Difference between revisions of "Part:BBa K4601105"

Revision as of 18:05, 2 October 2023

Synthetic RBS designed for NpSR

This part is a synthetic RBS specifically designed for the NpSRII sensory rhodopsin (BBa_K4601005) using the Salis Lab RBS Library Calculator v2.0 [1-3].

Usage and Biology

This RBS was used to drive the expression of NpSRII (BBa_K4601005) under the control of the T7 promoter (BBa_K2150031) in the composite part BBa_K4601205.

Using the Salis Lab RBS Library Calculator v2.0 [1-3], the predicted features of this RBS are:

Translation Initiation Rate (au)	:	9563,49
dG_total (kcal/mol)	:	-4,55
dG_mRNA_rRNA (kcal/mol)	:	-11.60
dG_spacing (kcal/mol)	:	0
dG_stacking (kcal/mol)	:	0
dG_standby (kcal/mol)	:	0.87
dG_start (kcal/mol)	:	-2.76
dG_mRNA (kcal/mol)	:	-9.37
Warnings	:	none

This RBS was selected as predicted to have a Translation Initiation Rate (TIR) of about 10000 au from a library of 64 RBSes (GGGGAAAMTTAAATTMAGGMGGTWKTAM) for which the estimated TIR range from 3891.73 to 649251.13.

References

[1] Reis AC, Salis HM. An automated model test system for systematic development and improvement of gene expression models. ACS synthetic biology (2020) 9: 3145–3156.

[2] Farasat I, Kushwaha M, Collens J, Easterbrook M, Guido M, Salis HM. Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria. Molecular Systems Biology (2014) 10: 731.

[3] Ng CY, Farasat I, Maranas CD, Salis HM. Rational design of a synthetic Entner-Doudoroff pathway for improved and controllable NADPH regeneration. Metabolic Engineering (2015) 29: 86–96.

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
COMPATIBLE WITH RFC[25]
1000
COMPATIBLE WITH RFC[1000]

@@ Line 3: / Line 3: @@
 <partinfo>BBa_K4601105 short</partinfo>
-to do
+This part is a synthetic RBS specifically designed for the NpSRII sensory rhodopsin ([[Part:BBa_K4601005|BBa_K4601005]]) using the [https://www.denovodna.com/ Salis Lab RBS Library Calculator v2.0] [1-3].
-<!-- Add more about the biology of this part here
 ===Usage and Biology===
+This RBS was used to drive the expression of NpSRII ([[Part:BBa_K4601005|BBa_K4601005]]) under the control of the T7 promoter ([[Part:BBa_K2150031|BBa_K2150031]]) in the composite part [[Part:BBa_K4601205|BBa_K4601205]].
+Using the Salis Lab RBS Library Calculator v2.0 [1-3], the predicted features of this RBS are:
+ Translation Initiation Rate (au)	:	9563,49
+ dG_total (kcal/mol)	:	-4,55
+ dG_mRNA_rRNA (kcal/mol)	:	-11.60
+ dG_spacing (kcal/mol)	:	0
+ dG_stacking (kcal/mol)	:	0
+ dG_standby (kcal/mol)	:	0.87
+ dG_start (kcal/mol)	:	-2.76
+ dG_mRNA (kcal/mol)	:	-9.37
+ Warnings	:	none
+This RBS was selected as predicted to have a Translation Initiation Rate (TIR) of about 10000 au from a library of 64 RBSes (GGGGAAAMTTAAATTMAGGMGGTWKTAM) for which the estimated TIR range from 3891.73 to 649251.13.
+===References===
+[1] Reis AC, Salis HM. An automated model test system for systematic development and improvement of gene expression models. ACS synthetic biology (2020) 9: 3145–3156.
+[2] Farasat I, Kushwaha M, Collens J, Easterbrook M, Guido M, Salis HM. Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria. Molecular Systems Biology (2014) 10: 731.
+[3] Ng CY, Farasat I, Maranas CD, Salis HM. Rational design of a synthetic Entner-Doudoroff pathway for improved and controllable NADPH regeneration. Metabolic Engineering (2015) 29: 86–96.
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