Team:Heidelberg/Part Collection
The RBP Collection
Enabling Modular RBP Design
We used the modular RNA binding Pentatricopeptide Repeat and Pumby proteins on many different applications in our experiment, or implementation design. May it be the tethering together of functional protein subunits, mRNA translation inhibition or completely different applications, like the fluorescent marking of specific RNA motifs - whenever a specific RNA motif has to be bound by a protein Pumby or PPR proteins are the simple answer.
In our page about Pumby and PPR proteins we already talked about the structure and biology of these proteins. If you want to design your own PPR or Pumby proteins, simply concatenate the subunits listed underneath in the same order than the RNA motif of your choice. When designing PPR proteins, you have to additionally cap the N-terminal end with BBa_K3657010 and add to the C-terminus the solubility helix BBa_K3657010, as PPR proteins are naturally very unsuable.
In theory PPR and Pumby proteins of any length can be created. For the pumby proteins, it has already been shown that 18-mers can be created without loosing binding specifity to their corresponding RNA motif
Modular RNA Binding
Table 1: The modular RBP Collection
| Name | Type | Description | Length |
|---|---|---|---|
| BBa_K3657000 | Coding | RNA binding Pumilio Homology Domain (Adenine) | 111 |
| BBa_K3657001 | Coding | RNA binding Pumilio Homology Domain (Guanine) | 111 |
| BBa_K3657002 | Coding | RNA binding Pumilio Homology Domain (Uracil) | 111 |
| BBa_K3657003 | Coding | RNA binding Pumilio Homology Domain (Cytosine) | 111 |
| BBa_K3657004 | Coding | RNA binding Pumby Protein - Motif AUAGAU | 675 |
| BBa_K3657005 | Coding | RNA binding Pumby Protein - Motif AUGGUU | 669 |
| BBa_K3657006 | Coding | RNA binding Pentatricopeptide Repeat Protein (Adenin) | 105 |
| BBa_K3657007 | Coding | RNA binding Pentatricopeptide Repeat Protein (Uracil) | 105 |
| BBa_K3657008 | Coding | RNA binding Pentatricopeptide Repeat Protein (Cytosine) | 105 |
| BBa_K3657009 | Coding | RNA binding Pentatricopeptide Repeat Protein (Guanine) | 105 |
| BBa_K3657010 | Coding | N-Terminal Cap for Pentatricopeptide Repeat Proteins | 9 |
| BBa_K3657011 | Coding | Solubility Helix for Pentatricopeptide Repeat Proteins | 45 |
| BBa_K3657012 | Coding | RNA binding Pentatricopeptide Repeat Protein - Motif ACACAG | 684 |
| BBa_K3657013 | Coding | RNA binding Pentatricopeptide Repeat Protein - Motif GUAGAG | 684 |
| BBa_K3657037 | RNA | RNA Linker binding Pumby AUAGAU and Pumby AUGGUU | 103 |