Part:BBa_K3743009

30x degredation motifs

Part Description

These motifs are interchangeable and only active within 3′ UTRs, where they are typically preferentially conserved; they are also found in hundreds of transcripts, many of which encode regulatory proteins. The CCR4–NOT complex mediates mRNA deadenylation, which results in degradation.

Usage

This is an addition to the downstream toehold switch, which binds to tumor-suppressing miRNA. By replacing the liker with malate 1 triplex and adding 30X degradation motifs downstream, the toehold switch is modified. This enables degradation of the transcripts to decrease the yield of the vaccine after suppressing the tumor.

Structural Characterization

In order to model the structural stability of DegraderToeHold switch, we used RNAfold tool that predicts secondary structures of single stranded RNA.

The free energy of the thermodynamic ensemble is -124.84 kcal/mol.

The frequency of the MFE structure in the ensemble is 0.09 %.

The ensemble diversity is 60.44 .

Figure 1.Structural Characterization of Toehold.

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]