Difference between revisions of "Part:BBa K3657017:Design"

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===Design Notes===
 
===Design Notes===
 
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The part was designed based on the original Broccoli aptamer with the use of <a href="">DesignSimple</a> in order to exclude the BsmbI cutting site and introduce the GUAGAG loop.
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The part was designed based on the original Broccoli aptamer with the use of <a href="https://github.com/igemsoftware2020/Heidelberg_2020/blob/main/CoNcoRDe/CoNcoRDe/rnasupport/scripts/design_simple.py">DesignSimple</a> in order to exclude the BsmbI cutting site and introduce the GUAGAG loop.
 
<p>Due to the COVID pandemic we were not able to experimentally prove that this Broccoli modification binds DFHBI correctly <i>in vitro</i>.</p>
 
<p>Due to the COVID pandemic we were not able to experimentally prove that this Broccoli modification binds DFHBI correctly <i>in vitro</i>.</p>
 
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===References===
 
===References===
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Wenjiao S, Strack R L, Nina S, et al. Plug-and-play fluorophores extend the spectral properties of Spinach.[J]. Journal of the American Chemical Society, 2014, 136(4):1198-1201. Filonov G S, Moon J D, Nina S, et al. Broccoli: Rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution.[J]. Journal of the American Chemical Society, 2014, 136.

Latest revision as of 23:47, 27 October 2020


Broccoli Aptamer with added GUAGAG RNA Loop


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]


Design Notes

The part was designed based on the original Broccoli aptamer with the use of DesignSimple in order to exclude the BsmbI cutting site and introduce the GUAGAG loop.

Due to the COVID pandemic we were not able to experimentally prove that this Broccoli modification binds DFHBI correctly in vitro.

Source

Synthetic

References

Wenjiao S, Strack R L, Nina S, et al. Plug-and-play fluorophores extend the spectral properties of Spinach.[J]. Journal of the American Chemical Society, 2014, 136(4):1198-1201. Filonov G S, Moon J D, Nina S, et al. Broccoli: Rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution.[J]. Journal of the American Chemical Society, 2014, 136.