Part:BBa_K1520002

Riboswitch MC31

It is a putative riboswitch designed by our team. We designed a lot of riboswitch for microcystin, and then choose a excellent ones, MC31 by modeling. They are riboswitches based on the stability of mRNA. The structure of them includes a hammerhead ribozyme and a microcystin aptamer. Users can connect them to the downstream of promoters to use them.

Sometimes, the promoter of the target molecule cannot be found, thus we use this tested design strategy to design the sequence of the riboswitches. Thus the synthetic riboswitch can substitute the promoter of the target molecule to control the expression of downstream genes. The designed sequence contains three parts, the hammerhead ribozyme, spacer sequence, and the aptamer. Firstly, the sequence of the hammerhead ribozyme has been given and tested by a published paper. Secondly, the spacer sequence, which isolate the riboswitch from the surrounding sequence. We combined the hammerhead ribozyme with the spacer sequence, and used RNAfold to simulate the secondary structure of it, and we have the structure as below:

Then we combined this structure with each aptamer of the microcistin separately, and used RNAfold to simulate their structure. According to the secondary structure and the modeling results, we found the most likely two riboswitches.

Using aptamer MC31:

We designed a synthetic riboswitch which has structure like this:

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
  COMPATIBLE WITH RFC[25]
• 1000
  COMPATIBLE WITH RFC[1000]