Part:BBa_K3657018

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]