Source:
Generated By: https://synbiohub.org/public/igem/igem2sbol/1
Created by: Iva Burova
Date created: 2014-10-15 11:00:00
Date modified: 2015-05-08 01:10:27
5' RdRP Promoter
| Types | DnaRegion |
| Roles | Other sequence_feature |
| Sequences | BBa_K1442118_sequence (Version 1) |
Description
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). It starts replication at the 3??? end of the HCV RNA strand. This 3??? UTR is a RNA promoter. After producing the minus strand of the HCV RNA, the RdRP ???recognises??? the reversed 5???UTR of the original RNA and initiates second replication which produces the viral RNA in is positive sense . Therefore, the reversed 5??? UTR (R5) of HCV is also a RNA promoter. The complete sequence was taken from the NCBI GenBank . It has been suggested that the first 125 nucleotides of the 5???UTR are sufficient for replication, but the inclusion of the entire 341 base-long region results in higher efficiency rates . Due to the fact that the 5???UTR and a part of the coding sequence constitute an IRES essential for the translation of the HCV, another 76 nucleotides from the coding DNA were included in the sequence for the promoter.Notes
RibozymeThe use of a ribozyme is necessitated due to the complicated binding process between the RNA template and the RdRP. In order to optimise the process and avoid any risk of unfavourable secondary structures or obstruction by unneeded nucleotides, a self-cleaving ribozyme was put after the RNA promoter. The rationale being that after transcription (either in vitro for human cell tests or in vivo for e-coli tests), any added bases as a result of the T7 polymerase would be removed from the main template strand. The chosen ribozyme taken from the Hepatitis Delta virus was investigated at length by the team of J. Doudna and is reported to be the fasted naturally occurring, independent and resistant to denaturants. Its close genetic origin also contribute to a better working and compatible system.
Source
Hepatitis C Virus| Sequence Annotation | Location | Component / Role(s) |
| Ribozyme RNA Promoter | 1,42 43,434 | engineered_region feature/BioBrick feature/promoter promoter |