Part:BBa_K3743012
Small Nuclear Ribonucleoprotein (snRNP) Riboswitch
Part Description & Usage
A riboswitch that inhibits transcription by binding of MS2 with the small nuclear ribonulceoprotein (U2-snRNP). MS2 is linked to the destabilising domain (DD) in our design via a Gly Ser linker, which may be stabilised following Trimethoprim administration (TMP). After stabilising DD, TMP, a small molecule inhibitor, will release the MS2. Free MS2 binds to U2-snRNP, which inhibits the circuit, allowing the transcription process to be controlled in severe situations such as cytokine storms or unexpected outcomes.
Characterization by Mathematical Modelling
In order to simulate the dynamics of the used riboswitches which acts as an essential safety switches in our vaccine design, Mathematical modeling is performed using ordinary differential equations (ODEs) and fitted parameters.
As shown in Figure(1), P2 which represents the binding state shown inhibition throughout the time which conclude inhibition of the circuit. On the other hand, P1 which represents removing the inhibitory effect of riboswitches showed increased transcription of the circuit which reach the steady state after about 200 seconds.
Structural Characterization
n order to model the structural stability of MS2-U2SNRP, we used RNAfold tool that predicts secondary structures of single stranded RNA.
The final result was that the free energy of the thermodynamic ensemble is -9.13 kcal/mol.
The frequency of the MFE structure in the ensemble is 35.78 %.
The ensemble diversity is 3.86.
The final result was that the free energy of the thermodynamic ensemble is -54.19 kcal/mol.
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
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