Difference between revisions of "Part:BBa K3657018"

 
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<partinfo>BBa_K3657018 short</partinfo>
 
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This part is a modification of the Broccoli dimer (<a href="https://parts.igem.org/Part:BBa_K1713020">BBa_K1713020</a>). It was re-engineered to exclude the BsmbI cutting site and GUAGAG RNA loop.
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===Usage and Biology===
 
===Usage and Biology===
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Broccoli is an aptamer that forms a stable secondary structure and binds the fluorogen DFHBI, which results in green fluorescence. The absence of BsmbI site allows cloning of this part with <a href="http://2018.igem.org/Team:Marburg/Part_Collection">Marburg Collection system</a>. The GUAGAG loop was introduced in order to allow PPR protein specific to GUAGAG (<a href="https://parts.igem.org/Part:BBa_K3657013">BBa_K3657013</a>) to bind to the part, since PPR can only bind single stranded RNA.
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Concatenating two Broccoli aptamers together results in higher fluorescent activity.
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<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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<img style="width:20%"src="https://static.igem.org/mediawiki/parts/a/ab/T--Heidelberg--Parts-BBa_K3657018.jpg"
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<p><b>Figure 1:</b> Secondary structure of the part.</p>
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<span class='h3bb'>Sequence and Features</span>
 
<span class='h3bb'>Sequence and Features</span>
 
<partinfo>BBa_K3657018 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K3657018 SequenceAndFeatures</partinfo>

Latest revision as of 03:45, 28 October 2020


dBroccoli Aptamer with added GUAGAG RNA Loop

This part is a modification of the Broccoli dimer (BBa_K1713020). It was re-engineered to exclude the BsmbI cutting site and GUAGAG RNA loop.

Usage and Biology

Broccoli is an aptamer that forms a stable secondary structure and binds the fluorogen DFHBI, which results in green fluorescence. The absence of BsmbI site allows cloning of this part with Marburg Collection system. The GUAGAG loop was introduced in order to allow PPR protein specific to GUAGAG (BBa_K3657013) to bind to the part, since PPR can only bind single stranded RNA. Concatenating two Broccoli aptamers together results in higher fluorescent activity.

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

Figure 1: Secondary structure of the part.


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
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 23
  • 1000
    COMPATIBLE WITH RFC[1000]