Difference between revisions of "Part:BBa K1442304"

Latest revision as of 18:54, 16 October 2014

SLD3 RdRP Promoter 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 SLD3 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-directed Replication for further details.

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

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
COMPATIBLE WITH RFC[21]
23
COMPATIBLE WITH RFC[23]
25
INCOMPATIBLE WITH RFC[25]
Illegal NgoMIV site found at 13
Illegal NgoMIV site found at 41
Illegal NgoMIV site found at 70
1000
INCOMPATIBLE WITH RFC[1000]
Illegal BsaI.rc site found at 34

@@ Line 1: / Line 1: @@
 __NOTOC__
 <partinfo>BBa_K1442304 short</partinfo>
-This is a promoter we tested with our RdRp that was derived from the 3' untranslated region of the Brome Mosaic Virus and forms a stem loop that forms an additional canonical structure that attracts the polymerase.
+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 SLD3 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-directed Replication for further details.
+== Usage ==
+Used as an RNA promoter to direct replication by RdRP.
+[[File:Promoters_Diagram.jpg]]
+=== RdRP-directed Replication ===
+[[File:FF.png]]
+. The DNA strand gets transcribed and then translated, whereby the RdRP protein is produced.
+. The active RdRP binds to the 3’ end of the transcribed plus –sense RNA strand. It produces its complementary minus-sense RNA strand.
+. 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'''
-<!-- Add more about the biology of this part here
+[[File:ModEq.png]]
-===Usage and Biology===
+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.
 <!-- -->
 <span class='h3bb'>Sequence and Features</span>