Part:BBa_K1442117
Sldel+8 3
Each unique RNA dependent RNA polymerase (RdRP) initiates de novo replication of a RNA strand by interacting with RdRP-specific RNA sequences, henceforth called RdRP/RNA promoters. The RdRP chosen for our project is taken from the Hepatitis C virus (HCV). The SLdel+8 RNA promoter was identified as such by Heinz, Kao (2000) , along with a number of other sequences. All of them possess a few common characteristics: an initiation cytidylate at the 3’ end, where the replication starts; and a stable secondary structure- single stranded tail and a stem of various length. Replication stops at the 5’ end. Please refer to Section: RdRP function for further details.
This is a genomic plus-strand RNA that can direct BMV minus-strand initiation. This has 8 nucleotides at the 5’end deleted and shows that the 5’ end is not essential for NS5B action.
Usage
Used as an RNA promoter to direct replication by RdRP.
RdRP-directed Replication
1. The DNA strand gets transcribed and then translated, whereby the RdRP protein is produced.
2. The active RdRP binds to the 3’ end of the transcribed plus –sense RNA strand. It produces its complementary minus-sense RNA strand.
3. The RdRP interacts with the 5’ end of the replicated minus-sense RNA strand. It produces the plus-sense RNA strand again and completes the full replication of the RNA. The new RNA strand can act as a template as well and the process of replication can start over.
Mathematical Modelling
E-coli
Where c, α-,β are constants, E stands for the RdRP, G – for GFP. R- is amount of minus-sense RNA strands, R+ amount of plus-sense RNA strands; µ- is degradation rate of the minus-sense strands and µ+of the plus-sense.
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25INCOMPATIBLE WITH RFC[25]Illegal NgoMIV site found at 38
Illegal NgoMIV site found at 67 - 1000COMPATIBLE WITH RFC[1000]
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