RNA thermometer structure at 25 °C.</p>
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<img src="https://2019.igem.org/wiki/images/c/c0/T--Rice--0430.png" width = 60%>
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<p><b>Figure 1b.</b> Predicted RNA thermometer structure at 30 °C.</p>
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<img src="https://2019.igem.org/wiki/images/4/45/T--Rice--0437.png" width = 60%>
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<p><b>Figure 1c.</b> Predicted RNA thermometer structure at 37 °C.</p>
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===Characterization===
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<img src="https://2019.igem.org/wiki/images/c/c2/T--Rice--Nochill4.png" width = 60%>
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<p><b>Figure 2.</b> Fluorescence intensity at 25 °C, 30 °C, and 37 °C.</p>
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<partinfo>BBa_K3247003 SequenceAndFeatures</partinfo>
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===Source===
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The thermometers were designed de novo using NUPACK and VSAlgorithm
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===References===
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J. N. Zadeh, C. D. Steenberg, J. S. Bois, B. R. Wolfe, M. B. Pierce, A. R. Khan, R. M. Dirks, N. A. Pierce. NUPACK: analysis and design of nucleic acid systems. J Comput Chem, 32:170–173, 2011. (pdf)

Latest revision as of 00:05, 22 October 2019

RNA Thermometer NoChill-04

RNA thermometers are a form of translational regulation. Our RNA thermometers were designed to have a high fold change between 25°C and 30°C, which is a significantly lower temperature range than existing thermometers that are generally optimized for expression at 37°C or higher.

Design Notes

The stem-loop structure of the thermometer was created by taking the complement of the ribosome binding site (RBS) and adding nucleotides to either side. The additional bases were mutated; the resulting altered sequence is known as the variable region. Mutating the variable region keeps the RBS intact while modifying the RNA thermometer secondary structure to change the melting temperature. There is no internal BsaI cut site, since it would render the thermometer incompatible with our assembly method. The part is TypeIIS compatible. Figure 1a-c showing the RNA thermometer structures were designed using NUPACK software.

Figure 1a. Predicted RNA thermometer structure at 25 °C.

Figure 1b. Predicted RNA thermometer structure at 30 °C.

Figure 1c. Predicted RNA thermometer structure at 37 °C.

Characterization

Figure 2. Fluorescence intensity at 25 °C, 30 °C, and 37 °C.


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]

Source

The thermometers were designed de novo using NUPACK and VSAlgorithm


References

J. N. Zadeh, C. D. Steenberg, J. S. Bois, B. R. Wolfe, M. B. Pierce, A. R. Khan, R. M. Dirks, N. A. Pierce. NUPACK: analysis and design of nucleic acid systems. J Comput Chem, 32:170–173, 2011. (pdf)